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.venv_haddock/include/site/python3.12/freesasa/classifier.c

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+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <assert.h>
+#include <stdlib.h>
+#if HAVE_STRINGS_H
+#include <strings.h>
+#endif
+#include <errno.h>
+
+#include "classifier.h"
+#include "freesasa_internal.h"
+#include "pdb.h"
+
+#define STD_CLASSIFIER_NAME "no-name-given"
+
+#define MAX_LINE_LEN 256
+
+/**
+    In this file the concept class refers to polar/apolar and type to
+    aliphatic/aromatic/etc. See the example configurations in share/.
+ */
+
+static const struct classifier_types empty_types = {0, NULL, NULL, NULL};
+
+static const struct classifier_residue empty_residue = {0, NULL, NULL, NULL, NULL, {NULL, 0, 0, 0, 0, 0}};
+
+static const struct freesasa_classifier empty_config = {0, NULL, NULL, NULL};
+
+struct classifier_types *
+freesasa_classifier_types_new(void)
+{
+    struct classifier_types *t = malloc(sizeof(struct classifier_types));
+    if (t == NULL)
+        mem_fail();
+    else
+        *t = empty_types;
+    return t;
+}
+
+void freesasa_classifier_types_free(struct classifier_types *t)
+{
+    int i;
+
+    if (t != NULL) {
+        free(t->type_radius);
+        free(t->type_class);
+        if (t->name)
+            for (i = 0; i < t->n_types; ++i)
+                free(t->name[i]);
+        free(t->name);
+
+        free(t);
+    }
+}
+
+struct classifier_residue *
+freesasa_classifier_residue_new(const char *name)
+{
+    struct classifier_residue *res;
+    assert(strlen(name) > 0);
+
+    res = malloc(sizeof(struct classifier_residue));
+
+    if (res == NULL)
+        mem_fail();
+    else {
+        *res = empty_residue;
+        res->name = strdup(name);
+        if (res->name == NULL) {
+            mem_fail();
+            free(res);
+            res = NULL;
+        }
+    }
+    return res;
+}
+
+void freesasa_classifier_residue_free(struct classifier_residue *res)
+{
+    int i;
+    if (res != NULL) {
+        free(res->name);
+
+        if (res->atom_name)
+            for (i = 0; i < res->n_atoms; ++i)
+                free(res->atom_name[i]);
+        free(res->atom_name);
+
+        free(res->atom_radius);
+        free(res->atom_class);
+
+        free(res);
+    }
+}
+
+freesasa_classifier *
+freesasa_classifier_new()
+{
+    struct freesasa_classifier *cfg = malloc(sizeof(struct freesasa_classifier));
+    if (cfg == NULL)
+        mem_fail();
+    else
+        *cfg = empty_config;
+    return cfg;
+}
+
+void freesasa_classifier_free(freesasa_classifier *c)
+{
+    int i;
+    if (c != NULL) {
+        if (c->residue)
+            for (i = 0; i < c->n_residues; ++i)
+                freesasa_classifier_residue_free(c->residue[i]);
+        free(c->residue);
+        free(c->residue_name);
+        free(c->name);
+        free(c);
+    }
+}
+
+/* check if array of strings has a string that matches key,
+   ignores trailing and leading whitespace */
+static int
+find_string(char **array,
+            const char *key,
+            int array_size)
+{
+    int n, i, found = 0;
+    char *key_trimmed;
+
+    if (array == NULL || array_size == 0) return -1;
+
+    n = strlen(key);
+    key_trimmed = malloc(n + 1);
+
+    if (key_trimmed == NULL) return mem_fail();
+
+    /* remove trailing and leading whitespace */
+    sscanf(key, "%s", key_trimmed);
+
+    for (i = 0; i < array_size; ++i) {
+        assert(array[i]);
+        if (strcmp(array[i], key_trimmed) == 0) {
+            found = 1;
+            break;
+        }
+    }
+
+    free(key_trimmed);
+
+    if (found) return i;
+    return FREESASA_FAIL;
+}
+
+/**
+   Removes comments and strips leading and trailing
+   whitespace. Returns the length of the stripped line on success,
+   FREESASA_FAIL if malloc/realloc fails. Result will be stored in
+   the string line, which is assumed to have size MAX_LINE_LEN + 1.
+ */
+static int
+strip_line(char *line,
+           const char *input)
+{
+    char *comment, *first, *last;
+    char linebuf[MAX_LINE_LEN + 1];
+
+    assert(strlen(input) <= MAX_LINE_LEN);
+
+    strcpy(linebuf, input);
+    comment = strchr(linebuf, '#');
+    if (comment) *comment = '\0'; /* skip comments */
+
+    first = linebuf;
+    last = linebuf + strlen(linebuf) - 1;
+    while (*first == ' ' || *first == '\t')
+        ++first;
+
+    if (last > first)
+        while (*last == ' ' || *last == '\t' || *last == '\n')
+            --last;
+
+    if (first >= last) {
+        line[0] = '\0';
+        return 0;
+    }
+
+    *(last + 1) = '\0';
+    strncpy(line, first, MAX_LINE_LEN);
+
+    return strlen(line);
+}
+
+/**
+    Essentially a safer fscanf(input, "%s", str) limited to the
+    current line in input.  Stores the result in 'str' (which should
+    be able to store a string of length MAX_LINE_LEN)
+*/
+static int
+get_next_string(FILE *input, char *str)
+{
+    char line[MAX_LINE_LEN + 1];
+    long pos = ftell(input);
+
+    if (fgets(line, MAX_LINE_LEN + 1, input) == NULL) {
+        if (ferror(input)) {
+            return freesasa_fail(strerror(errno));
+        }
+        return 0;
+    }
+
+    str[0] = '\0';
+
+    sscanf(line, "%s", str);
+
+    fseek(input, pos + strlen(str), SEEK_SET);
+    return strlen(str);
+}
+
+/**
+    Allocates space and stores a line stripped of comments in the line
+    pointer. Returns the length of the line on success, FREESASA_FAIL
+    for I/O errors.
+ */
+static int
+next_line(char *line,
+          FILE *fp)
+{
+    char linebuf[MAX_LINE_LEN + 1];
+
+    if (fgets(linebuf, MAX_LINE_LEN + 1, fp) == NULL) {
+        if (ferror(fp)) {
+            return fail_msg(strerror(errno));
+        }
+
+        if (feof(fp)) {
+            line[0] = '\0';
+            return 0;
+        }
+    }
+
+    return strip_line(line, linebuf);
+}
+
+/**
+    Find offset of str in line, returns -1 if not found
+    Ignores comments
+*/
+static inline int
+locate_string(const char *line,
+              const char *str)
+{
+    int NOT_FOUND = -1;
+    char *loc, buf[MAX_LINE_LEN + 1];
+
+    assert(line);
+    assert(strlen(line) <= MAX_LINE_LEN);
+    assert(str);
+
+    if (strlen(line) == 0) {
+        return NOT_FOUND;
+    }
+
+    strcpy(buf, line);
+
+    /* skip comments */
+    loc = strstr(buf, "#");
+    if (loc == buf) {
+        return NOT_FOUND;
+    } else if (loc != NULL) {
+        *loc = '\0';
+    }
+
+    loc = strstr(buf, str);
+    if (loc != NULL) {
+        return loc - buf;
+    }
+
+    return NOT_FOUND;
+}
+
+/**
+    If string exists on line its location is stored in this_range, and
+    if prev_range is non-null it is set to end at the same location.
+ */
+static inline int
+try_register_stringloc(const char *line,
+                       const char *str,
+                       long last_tell,
+                       struct file_range *this_range,
+                       struct file_range **prev_range)
+{
+    int pos, NOT_FOUND = -1;
+
+    if (strlen(line) == 0) return NOT_FOUND;
+
+    pos = locate_string(line, str);
+    if (pos >= 0) {
+        this_range->begin = last_tell + pos;
+        if (*prev_range) (*prev_range)->end = last_tell + pos;
+        (*prev_range) = this_range;
+        return last_tell + pos;
+    }
+    return NOT_FOUND;
+}
+
+/**
+    Checks that input file has the required fields and locates the
+    'types' and 'atoms' sections. No syntax checking. Return
+    FREESASA_SUCCESS if file seems ok, FREESASA_FAIL if either/both of
+    the sections are missing, or file invalid in some other way, or there was an error reading the file.
+ */
+static int
+check_file(FILE *input,
+           struct file_range *types,
+           struct file_range *atoms,
+           struct file_range *name)
+{
+    long last_tell;
+    char line[MAX_LINE_LEN + 1];
+    struct file_range *last_range = NULL;
+
+    assert(input);
+    assert(types);
+    assert(atoms);
+
+    last_tell = ftell(input);
+
+    /* this allows us to detect wether a section wasn't found later */
+    types->begin = atoms->begin = name->begin = -1;
+
+    while (fgets(line, MAX_LINE_LEN + 1, input)) {
+        try_register_stringloc(line, "types:", last_tell, types, &last_range);
+        try_register_stringloc(line, "atoms:", last_tell, atoms, &last_range);
+        try_register_stringloc(line, "name:", last_tell, name, &last_range);
+        last_tell = ftell(input);
+
+        if (strlen(line) == MAX_LINE_LEN &&
+            line[MAX_LINE_LEN - 1] != '\n') {
+            return fail_msg("Lines in classifier files can only be %d characters or less",
+                            MAX_LINE_LEN);
+        }
+    }
+
+    if (ferror(input)) {
+        return fail_msg(strerror(errno));
+    }
+
+    if (last_range != NULL) {
+        last_range->end = last_tell;
+    }
+    rewind(input);
+
+    if (name->begin == -1) {
+        freesasa_warn("input configuration lacks the entry 'name:', "
+                      "will use '" STD_CLASSIFIER_NAME "'");
+    }
+
+    if ((types->begin == -1) ||
+        (atoms->begin == -1)) {
+        return fail_msg("input configuration lacks (at least) one of "
+                        "the entries 'types:' or 'atoms:'");
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_classifier_parse_class(const char *name)
+{
+#if HAVE_STRNCASECMP
+    if (strncasecmp(name, "apolar", 6) == 0) {
+        return FREESASA_ATOM_APOLAR;
+    } else if (strncasecmp(name, "polar", 5) == 0) {
+        return FREESASA_ATOM_POLAR;
+    } else {
+        return fail_msg("only atom classes allowed are 'polar' and 'apolar'"
+                        " (case insensitive)");
+    }
+#else
+    if (strncmp(name, "apolar", 6) == 0) {
+        return FREESASA_ATOM_APOLAR;
+    } else if (strncmp(name, "polar", 5) == 0) {
+        return FREESASA_ATOM_POLAR;
+    } else {
+        return fail_msg("only atom classes allowed are 'polar' and 'apolar'");
+    }
+#endif
+}
+
+/**
+    Add type. Returns the index of the new type on success,
+    FREESASA_FAIL if realloc/strdup fails, FREESASA_WARN if type
+    already known (ignore duplicates).
+ */
+int freesasa_classifier_add_type(struct classifier_types *types,
+                                 const char *type_name,
+                                 const char *class_name,
+                                 double r)
+{
+    int the_class;
+    int n = types->n_types + 1;
+    char **tn = types->name;
+    double *tr = types->type_radius;
+    freesasa_atom_class *tc = types->type_class;
+
+    if (find_string(types->name, type_name, types->n_types) >= 0)
+        return freesasa_warn("ignoring duplicate configuration entry for '%s'", type_name);
+
+    the_class = freesasa_classifier_parse_class(class_name);
+    if (the_class == FREESASA_FAIL) return fail_msg("");
+
+    if ((types->name = realloc(tn, sizeof(char *) * n)) == NULL) {
+        types->name = tn;
+        return mem_fail();
+    }
+
+    if ((types->type_radius = realloc(tr, sizeof(double) * n)) == NULL) {
+        types->type_radius = tr;
+        return mem_fail();
+    }
+
+    if ((types->type_class = realloc(tc, sizeof(int) * n)) == NULL) {
+        types->type_class = tc;
+        return mem_fail();
+    }
+
+    if ((types->name[n - 1] = strdup(type_name)) == NULL) {
+        return mem_fail();
+    }
+
+    types->n_types++;
+    types->type_radius[types->n_types - 1] = r;
+    types->type_class[types->n_types - 1] = the_class;
+
+    return types->n_types - 1;
+}
+
+/**
+    Read a line specifying a type, store it in the config. Returns
+    warning for duplicates, failures for syntax errors or memory
+    allocation errors.
+ */
+static int
+read_types_line(struct classifier_types *types,
+                const char *line)
+{
+    int the_type, ret = FREESASA_SUCCESS;
+    double r;
+    char buf1[MAX_LINE_LEN + 1], buf2[MAX_LINE_LEN + 1];
+
+    assert(strlen(line) <= MAX_LINE_LEN);
+
+    if (sscanf(line, "%s %lf %s", buf1, &r, buf2) == 3) {
+        the_type = freesasa_classifier_add_type(types, buf1, buf2, r);
+        if (the_type == FREESASA_FAIL) ret = fail_msg("");
+        if (the_type == FREESASA_WARN) ret = FREESASA_WARN;
+    } else {
+        ret = fail_msg("could not parse line '%s' in configuration, "
+                       "expecting triplet of type 'TYPE [RADIUS] CLASS' for "
+                       "example 'C_ALI 2.00 apolar'",
+                       line);
+    }
+
+    return ret;
+}
+
+/**
+    Reads info about types from the user config. Associates each type
+    with a class and a radius in the config struct. Returns
+    FREESASA_SUCCESS on success, FREESASA_FAIL on syntax or memory
+    allocation errors.
+ */
+static int
+read_types(struct classifier_types *types,
+           FILE *input,
+           struct file_range fi)
+{
+    char line[MAX_LINE_LEN + 1];
+    int ret = FREESASA_SUCCESS, nl;
+
+    fseek(input, fi.begin, SEEK_SET);
+
+    /* read command (and discard) */
+    if (next_line(line, input) > 0) {
+        char buf[7]; /* we should not get here if the line isn't "types:" (plus whitespace) */
+        if (sscanf(line, "%6s", buf) == 0) return FREESASA_FAIL;
+        assert(strcmp(buf, "types:") == 0);
+    } else {
+        return FREESASA_FAIL;
+    }
+
+    while (ftell(input) < fi.end) {
+        nl = next_line(line, input);
+        if (nl == 0) continue;
+        if (nl == FREESASA_FAIL) {
+            ret = nl;
+            break;
+        };
+        ret = read_types_line(types, line);
+        if (ret == FREESASA_FAIL) break;
+    }
+
+    return ret;
+}
+
+/**
+    Add atom to residue. Returns index of the new atom on
+    success. FREESASA_FAIL if memory allocation fails. FREESASA_WARN
+    if the atom has already been added.
+ */
+int freesasa_classifier_add_atom(struct classifier_residue *res,
+                                 const char *name,
+                                 double radius,
+                                 int the_class)
+{
+    int n;
+    char **an = res->atom_name;
+    double *ar = res->atom_radius;
+    freesasa_atom_class *ac = res->atom_class;
+
+    if (find_string(res->atom_name, name, res->n_atoms) >= 0)
+        return freesasa_warn("ignoring duplicate configuration entry for atom '%s %s'",
+                             res->name, name);
+    n = res->n_atoms + 1;
+
+    if ((res->atom_name = realloc(res->atom_name, sizeof(char *) * n)) == NULL) {
+        res->atom_name = an;
+        return mem_fail();
+    }
+    if ((res->atom_radius = realloc(res->atom_radius, sizeof(double) * n)) == NULL) {
+        res->atom_radius = ar;
+        return mem_fail();
+    }
+    if ((res->atom_class = realloc(res->atom_class, sizeof(int) * n)) == NULL) {
+        res->atom_class = ac;
+        return mem_fail();
+    }
+    if ((res->atom_name[n - 1] = strdup(name)) == NULL)
+        return mem_fail();
+
+    ++res->n_atoms;
+    res->atom_radius[n - 1] = radius;
+    res->atom_class[n - 1] = the_class;
+
+    return n - 1;
+}
+
+/**
+    Add residue to config. If the residue already exists, it returns
+    the index of that residue, else it returns the index of the new
+    residue. Returns FREESASA_FAILURE if realloc/strdup fails.
+ */
+int freesasa_classifier_add_residue(struct freesasa_classifier *c,
+                                    const char *name)
+{
+    char **rn = c->residue_name;
+    struct classifier_residue **cr = c->residue;
+    int res = find_string(c->residue_name, name, c->n_residues);
+
+    if (res >= 0) return res;
+
+    res = c->n_residues + 1;
+
+    if ((c->residue_name = realloc(rn, sizeof(char *) * res)) == NULL) {
+        c->residue_name = rn;
+        return mem_fail();
+    }
+
+    if ((c->residue = realloc(cr, sizeof(struct classifier_residue *) * res)) == NULL) {
+        c->residue = cr;
+        return mem_fail();
+    }
+
+    if ((c->residue[res - 1] = freesasa_classifier_residue_new(name)) == NULL) {
+        return mem_fail();
+    }
+
+    ++c->n_residues;
+    c->residue_name[res - 1] = c->residue[res - 1]->name;
+    return res - 1;
+}
+
+/**
+    Read a line specifying an atom, store it in the config. Use
+    supplied types to add assign radius and class. Returns
+    FREESASA_WARN for duplicates. Returns FREESASA_FAIL for syntax
+    errors or memory allocation errors. FREESASA_SUCCESS else.
+ */
+static int
+read_atoms_line(struct freesasa_classifier *c,
+                const struct classifier_types *types,
+                const char *line)
+{
+    char buf1[MAX_LINE_LEN + 1], buf2[MAX_LINE_LEN + 1], buf3[MAX_LINE_LEN + 1];
+    int res, type, atom;
+
+    assert(strlen(line) <= MAX_LINE_LEN);
+
+    if (sscanf(line, "%s %s %s", buf1, buf2, buf3) == 3) {
+        if (strlen(buf1) > PDB_ATOM_RES_NAME_STRL) {
+            return fail_msg("residue name %s is too long in classifier file", buf1);
+        }
+
+        if (strlen(buf2) > PDB_ATOM_NAME_STRL) {
+            return fail_msg("atom name %s is too long in classifier file", buf2);
+        }
+
+        type = find_string(types->name, buf3, types->n_types);
+
+        if (type < 0) {
+            return fail_msg("unknown atom type '%s' in configuration, line '%s'",
+                            buf3, line);
+        }
+
+        res = freesasa_classifier_add_residue(c, buf1);
+
+        if (res == FREESASA_FAIL) return fail_msg("");
+
+        atom = freesasa_classifier_add_atom(c->residue[res],
+                                            buf2,
+                                            types->type_radius[type],
+                                            types->type_class[type]);
+
+        if (atom == FREESASA_FAIL) return fail_msg("");
+        if (atom == FREESASA_WARN) return FREESASA_WARN;
+
+    } else {
+        return fail_msg("could not parse configuration, line '%s', "
+                        "expecting triplet of type "
+                        "'RESIDUE ATOM CLASS', for example 'ALA CB C_ALI'",
+                        line);
+    }
+    return FREESASA_SUCCESS;
+}
+
+/**
+    Reads atom configurations from config-file. Associates each atom
+    with a radius and class using the types that should already have
+    been stored in the config struct.
+ */
+static int
+read_atoms(struct freesasa_classifier *c,
+           struct classifier_types *types,
+           FILE *input,
+           struct file_range fi)
+{
+    char line[MAX_LINE_LEN + 1], buf[MAX_LINE_LEN + 1];
+    int ret = FREESASA_SUCCESS, nl;
+
+    fseek(input, fi.begin, SEEK_SET);
+
+    /* read command (and discard) */
+    if (next_line(line, input) > 0) {
+        assert(strlen(line) <= MAX_LINE_LEN);
+        if (sscanf(line, "%s", buf) == 0) return FREESASA_FAIL;
+        assert(strcmp(buf, "atoms:") == 0);
+    } else {
+        return FREESASA_FAIL;
+    }
+
+    while (ftell(input) < fi.end) {
+        nl = next_line(line, input);
+        if (nl == 0) continue;
+        if (nl == FREESASA_FAIL) return fail_msg("");
+        ret = read_atoms_line(c, types, line);
+        if (ret == FREESASA_FAIL) break;
+    }
+
+    return ret;
+}
+
+static int
+read_name(struct freesasa_classifier *classifier,
+          FILE *input,
+          struct file_range fi)
+{
+    char buf[MAX_LINE_LEN + 1];
+
+    if (fi.begin < 0)
+        return FREESASA_SUCCESS; /* name not set? */
+
+    fseek(input, fi.begin, SEEK_SET);
+    if (get_next_string(input, buf) <= 0)
+        return fail_msg("");
+
+    assert(strcmp(buf, "name:") == 0);
+
+    if (get_next_string(input, buf) <= 0) {
+        return fail_msg("empty name for configuration?");
+    }
+
+    classifier->name = strdup(buf);
+    if (classifier->name == NULL) {
+        return mem_fail();
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+static struct freesasa_classifier *
+read_config(FILE *input)
+{
+    struct file_range types_section, atoms_section, name_section;
+    struct freesasa_classifier *classifier = NULL;
+    struct classifier_types *types = NULL;
+
+    assert(input);
+
+    if (!(types = freesasa_classifier_types_new()))
+        goto cleanup;
+    if (!(classifier = freesasa_classifier_new()))
+        goto cleanup;
+    if (check_file(input, &types_section, &atoms_section, &name_section))
+        goto cleanup;
+    if (read_name(classifier, input, name_section))
+        goto cleanup;
+    if (read_types(types, input, types_section))
+        goto cleanup;
+    if (read_atoms(classifier, types, input, atoms_section))
+        goto cleanup;
+
+    freesasa_classifier_types_free(types);
+
+    return classifier;
+
+cleanup:
+    freesasa_classifier_free(classifier);
+    freesasa_classifier_types_free(types);
+    return NULL;
+}
+
+/**
+    See if an atom_name has been defined for the residue ANY (writes
+    indices to the provided pointers).
+ */
+static void
+find_any(const struct freesasa_classifier *c,
+         const char *atom_name,
+         int *res, int *atom)
+{
+    *res = find_string(c->residue_name, "ANY", c->n_residues);
+    if (*res >= 0) {
+        *atom = find_string(c->residue[*res]->atom_name,
+                            atom_name,
+                            c->residue[*res]->n_atoms);
+    }
+}
+/**
+    Find the residue and atom index of an atom in the supplied
+    configuration. Prints error and returns FREESASA_WARN if not
+    found.
+ */
+static int
+find_atom(const struct freesasa_classifier *c,
+          const char *res_name,
+          const char *atom_name,
+          int *res,
+          int *atom)
+{
+    const struct classifier_residue *residue;
+    *atom = -1;
+    *res = find_string(c->residue_name, res_name, c->n_residues);
+    if (*res < 0) {
+        find_any(c, atom_name, res, atom);
+    } else {
+        residue = c->residue[*res];
+        *atom = find_string(residue->atom_name, atom_name, residue->n_atoms);
+        if (*atom < 0) {
+            find_any(c, atom_name, res, atom);
+        }
+    }
+    if (*atom < 0) {
+        return FREESASA_WARN;
+    }
+    return FREESASA_SUCCESS;
+}
+
+double
+freesasa_classifier_radius(const freesasa_classifier *classifier,
+                           const char *res_name,
+                           const char *atom_name)
+{
+    int res, atom, status;
+
+    assert(classifier);
+    assert(res_name);
+    assert(atom_name);
+
+    status = find_atom(classifier, res_name, atom_name, &res, &atom);
+    if (status == FREESASA_SUCCESS)
+        return classifier->residue[res]->atom_radius[atom];
+    return -1.0;
+}
+
+freesasa_atom_class
+freesasa_classifier_class(const freesasa_classifier *classifier,
+                          const char *res_name,
+                          const char *atom_name)
+{
+    int res, atom, status;
+
+    assert(classifier);
+    assert(res_name);
+    assert(atom_name);
+
+    status = find_atom(classifier, res_name, atom_name, &res, &atom);
+    if (status == FREESASA_SUCCESS)
+        return classifier->residue[res]->atom_class[atom];
+    return FREESASA_ATOM_UNKNOWN;
+}
+
+const char *
+freesasa_classifier_class2str(freesasa_atom_class atom_class)
+{
+    switch (atom_class) {
+    case FREESASA_ATOM_APOLAR:
+        return "Apolar";
+    case FREESASA_ATOM_POLAR:
+        return "Polar";
+    case FREESASA_ATOM_UNKNOWN:
+        return "Unknown";
+    }
+    fail_msg("invalid atom class");
+    return NULL;
+}
+
+freesasa_nodearea
+freesasa_result_classes(const freesasa_structure *structure,
+                        const freesasa_result *result)
+{
+    freesasa_nodearea area = {"whole-structure", 0, 0, 0, 0, 0};
+    freesasa_range_nodearea(&area, structure, result,
+                            0, freesasa_structure_n(structure) - 1);
+    return area;
+}
+
+freesasa_classifier *
+freesasa_classifier_from_file(FILE *file)
+{
+    struct freesasa_classifier *classifier = read_config(file);
+
+    if (classifier == NULL) {
+        fail_msg("");
+        return NULL;
+    }
+
+    return classifier;
+}
+
+const freesasa_nodearea *
+freesasa_classifier_residue_reference(const freesasa_classifier *classifier,
+                                      const char *res_name)
+{
+    int res = find_string(classifier->residue_name, res_name, classifier->n_residues);
+
+    if (res < 0) return NULL;
+
+    return &classifier->residue[res]->max_area;
+}
+
+const char *
+freesasa_classifier_name(const freesasa_classifier *classifier)
+{
+    return classifier->name;
+}
+
+struct symbol_radius {
+    const char symbol[3];
+    double radius;
+};
+
+/* Taken from:
+
+   Mantina et al. "Consistent van der Waals Radii for
+   the Whole Main Group". J. Phys. Chem. A, 2009, 113 (19), pp
+   5806–5812.
+
+   Many of these elements, if they occur in a PDB file, should
+   probably rather be skipped than used in a SASA calculation, and
+   ionization will change the effective radius.
+
+*/
+static const struct symbol_radius symbol_radius[] = {
+    /* elements that actually occur in the regular amino acids and nucleotides */
+    {" H", 1.10},
+    {" C", 1.70},
+    {" N", 1.55},
+    {" O", 1.52},
+    {" P", 1.80},
+    {" S", 1.80},
+    {"SE", 1.90},
+    /* some others, values pulled from gemmi elem.hpp */
+    /* Halogens */
+    {" F", 1.47},
+    {"CL", 1.75},
+    {"BR", 1.83},
+    {" I", 1.98},
+    /* Alkali and Alkali Earth metals */
+    {"LI", 1.81},
+    {"BE", 1.53},
+    {"NA", 2.27},
+    {"MG", 1.73},
+    {" K", 2.75},
+    {"CA", 2.31},
+    {"RB", 3.03},
+    {"SR", 2.49},
+    {"CS", 3.43},
+    {"BA", 2.68},
+    {"FR", 3.48},
+    {"RA", 2.83},
+    /* Transition metals */
+    {"SC", 2.11},
+    {"TI", 1.95},
+    {" V", 1.06},
+    {"CR", 1.13},
+    {"MN", 1.19},
+    {"FE", 1.26},
+    {"CO", 1.13},
+    {"NI", 1.63},
+    {"CU", 1.40},
+    {"ZN", 1.39},
+    {" Y", 1.61},
+    {"ZR", 1.42},
+    {"NB", 1.33},
+    {"MO", 1.75},
+    {"TC", 2.00},
+    {"RU", 1.20},
+    {"RH", 1.22},
+    {"PD", 1.63},
+    {"AG", 1.72},
+    {"CD", 1.58},
+    {"HF", 1.40},
+    {"TA", 1.22},
+    {" W", 1.26},
+    {"RE", 1.30},
+    {"OS", 1.58},
+    {"IR", 1.22},
+    {"PT", 1.75},
+    {"AU", 1.66},
+    {"HG", 1.55},
+    /* Post-Transition metals */
+    {"AL", 1.84},
+    {"GA", 1.87},
+    {"IN", 1.93},
+    {"SN", 2.17},
+    {"TL", 1.96},
+    {"PB", 2.02},
+    {"BI", 2.07},
+    {"PO", 1.97},
+    /* Metalloid */
+    {" B", 1.92},
+    {"SI", 2.10},
+    {"GE", 2.11},
+    {"AS", 1.85},
+    {"SB", 2.06},
+    {"TE", 2.06},
+    {"AT", 2.02},
+    /* Noble gases */
+    {"HE", 1.40},
+    {"NE", 1.54},
+    {"AR", 1.88},
+    {"KR", 2.02},
+    {"XE", 2.16},
+    {"RN", 2.20},
+    /* Lanthanoids */
+    {"LA", 1.83},
+    {"CE", 1.86},
+    {"PR", 1.62},
+    {"ND", 1.79},
+    {"PM", 1.76},
+    {"SM", 1.74},
+    {"EU", 1.96},
+    {"GD", 1.69},
+    {"TB", 1.66},
+    {"DY", 1.63},
+    {"HO", 1.61},
+    {"ER", 1.59},
+    {"TM", 1.57},
+    {"YB", 1.54},
+    {"LU", 1.53},
+    /* Actinoids */
+    {"AC", 2.12},
+    {"TH", 1.84},
+    {"PA", 1.60},
+    {" U", 1.86},
+    {"NP", 1.71},
+    {"PU", 1.67},
+    {"AM", 1.66},
+    {"CM", 1.65},
+    {"BK", 1.64},
+    {"CF", 1.63},
+    {"ES", 1.62},
+    {"FM", 1.61},
+    {"MD", 1.60},
+    {"NO", 1.59},
+    {"LR", 1.58},
+};
+
+double
+freesasa_guess_radius(const char *input_symbol)
+{
+    int n_symbol, i;
+    char symbol[3];
+
+    assert(input_symbol);
+    snprintf(symbol, 3, "%2s", input_symbol);
+
+    n_symbol = sizeof(symbol_radius) / sizeof(struct symbol_radius);
+
+    for (i = 0; i < n_symbol; ++i) {
+        if (strcmp(symbol, symbol_radius[i].symbol) == 0)
+            return symbol_radius[i].radius;
+    }
+    return -1.0;
+}
+
+// clang-format off
+/* The residue types that are returned by freesasa_classify_residue() */
+enum residue {
+    /* Regular amino acids */
+    ALA = 0, ARG, ASN, ASP,
+    CYS, GLN, GLU, GLY,
+    HIS, ILE, LEU, LYS,
+    MET, PHE, PRO, SER,
+    THR, TRP, TYR, VAL,
+    /* some non-standard ones */
+    CSE, SEC, PYL, PYH, ASX, GLX,
+    /* residue unknown */
+    RES_UNK,
+    /* capping N- and C-terminal groups (usually HETATM) */
+    ACE, NH2,
+    /* DNA */
+    DA, DC, DG, DT, DU, DI,
+    /* RNA (avoid one-letter enums) */
+    RA, RC, RG, RU, RI, RT,
+    /* generic nucleotide */
+    NN
+};
+
+/* Residue types, make sure this always matches the corresponding enum. */
+static const char *residue_names[] = {
+    /* amino acids */
+    "ALA", "ARG", "ASN", "ASP",
+    "CYS", "GLN", "GLU", "GLY",
+    "HIS", "ILE", "LEU", "LYS",
+    "MET", "PHE", "PRO", "SER",
+    "THR", "TRP", "TYR", "VAL",
+    /* non-standard amino acids */
+    "CSE", "SEC", "PYL", "PYH", /* SEC and PYL are standard names, CSE and PYH are found in some early files */
+    "ASX", "GLX",
+    "UNK",
+    /* capping groups */
+    "ACE", "NH2",
+    /* DNA */
+    "DA", "DC", "DG", "DT", "DU", "DI",
+    /* RNA */
+    "A", "C", "G", "U", "I", "T",
+    /* General nucleotide */
+    "N"};
+// clang-format on
+
+int freesasa_classify_n_residue_types()
+{
+    return NN + 1;
+}
+
+int freesasa_classify_residue(const char *res_name)
+{
+    int i;
+    char cpy[PDB_ATOM_RES_NAME_STRL + 1];
+
+    sscanf(res_name, "%s", cpy);
+
+    for (i = ALA; i < freesasa_classify_n_residue_types(); ++i) {
+        if (strcmp(cpy, residue_names[i]) == 0) return i;
+    }
+
+    return RES_UNK;
+}
+
+const char *
+freesasa_classify_residue_name(int residue_type)
+{
+    assert(residue_type >= 0 && residue_type <= NN);
+    return residue_names[residue_type];
+}
+
+int freesasa_atom_is_backbone(const char *atom_name)
+{
+    const char *bb[] = {"CA", "N", "O", "C", "OXT",
+                        "P", "OP1", "OP2", "O5'", "C5'", "C4'",
+                        "O4'", "C3'", "O3'", "C2'", "C1'"};
+    char name[PDB_ATOM_NAME_STRL + 1];
+    int i;
+
+    name[0] = '\0';
+    sscanf(atom_name, "%s", name); /* trim whitespace */
+
+    if (strlen(name) == 0) return 0;
+    for (i = 0; i < sizeof(bb) / sizeof(const char *); ++i) {
+        if (strcmp(name, bb[i]) == 0) {
+            return 1;
+        }
+    }
+    return 0;
+}
+
+#if USE_CHECK
+#include <check.h>
+#include <math.h>
+
+START_TEST(test_classifier)
+{
+    struct classifier_types *types = freesasa_classifier_types_new();
+    struct classifier_residue *residue_cfg = freesasa_classifier_residue_new("ALA");
+    struct freesasa_classifier *clf = freesasa_classifier_new();
+
+    freesasa_set_verbosity(FREESASA_V_SILENT);
+
+    ck_assert_int_eq(freesasa_classifier_parse_class("A"), FREESASA_FAIL);
+#if HAVE_STRNCASECMP
+    ck_assert_int_eq(freesasa_classifier_parse_class("POLAR"), FREESASA_ATOM_POLAR);
+    ck_assert_int_eq(freesasa_classifier_parse_class("APOLAR"), FREESASA_ATOM_APOLAR);
+#endif
+    ck_assert_int_eq(freesasa_classifier_parse_class("polar"), FREESASA_ATOM_POLAR);
+    ck_assert_int_eq(freesasa_classifier_parse_class("apolar"), FREESASA_ATOM_APOLAR);
+
+    ck_assert_int_eq(types->n_types, 0);
+    ck_assert_int_eq(freesasa_classifier_add_type(types, "a", "A", 1.0), FREESASA_FAIL);
+    ck_assert_int_eq(freesasa_classifier_add_type(types, "a", "polar", 1.0), 0);
+    ck_assert_int_eq(freesasa_classifier_add_type(types, "b", "apolar", 2.0), 1);
+    ck_assert_int_eq(freesasa_classifier_add_type(types, "b", "polar", 1.0), FREESASA_WARN);
+    ck_assert_int_eq(freesasa_classifier_add_type(types, "c", "apolar", 3.0), 2);
+    ck_assert_int_eq(types->n_types, 3);
+    ck_assert_str_eq(types->name[0], "a");
+    ck_assert_str_eq(types->name[1], "b");
+    ck_assert_str_eq(types->name[2], "c");
+    ck_assert(fabs(types->type_radius[0] - 1.0) < 1e-10);
+    ck_assert(fabs(types->type_radius[1] - 2.0) < 1e-10);
+    ck_assert(fabs(types->type_radius[2] - 3.0) < 1e-10);
+
+    freesasa_classifier_types_free(types);
+    types = freesasa_classifier_types_new();
+
+    ck_assert_int_eq(read_types_line(types, ""), FREESASA_FAIL);
+    ck_assert_int_eq(read_types_line(types, "a"), FREESASA_FAIL);
+    ck_assert_int_eq(read_types_line(types, "a 1.0"), FREESASA_FAIL);
+    ck_assert_int_eq(read_types_line(types, "a b C"), FREESASA_FAIL);
+    ck_assert_int_eq(read_types_line(types, "a 1.0 C"), FREESASA_FAIL);
+    ck_assert_int_eq(read_types_line(types, "a 1.0 apolar"), FREESASA_SUCCESS);
+    ck_assert_int_eq(read_types_line(types, "b 2.0 polar"), FREESASA_SUCCESS);
+    ck_assert_int_eq(types->n_types, 2);
+    ck_assert_str_eq(types->name[0], "a");
+    ck_assert_str_eq(types->name[1], "b");
+    ck_assert(fabs(types->type_radius[0] - 1.0) < 1e-10);
+    ck_assert(fabs(types->type_radius[1] - 2.0) < 1e-10);
+
+    ck_assert_int_eq(freesasa_classifier_add_atom(residue_cfg, "C", 1.0, 0), 0);
+    ck_assert_int_eq(freesasa_classifier_add_atom(residue_cfg, "CB", 2.0, 0), 1);
+    ck_assert_int_eq(freesasa_classifier_add_atom(residue_cfg, "CB", 2.0, 0), FREESASA_WARN);
+    ck_assert_str_eq(residue_cfg->atom_name[0], "C");
+    ck_assert_str_eq(residue_cfg->atom_name[1], "CB");
+    ck_assert(fabs(residue_cfg->atom_radius[0] - 1.0) < 1e-10);
+    ck_assert(fabs(residue_cfg->atom_radius[1] - 2.0) < 1e-10);
+    freesasa_classifier_residue_free(residue_cfg);
+
+    ck_assert_int_eq(freesasa_classifier_add_residue(clf, "A"), 0);
+    ck_assert_int_eq(freesasa_classifier_add_residue(clf, "B"), 1);
+    ck_assert_int_eq(freesasa_classifier_add_residue(clf, "B"), 1);
+    ck_assert_int_eq(clf->n_residues, 2);
+    ck_assert_str_eq(clf->residue_name[0], "A");
+    ck_assert_str_eq(clf->residue_name[1], "B");
+    ck_assert_str_eq(clf->residue[0]->name, "A");
+
+    freesasa_classifier_free(clf);
+    clf = freesasa_classifier_new();
+
+    ck_assert_int_eq(read_atoms_line(clf, types, "A A"), FREESASA_FAIL);
+    ck_assert_int_eq(read_atoms_line(clf, types, "A A bla"), FREESASA_FAIL);
+    ck_assert_int_eq(read_atoms_line(clf, types, "ALA CA a"), FREESASA_SUCCESS);
+    ck_assert_int_eq(read_atoms_line(clf, types, "ALA CB b"), FREESASA_SUCCESS);
+    ck_assert_int_eq(read_atoms_line(clf, types, "ARG CA a"), FREESASA_SUCCESS);
+    ck_assert_int_eq(read_atoms_line(clf, types, "ARG CB b"), FREESASA_SUCCESS);
+    ck_assert_int_eq(read_atoms_line(clf, types, "ARG CG b"), FREESASA_SUCCESS);
+    ck_assert_int_eq(read_atoms_line(clf, types, "TOOLONGRESNAME CG b"), FREESASA_FAIL);
+    ck_assert_int_eq(read_atoms_line(clf, types, "ARG TOOLONGATOMNAME b"), FREESASA_FAIL);
+    ck_assert_int_eq(clf->n_residues, 2);
+    ck_assert_str_eq(clf->residue_name[0], "ALA");
+    ck_assert_str_eq(clf->residue_name[1], "ARG");
+    ck_assert_int_eq(clf->residue[0]->n_atoms, 2);
+    ck_assert_str_eq(clf->residue[0]->atom_name[0], "CA");
+    ck_assert_str_eq(clf->residue[0]->atom_name[1], "CB");
+    ck_assert(fabs(clf->residue[0]->atom_radius[0] - 1.0) < 1e-5);
+    ck_assert(fabs(clf->residue[0]->atom_radius[1] - 2.0) < 1e-5);
+
+    freesasa_classifier_free(clf);
+    freesasa_classifier_types_free(types);
+
+    freesasa_set_verbosity(FREESASA_V_NORMAL);
+}
+END_TEST
+
+START_TEST(test_classifier_utils)
+{
+    const char *strarr[] = {"A", "B", "C"};
+    const char *line[] = {"# Bla", " # Bla", "Bla # Bla", " Bla # Bla", "#Bla #Alb"};
+
+    char dummy_str[MAX_LINE_LEN + 1];
+    ck_assert_int_eq(find_string((char **)strarr, "A", 3), 0);
+    ck_assert_int_eq(find_string((char **)strarr, "B", 3), 1);
+    ck_assert_int_eq(find_string((char **)strarr, "C", 3), 2);
+    ck_assert_int_eq(find_string((char **)strarr, "D", 3), -1);
+    ck_assert_int_eq(find_string((char **)strarr, " C ", 3), 2);
+    ck_assert_int_eq(find_string((char **)strarr, "CC", 3), -1);
+
+    ck_assert_int_eq(strip_line(dummy_str, line[0]), 0);
+    ck_assert_int_eq(strip_line(dummy_str, line[1]), 0);
+    ck_assert_int_eq(strip_line(dummy_str, line[2]), 3);
+    ck_assert_str_eq(dummy_str, "Bla");
+
+    ck_assert_int_eq(strip_line(dummy_str, line[3]), 3);
+    ck_assert_str_eq(dummy_str, "Bla");
+
+    ck_assert_int_eq(strip_line(dummy_str, line[4]), 0);
+
+    const char *str = "foo bar # baz";
+    ck_assert_int_eq(locate_string(str, "Foo"), -1);
+    ck_assert_int_eq(locate_string(str, "foo"), 0);
+    ck_assert_int_eq(locate_string(str, "bar"), 4);
+    ck_assert_int_eq(locate_string(str, "baz"), -1);
+    ck_assert_int_eq(locate_string(str, "ar"), 5);
+
+    struct file_range this_range, *last_range = NULL;
+    ck_assert_int_eq(try_register_stringloc(str, "foo", 0, &this_range, &last_range), 0);
+    ck_assert_int_eq(this_range.begin, 0);
+    ck_assert_ptr_eq(last_range, &this_range);
+    ck_assert_int_eq(try_register_stringloc(str, "bar", 0, &this_range, &last_range), 4);
+    ck_assert_ptr_eq(last_range, &this_range);
+    ck_assert_int_eq(last_range->end, 4);
+    ck_assert_int_eq(try_register_stringloc(str, "baz", 0, &this_range, &last_range), -1);
+}
+END_TEST
+
+TCase *
+test_classifier_static()
+{
+    TCase *tc = tcase_create("classifier.c static");
+    tcase_add_test(tc, test_classifier);
+    tcase_add_test(tc, test_classifier_utils);
+
+    return tc;
+}
+
+#endif /** USE_CHECK */

.venv_haddock/include/site/python3.12/freesasa/classifier.h

@@ -0,0 +1,117 @@
+#ifndef CLASSIFIER_H
+#define CLASSIFIER_H
+
+#include "freesasa_internal.h"
+
+/**
+    This classifier only has the sasa_class() and class2str()
+    functions, which returns 1 for protein backbone atoms, and 0
+    else. Backbone atoms are CA, N, C and O.
+ */
+extern const freesasa_classifier freesasa_backbone_classifier;
+
+/** Classifier that classifies each atom according to residue */
+extern const freesasa_classifier freesasa_residue_classifier;
+
+/**
+    The following three structs and the following functions are only
+    exposed in a header because the autogenerated static classifiers
+    need to see them, they are not intended for use outside of this
+    context. Therefore the functions to modify the structs are hidden
+    inside classifier.c.
+
+    Names of classes, types, etc are stored in arrays to simplify
+    generic searching.
+*/
+
+/**
+    Struct to store information about the types-section in a user-config.
+ */
+struct classifier_types {
+    int n_types;                     /**< number of types */
+    char **name;                     /**< names of types */
+    double *type_radius;             /**< radius of type */
+    freesasa_atom_class *type_class; /**< class of each type */
+};
+
+/**
+     Configuration info for each residue type.
+ */
+struct classifier_residue {
+    int n_atoms;                     /**< Number of atoms */
+    char *name;                      /**< Name of residue */
+    char **atom_name;                /**< Names of atoms */
+    double *atom_radius;             /**< Atomic radii */
+    freesasa_atom_class *atom_class; /**< Classes of atoms */
+    freesasa_nodearea max_area;      /**< Maximum area (for RSA) */
+};
+
+/**
+    Stores a user-configuration as extracted from a configuration
+    file. No info about types, since those are only a tool used
+    intermediately in assigment of radii and classes.
+
+    An array of the names of residues is stored directly in the struct
+    to facilitate searching for residues. The class_name array should
+    be a clone of that found in struct types (can be done bye
+    config_copy_classes()).
+
+    Only for internal use.
+ */
+struct freesasa_classifier {
+    int n_residues;      /**< Number of residues */
+    char **residue_name; /**< Names of residues */
+    char *name;
+    struct classifier_residue **residue;
+};
+
+/**
+    Get the VdW radius of an element
+ */
+double
+freesasa_guess_radius(const char *symbol);
+
+const freesasa_nodearea *
+freesasa_classifier_residue_reference(const freesasa_classifier *classifier,
+                                      const char *res_name);
+
+/* The functions below are only exposed to allow testing */
+freesasa_classifier *
+freesasa_classifier_new(void);
+
+struct classifier_types *
+freesasa_classifier_types_new(void);
+
+void freesasa_classifier_types_free(struct classifier_types *t);
+
+struct classifier_residue *
+freesasa_classifier_residue_new(const char *name);
+
+void freesasa_classifier_residue_free(struct classifier_residue *res);
+
+int freesasa_classifier_add_residue(struct freesasa_classifier *c,
+                                    const char *name);
+
+int freesasa_classifier_add_atom(struct classifier_residue *res,
+                                 const char *name,
+                                 double radius,
+                                 int the_class);
+
+int freesasa_classifier_add_type(struct classifier_types *types,
+                                 const char *type_name,
+                                 const char *class_name,
+                                 double r);
+
+int freesasa_classifier_add_class(struct classifier_types *types,
+                                  const char *name);
+
+/* These three are used to calculate residue type areas */
+
+int freesasa_classify_n_residue_types(void);
+
+int freesasa_classify_residue(const char *res_name);
+
+const char *
+freesasa_classify_residue_name(int residue_type);
+
+#endif /* CLASSIFIER_H */

.venv_haddock/include/site/python3.12/freesasa/classifier_naccess.c

@@ -0,0 +1,434 @@
+#include "classifier.h"
+
+/* Autogenerated code from the script config2c.pl */
+
+static const char *naccess_residue_name[] = {"A", "ALA", "ANY", "ARG", "ASN", "ASP", "C", "CYS", "DA", "DC", "DG", "DI", "DT", "DU", "G", "GLN", "GLU", "GLY", "HIS", "I", "ILE", "LEU", "LYS", "MET", "MSE", "PHE", "PRO", "SEC", "SER", "T", "THR", "TRP", "TYR", "U", "VAL", };
+static const char *naccess_A_atom_name[] = {"C2", "C6", "C4", "N7", "N9", "C5", "C8", "N3", "N6", "N1", };
+static double naccess_A_atom_radius[] = {1.80, 1.80, 1.80, 1.60, 1.60, 1.80, 1.80, 1.60, 1.60, 1.60, };
+static int naccess_A_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_A_cfg = {
+    10,
+ "A",
+    (char**) naccess_A_atom_name,
+    (double*) naccess_A_atom_radius,
+    (freesasa_atom_class*) naccess_A_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_ALA_atom_name[] = {"CB", };
+static double naccess_ALA_atom_radius[] = {1.87, };
+static int naccess_ALA_atom_class[] = {FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_ALA_cfg = {
+    1,
+ "ALA",
+    (char**) naccess_ALA_atom_name,
+    (double*) naccess_ALA_atom_radius,
+    (freesasa_atom_class*) naccess_ALA_atom_class,
+ {"ALA", 107.89, 43.94, 63.94, 36.71, 71.17, 0},
+};
+
+static const char *naccess_ANY_atom_name[] = {"C3'", "OP1", "C", "O5'", "OXT", "C1'", "CA", "C5'", "C4'", "O2'", "O", "OP2", "CB", "N", "P", "O4'", "OP3", "C2'", "O3'", };
+static double naccess_ANY_atom_radius[] = {1.80, 1.40, 1.76, 1.40, 1.40, 1.80, 1.87, 1.80, 1.80, 1.40, 1.40, 1.40, 1.87, 1.65, 1.90, 1.40, 1.40, 1.80, 1.40, };
+static int naccess_ANY_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_ANY_cfg = {
+    19,
+ "ANY",
+    (char**) naccess_ANY_atom_name,
+    (double*) naccess_ANY_atom_radius,
+    (freesasa_atom_class*) naccess_ANY_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_ARG_atom_name[] = {"CG", "CD", "NH1", "NE", "NH2", "CZ", };
+static double naccess_ARG_atom_radius[] = {1.87, 1.87, 1.65, 1.65, 1.65, 1.76, };
+static int naccess_ARG_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_ARG_cfg = {
+    6,
+ "ARG",
+    (char**) naccess_ARG_atom_name,
+    (double*) naccess_ARG_atom_radius,
+    (freesasa_atom_class*) naccess_ARG_atom_class,
+ {"ARG", 238.33, 41.72, 196.61, 161.10, 77.23, 0},
+};
+
+static const char *naccess_ASN_atom_name[] = {"OD1", "CG", "ND2", };
+static double naccess_ASN_atom_radius[] = {1.40, 1.76, 1.65, };
+static int naccess_ASN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_ASN_cfg = {
+    3,
+ "ASN",
+    (char**) naccess_ASN_atom_name,
+    (double*) naccess_ASN_atom_radius,
+    (freesasa_atom_class*) naccess_ASN_atom_class,
+ {"ASN", 143.97, 41.03, 102.94, 97.83, 46.14, 0},
+};
+
+static const char *naccess_ASP_atom_name[] = {"OD1", "CG", "OD2", };
+static double naccess_ASP_atom_radius[] = {1.40, 1.76, 1.40, };
+static int naccess_ASP_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_ASP_cfg = {
+    3,
+ "ASP",
+    (char**) naccess_ASP_atom_name,
+    (double*) naccess_ASP_atom_radius,
+    (freesasa_atom_class*) naccess_ASP_atom_class,
+ {"ASP", 140.48, 41.76, 98.72, 91.19, 49.29, 0},
+};
+
+static const char *naccess_C_atom_name[] = {"C5", "C6", "C4", "C2", "N1", "N4", "O2", "N3", };
+static double naccess_C_atom_radius[] = {1.80, 1.80, 1.80, 1.80, 1.60, 1.60, 1.40, 1.60, };
+static int naccess_C_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_C_cfg = {
+    8,
+ "C",
+    (char**) naccess_C_atom_name,
+    (double*) naccess_C_atom_radius,
+    (freesasa_atom_class*) naccess_C_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_CYS_atom_name[] = {"SG", };
+static double naccess_CYS_atom_radius[] = {1.85, };
+static int naccess_CYS_atom_class[] = {FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_CYS_cfg = {
+    1,
+ "CYS",
+    (char**) naccess_CYS_atom_name,
+    (double*) naccess_CYS_atom_radius,
+    (freesasa_atom_class*) naccess_CYS_atom_class,
+ {"CYS", 134.24, 41.92, 92.33, 36.49, 97.75, 0},
+};
+
+static const char *naccess_DA_atom_name[] = {"N6", "N1", "C8", "N3", "N9", "N7", "C5", "C2", "C6", "C4", };
+static double naccess_DA_atom_radius[] = {1.60, 1.60, 1.80, 1.60, 1.60, 1.60, 1.80, 1.80, 1.80, 1.80, };
+static int naccess_DA_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_DA_cfg = {
+    10,
+ "DA",
+    (char**) naccess_DA_atom_name,
+    (double*) naccess_DA_atom_radius,
+    (freesasa_atom_class*) naccess_DA_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_DC_atom_name[] = {"C2", "C4", "C6", "C5", "O2", "N3", "N4", "N1", };
+static double naccess_DC_atom_radius[] = {1.80, 1.80, 1.80, 1.80, 1.40, 1.60, 1.60, 1.60, };
+static int naccess_DC_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_DC_cfg = {
+    8,
+ "DC",
+    (char**) naccess_DC_atom_name,
+    (double*) naccess_DC_atom_radius,
+    (freesasa_atom_class*) naccess_DC_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_DG_atom_name[] = {"C8", "N3", "N1", "N2", "C2", "C6", "C4", "C5", "N9", "N7", "O6", };
+static double naccess_DG_atom_radius[] = {1.80, 1.60, 1.60, 1.60, 1.80, 1.80, 1.80, 1.80, 1.60, 1.60, 1.40, };
+static int naccess_DG_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_DG_cfg = {
+    11,
+ "DG",
+    (char**) naccess_DG_atom_name,
+    (double*) naccess_DG_atom_radius,
+    (freesasa_atom_class*) naccess_DG_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_DI_atom_name[] = {"N7", "N9", "C5", "O6", "C2", "C4", "C6", "N1", "C8", "N3", };
+static double naccess_DI_atom_radius[] = {1.60, 1.60, 1.80, 1.40, 1.80, 1.80, 1.80, 1.60, 1.80, 1.60, };
+static int naccess_DI_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_DI_cfg = {
+    10,
+ "DI",
+    (char**) naccess_DI_atom_name,
+    (double*) naccess_DI_atom_radius,
+    (freesasa_atom_class*) naccess_DI_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_DT_atom_name[] = {"C7", "N3", "O2", "N1", "C2", "O4", "C6", "C4", "C5", };
+static double naccess_DT_atom_radius[] = {1.80, 1.60, 1.40, 1.60, 1.80, 1.40, 1.80, 1.80, 1.80, };
+static int naccess_DT_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_DT_cfg = {
+    9,
+ "DT",
+    (char**) naccess_DT_atom_name,
+    (double*) naccess_DT_atom_radius,
+    (freesasa_atom_class*) naccess_DT_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_DU_atom_name[] = {"N3", "O2", "N1", "C6", "C4", "O4", "C2", "C5", };
+static double naccess_DU_atom_radius[] = {1.60, 1.40, 1.60, 1.80, 1.80, 1.40, 1.80, 1.80, };
+static int naccess_DU_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_DU_cfg = {
+    8,
+ "DU",
+    (char**) naccess_DU_atom_name,
+    (double*) naccess_DU_atom_radius,
+    (freesasa_atom_class*) naccess_DU_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_G_atom_name[] = {"N2", "C2", "C6", "C4", "N9", "N7", "C5", "O6", "C8", "N3", "N1", };
+static double naccess_G_atom_radius[] = {1.60, 1.80, 1.80, 1.80, 1.60, 1.60, 1.80, 1.40, 1.80, 1.60, 1.60, };
+static int naccess_G_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_G_cfg = {
+    11,
+ "G",
+    (char**) naccess_G_atom_name,
+    (double*) naccess_G_atom_radius,
+    (freesasa_atom_class*) naccess_G_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_GLN_atom_name[] = {"NE2", "OE1", "CD", "CG", };
+static double naccess_GLN_atom_radius[] = {1.65, 1.40, 1.76, 1.87, };
+static int naccess_GLN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_GLN_cfg = {
+    4,
+ "GLN",
+    (char**) naccess_GLN_atom_name,
+    (double*) naccess_GLN_atom_radius,
+    (freesasa_atom_class*) naccess_GLN_atom_class,
+ {"GLN", 178.24, 41.72, 136.52, 126.35, 51.89, 0},
+};
+
+static const char *naccess_GLU_atom_name[] = {"OE2", "OE1", "CD", "CG", };
+static double naccess_GLU_atom_radius[] = {1.40, 1.40, 1.76, 1.87, };
+static int naccess_GLU_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_GLU_cfg = {
+    4,
+ "GLU",
+    (char**) naccess_GLU_atom_name,
+    (double*) naccess_GLU_atom_radius,
+    (freesasa_atom_class*) naccess_GLU_atom_class,
+ {"GLU", 172.09, 41.72, 130.37, 112.13, 59.96, 0},
+};
+
+static const char *naccess_GLY_atom_name[] = {"CA", };
+static double naccess_GLY_atom_radius[] = {1.87, };
+static int naccess_GLY_atom_class[] = {FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_GLY_cfg = {
+    1,
+ "GLY",
+    (char**) naccess_GLY_atom_name,
+    (double*) naccess_GLY_atom_radius,
+    (freesasa_atom_class*) naccess_GLY_atom_class,
+ {"GLY", 80.30, 80.30, 0.00, 42.62, 37.69, 0},
+};
+
+static const char *naccess_HIS_atom_name[] = {"CG", "NE2", "CE1", "ND1", "CD2", };
+static double naccess_HIS_atom_radius[] = {1.76, 1.65, 1.76, 1.65, 1.76, };
+static int naccess_HIS_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_HIS_cfg = {
+    5,
+ "HIS",
+    (char**) naccess_HIS_atom_name,
+    (double*) naccess_HIS_atom_radius,
+    (freesasa_atom_class*) naccess_HIS_atom_class,
+ {"HIS", 182.75, 38.76, 143.99, 85.61, 97.14, 0},
+};
+
+static const char *naccess_I_atom_name[] = {"N3", "C8", "N1", "C4", "C6", "C2", "O6", "C5", "N7", "N9", };
+static double naccess_I_atom_radius[] = {1.60, 1.80, 1.60, 1.80, 1.80, 1.80, 1.40, 1.80, 1.60, 1.60, };
+static int naccess_I_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_I_cfg = {
+    10,
+ "I",
+    (char**) naccess_I_atom_name,
+    (double*) naccess_I_atom_radius,
+    (freesasa_atom_class*) naccess_I_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_ILE_atom_name[] = {"CG1", "CG2", "CD1", };
+static double naccess_ILE_atom_radius[] = {1.87, 1.87, 1.87, };
+static int naccess_ILE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_ILE_cfg = {
+    3,
+ "ILE",
+    (char**) naccess_ILE_atom_name,
+    (double*) naccess_ILE_atom_radius,
+    (freesasa_atom_class*) naccess_ILE_atom_class,
+ {"ILE", 175.10, 41.16, 133.94, 36.10, 139.00, 0},
+};
+
+static const char *naccess_LEU_atom_name[] = {"CD2", "CD1", "CG", };
+static double naccess_LEU_atom_radius[] = {1.87, 1.87, 1.87, };
+static int naccess_LEU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_LEU_cfg = {
+    3,
+ "LEU",
+    (char**) naccess_LEU_atom_name,
+    (double*) naccess_LEU_atom_radius,
+    (freesasa_atom_class*) naccess_LEU_atom_class,
+ {"LEU", 178.40, 39.50, 138.90, 36.45, 141.95, 0},
+};
+
+static const char *naccess_LYS_atom_name[] = {"CD", "NZ", "CE", "CG", };
+static double naccess_LYS_atom_radius[] = {1.87, 1.50, 1.87, 1.87, };
+static int naccess_LYS_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_LYS_cfg = {
+    4,
+ "LYS",
+    (char**) naccess_LYS_atom_name,
+    (double*) naccess_LYS_atom_radius,
+    (freesasa_atom_class*) naccess_LYS_atom_class,
+ {"LYS", 200.21, 41.72, 158.49, 84.31, 115.90, 0},
+};
+
+static const char *naccess_MET_atom_name[] = {"CE", "CG", "SD", };
+static double naccess_MET_atom_radius[] = {1.87, 1.87, 1.85, };
+static int naccess_MET_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_MET_cfg = {
+    3,
+ "MET",
+    (char**) naccess_MET_atom_name,
+    (double*) naccess_MET_atom_radius,
+    (freesasa_atom_class*) naccess_MET_atom_class,
+ {"MET", 193.72, 41.72, 152.00, 36.45, 157.27, 0},
+};
+
+static const char *naccess_MSE_atom_name[] = {"SE", };
+static double naccess_MSE_atom_radius[] = {1.80, };
+static int naccess_MSE_atom_class[] = {FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_MSE_cfg = {
+    1,
+ "MSE",
+    (char**) naccess_MSE_atom_name,
+    (double*) naccess_MSE_atom_radius,
+    (freesasa_atom_class*) naccess_MSE_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_PHE_atom_name[] = {"CG", "CD1", "CE2", "CE1", "CZ", "CD2", };
+static double naccess_PHE_atom_radius[] = {1.76, 1.76, 1.76, 1.76, 1.76, 1.76, };
+static int naccess_PHE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_PHE_cfg = {
+    6,
+ "PHE",
+    (char**) naccess_PHE_atom_name,
+    (double*) naccess_PHE_atom_radius,
+    (freesasa_atom_class*) naccess_PHE_atom_class,
+ {"PHE", 199.40, 38.12, 161.27, 34.25, 165.14, 0},
+};
+
+static const char *naccess_PRO_atom_name[] = {"CG", "CD", };
+static double naccess_PRO_atom_radius[] = {1.87, 1.87, };
+static int naccess_PRO_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_PRO_cfg = {
+    2,
+ "PRO",
+    (char**) naccess_PRO_atom_name,
+    (double*) naccess_PRO_atom_radius,
+    (freesasa_atom_class*) naccess_PRO_atom_class,
+ {"PRO", 135.84, 27.09, 108.76, 15.17, 120.67, 0},
+};
+
+static const char *naccess_SEC_atom_name[] = {"SE", };
+static double naccess_SEC_atom_radius[] = {1.80, };
+static int naccess_SEC_atom_class[] = {FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_SEC_cfg = {
+    1,
+ "SEC",
+    (char**) naccess_SEC_atom_name,
+    (double*) naccess_SEC_atom_radius,
+    (freesasa_atom_class*) naccess_SEC_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_SER_atom_name[] = {"OG", };
+static double naccess_SER_atom_radius[] = {1.40, };
+static int naccess_SER_atom_class[] = {FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_SER_cfg = {
+    1,
+ "SER",
+    (char**) naccess_SER_atom_name,
+    (double*) naccess_SER_atom_radius,
+    (freesasa_atom_class*) naccess_SER_atom_class,
+ {"SER", 116.56, 43.38, 73.18, 68.03, 48.53, 0},
+};
+
+static const char *naccess_T_atom_name[] = {"C4", "C6", "O4", "C2", "C5", "N3", "C7", "O2", "N1", };
+static double naccess_T_atom_radius[] = {1.80, 1.80, 1.40, 1.80, 1.80, 1.60, 1.80, 1.40, 1.60, };
+static int naccess_T_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_T_cfg = {
+    9,
+ "T",
+    (char**) naccess_T_atom_name,
+    (double*) naccess_T_atom_radius,
+    (freesasa_atom_class*) naccess_T_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_THR_atom_name[] = {"CG2", "OG1", };
+static double naccess_THR_atom_radius[] = {1.87, 1.40, };
+static int naccess_THR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_THR_cfg = {
+    2,
+ "THR",
+    (char**) naccess_THR_atom_name,
+    (double*) naccess_THR_atom_radius,
+    (freesasa_atom_class*) naccess_THR_atom_class,
+ {"THR", 139.25, 41.70, 97.55, 63.50, 75.75, 0},
+};
+
+static const char *naccess_TRP_atom_name[] = {"CD1", "CZ2", "CE2", "NE1", "CG", "CE3", "CH2", "CZ3", "CD2", };
+static double naccess_TRP_atom_radius[] = {1.76, 1.76, 1.76, 1.65, 1.76, 1.76, 1.76, 1.76, 1.76, };
+static int naccess_TRP_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_TRP_cfg = {
+    9,
+ "TRP",
+    (char**) naccess_TRP_atom_name,
+    (double*) naccess_TRP_atom_radius,
+    (freesasa_atom_class*) naccess_TRP_atom_class,
+ {"TRP", 248.97, 42.38, 206.59, 59.83, 189.14, 0},
+};
+
+static const char *naccess_TYR_atom_name[] = {"CG", "CZ", "CE1", "CE2", "CD1", "OH", "CD2", };
+static double naccess_TYR_atom_radius[] = {1.76, 1.76, 1.76, 1.76, 1.76, 1.40, 1.76, };
+static int naccess_TYR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_TYR_cfg = {
+    7,
+ "TYR",
+    (char**) naccess_TYR_atom_name,
+    (double*) naccess_TYR_atom_radius,
+    (freesasa_atom_class*) naccess_TYR_atom_class,
+ {"TYR", 212.23, 38.13, 174.10, 76.34, 135.89, 0},
+};
+
+static const char *naccess_U_atom_name[] = {"C2", "C4", "C6", "O4", "C5", "N3", "O2", "N1", };
+static double naccess_U_atom_radius[] = {1.80, 1.80, 1.80, 1.40, 1.80, 1.60, 1.40, 1.60, };
+static int naccess_U_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue naccess_U_cfg = {
+    8,
+ "U",
+    (char**) naccess_U_atom_name,
+    (double*) naccess_U_atom_radius,
+    (freesasa_atom_class*) naccess_U_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *naccess_VAL_atom_name[] = {"CG2", "CG1", };
+static double naccess_VAL_atom_radius[] = {1.87, 1.87, };
+static int naccess_VAL_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue naccess_VAL_cfg = {
+    2,
+ "VAL",
+    (char**) naccess_VAL_atom_name,
+    (double*) naccess_VAL_atom_radius,
+    (freesasa_atom_class*) naccess_VAL_atom_class,
+ {"VAL", 151.40, 41.17, 110.23, 36.12, 115.28, 0},
+};
+
+static struct classifier_residue *naccess_residue_cfg[] = {
+    &naccess_A_cfg, &naccess_ALA_cfg, &naccess_ANY_cfg, &naccess_ARG_cfg, &naccess_ASN_cfg, &naccess_ASP_cfg, &naccess_C_cfg, &naccess_CYS_cfg, &naccess_DA_cfg, &naccess_DC_cfg, &naccess_DG_cfg, &naccess_DI_cfg, &naccess_DT_cfg, &naccess_DU_cfg, &naccess_G_cfg, &naccess_GLN_cfg, &naccess_GLU_cfg, &naccess_GLY_cfg, &naccess_HIS_cfg, &naccess_I_cfg, &naccess_ILE_cfg, &naccess_LEU_cfg, &naccess_LYS_cfg, &naccess_MET_cfg, &naccess_MSE_cfg, &naccess_PHE_cfg, &naccess_PRO_cfg, &naccess_SEC_cfg, &naccess_SER_cfg, &naccess_T_cfg, &naccess_THR_cfg, &naccess_TRP_cfg, &naccess_TYR_cfg, &naccess_U_cfg, &naccess_VAL_cfg, };
+
+const freesasa_classifier freesasa_naccess_classifier = {
+    35,    (char**) naccess_residue_name,
+    "NACCESS",
+    (struct classifier_residue **) naccess_residue_cfg,
+};
+

.venv_haddock/include/site/python3.12/freesasa/classifier_oons.c

@@ -0,0 +1,350 @@
+#include "classifier.h"
+
+/* Autogenerated code from the script config2c.pl */
+
+static const char *oons_residue_name[] = {"ACE", "ANY", "ARG", "ASN", "ASP", "ASX", "CSE", "CYS", "GLN", "GLU", "GLX", "HIS", "HOH", "ILE", "LEU", "LYS", "MET", "MSE", "NH2", "PHE", "PRO", "PYL", "SEC", "SER", "THR", "TRP", "TYR", "VAL", };
+static const char *oons_ACE_atom_name[] = {"CH3", };
+static double oons_ACE_atom_radius[] = {2.00, };
+static int oons_ACE_atom_class[] = {FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_ACE_cfg = {
+    1,
+ "ACE",
+    (char**) oons_ACE_atom_name,
+    (double*) oons_ACE_atom_radius,
+    (freesasa_atom_class*) oons_ACE_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *oons_ANY_atom_name[] = {"N3", "O2", "N4", "N7", "CM2", "N9", "C5'", "C3'", "C1'", "C7", "OXT", "OP3", "C2", "C4'", "C5", "C8", "N1", "OP2", "C4", "N6", "C", "CB", "N2", "P", "OP1", "O2'", "O6", "O4'", "O5'", "O", "C2'", "CA", "O4", "O3'", "C6", "N", };
+static double oons_ANY_atom_radius[] = {1.55, 1.40, 1.55, 1.55, 2.00, 1.55, 2.00, 1.75, 1.75, 1.75, 1.40, 1.40, 1.75, 1.75, 1.75, 1.75, 1.55, 1.40, 1.75, 1.55, 1.55, 2.00, 1.55, 1.80, 1.40, 1.40, 1.40, 1.40, 1.40, 1.40, 1.75, 2.00, 1.40, 1.40, 1.75, 1.55, };
+static int oons_ANY_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_ANY_cfg = {
+    36,
+ "ANY",
+    (char**) oons_ANY_atom_name,
+    (double*) oons_ANY_atom_radius,
+    (freesasa_atom_class*) oons_ANY_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *oons_ARG_atom_name[] = {"NH1", "NH2", "CZ", "CD", "CG", "NE", };
+static double oons_ARG_atom_radius[] = {1.55, 1.55, 2.00, 2.00, 2.00, 1.55, };
+static int oons_ARG_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_ARG_cfg = {
+    6,
+ "ARG",
+    (char**) oons_ARG_atom_name,
+    (double*) oons_ARG_atom_radius,
+    (freesasa_atom_class*) oons_ARG_atom_class,
+ {"ARG", 235.30, 38.31, 196.99, 125.27, 110.03, 0},
+};
+
+static const char *oons_ASN_atom_name[] = {"ND2", "OD1", "CG", };
+static double oons_ASN_atom_radius[] = {1.55, 1.40, 1.55, };
+static int oons_ASN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_ASN_cfg = {
+    3,
+ "ASN",
+    (char**) oons_ASN_atom_name,
+    (double*) oons_ASN_atom_radius,
+    (freesasa_atom_class*) oons_ASN_atom_class,
+ {"ASN", 143.47, 38.26, 105.21, 97.51, 45.97, 0},
+};
+
+static const char *oons_ASP_atom_name[] = {"OD1", "CG", "OD2", };
+static double oons_ASP_atom_radius[] = {1.40, 1.55, 1.40, };
+static int oons_ASP_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_ASP_cfg = {
+    3,
+ "ASP",
+    (char**) oons_ASP_atom_name,
+    (double*) oons_ASP_atom_radius,
+    (freesasa_atom_class*) oons_ASP_atom_class,
+ {"ASP", 141.20, 38.87, 102.33, 95.17, 46.03, 0},
+};
+
+static const char *oons_ASX_atom_name[] = {"XD1", "AD2", "XD2", "AD1", "CG", };
+static double oons_ASX_atom_radius[] = {1.5, 1.5, 1.5, 1.5, 1.55, };
+static int oons_ASX_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_ASX_cfg = {
+    5,
+ "ASX",
+    (char**) oons_ASX_atom_name,
+    (double*) oons_ASX_atom_radius,
+    (freesasa_atom_class*) oons_ASX_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *oons_CSE_atom_name[] = {"SE", };
+static double oons_CSE_atom_radius[] = {1.90, };
+static int oons_CSE_atom_class[] = {FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_CSE_cfg = {
+    1,
+ "CSE",
+    (char**) oons_CSE_atom_name,
+    (double*) oons_CSE_atom_radius,
+    (freesasa_atom_class*) oons_CSE_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *oons_CYS_atom_name[] = {"SG", };
+static double oons_CYS_atom_radius[] = {2.00, };
+static int oons_CYS_atom_class[] = {FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_CYS_cfg = {
+    1,
+ "CYS",
+    (char**) oons_CYS_atom_name,
+    (double*) oons_CYS_atom_radius,
+    (freesasa_atom_class*) oons_CYS_atom_class,
+ {"CYS", 140.29, 38.44, 101.85, 98.30, 41.99, 0},
+};
+
+static const char *oons_GLN_atom_name[] = {"CD", "NE2", "OE1", "CG", };
+static double oons_GLN_atom_radius[] = {1.55, 1.55, 1.40, 2.00, };
+static int oons_GLN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_GLN_cfg = {
+    4,
+ "GLN",
+    (char**) oons_GLN_atom_name,
+    (double*) oons_GLN_atom_radius,
+    (freesasa_atom_class*) oons_GLN_atom_class,
+ {"GLN", 176.23, 38.31, 137.92, 122.17, 54.06, 0},
+};
+
+static const char *oons_GLU_atom_name[] = {"CD", "OE1", "CG", "OE2", };
+static double oons_GLU_atom_radius[] = {1.55, 1.40, 2.00, 1.40, };
+static int oons_GLU_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_GLU_cfg = {
+    4,
+ "GLU",
+    (char**) oons_GLU_atom_name,
+    (double*) oons_GLU_atom_radius,
+    (freesasa_atom_class*) oons_GLU_atom_class,
+ {"GLU", 172.43, 38.31, 134.11, 115.92, 56.51, 0},
+};
+
+static const char *oons_GLX_atom_name[] = {"XE1", "AE1", "AE2", "CD", "XE2", "CG", };
+static double oons_GLX_atom_radius[] = {1.5, 1.5, 1.5, 1.55, 1.5, 2.00, };
+static int oons_GLX_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_GLX_cfg = {
+    6,
+ "GLX",
+    (char**) oons_GLX_atom_name,
+    (double*) oons_GLX_atom_radius,
+    (freesasa_atom_class*) oons_GLX_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *oons_HIS_atom_name[] = {"ND1", "CE1", "NE2", "CG", "CD2", };
+static double oons_HIS_atom_radius[] = {1.55, 1.75, 1.55, 1.75, 1.75, };
+static int oons_HIS_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_HIS_cfg = {
+    5,
+ "HIS",
+    (char**) oons_HIS_atom_name,
+    (double*) oons_HIS_atom_radius,
+    (freesasa_atom_class*) oons_HIS_atom_class,
+ {"HIS", 180.78, 36.04, 144.74, 73.26, 107.52, 0},
+};
+
+static const char *oons_HOH_atom_name[] = {"O", };
+static double oons_HOH_atom_radius[] = {1.40, };
+static int oons_HOH_atom_class[] = {FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_HOH_cfg = {
+    1,
+ "HOH",
+    (char**) oons_HOH_atom_name,
+    (double*) oons_HOH_atom_radius,
+    (freesasa_atom_class*) oons_HOH_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *oons_ILE_atom_name[] = {"CG1", "CG2", "CD1", };
+static double oons_ILE_atom_radius[] = {2.00, 2.00, 2.00, };
+static int oons_ILE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_ILE_cfg = {
+    3,
+ "ILE",
+    (char**) oons_ILE_atom_name,
+    (double*) oons_ILE_atom_radius,
+    (freesasa_atom_class*) oons_ILE_atom_class,
+ {"ILE", 182.12, 37.96, 144.16, 31.67, 150.45, 0},
+};
+
+static const char *oons_LEU_atom_name[] = {"CD1", "CG", "CD2", };
+static double oons_LEU_atom_radius[] = {2.00, 2.00, 2.00, };
+static int oons_LEU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_LEU_cfg = {
+    3,
+ "LEU",
+    (char**) oons_LEU_atom_name,
+    (double*) oons_LEU_atom_radius,
+    (freesasa_atom_class*) oons_LEU_atom_class,
+ {"LEU", 185.43, 35.34, 150.08, 31.73, 153.69, 0},
+};
+
+static const char *oons_LYS_atom_name[] = {"NZ", "CE", "CG", "CD", };
+static double oons_LYS_atom_radius[] = {1.55, 2.00, 2.00, 2.00, };
+static int oons_LYS_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_LYS_cfg = {
+    4,
+ "LYS",
+    (char**) oons_LYS_atom_name,
+    (double*) oons_LYS_atom_radius,
+    (freesasa_atom_class*) oons_LYS_atom_class,
+ {"LYS", 205.80, 38.31, 167.49, 78.02, 127.78, 0},
+};
+
+static const char *oons_MET_atom_name[] = {"CE", "SD", "CG", };
+static double oons_MET_atom_radius[] = {2.00, 2.00, 2.00, };
+static int oons_MET_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_MET_cfg = {
+    3,
+ "MET",
+    (char**) oons_MET_atom_name,
+    (double*) oons_MET_atom_radius,
+    (freesasa_atom_class*) oons_MET_atom_class,
+ {"MET", 201.66, 38.31, 163.35, 78.68, 122.98, 0},
+};
+
+static const char *oons_MSE_atom_name[] = {"CE", "SE", "CG", };
+static double oons_MSE_atom_radius[] = {2.00, 1.90, 2.00, };
+static int oons_MSE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_MSE_cfg = {
+    3,
+ "MSE",
+    (char**) oons_MSE_atom_name,
+    (double*) oons_MSE_atom_radius,
+    (freesasa_atom_class*) oons_MSE_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *oons_NH2_atom_name[] = {"NH2", };
+static double oons_NH2_atom_radius[] = {1.55, };
+static int oons_NH2_atom_class[] = {FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_NH2_cfg = {
+    1,
+ "NH2",
+    (char**) oons_NH2_atom_name,
+    (double*) oons_NH2_atom_radius,
+    (freesasa_atom_class*) oons_NH2_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *oons_PHE_atom_name[] = {"CD1", "CZ", "CG", "CD2", "CE2", "CE1", };
+static double oons_PHE_atom_radius[] = {1.75, 1.75, 1.75, 1.75, 1.75, 1.75, };
+static int oons_PHE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_PHE_cfg = {
+    6,
+ "PHE",
+    (char**) oons_PHE_atom_name,
+    (double*) oons_PHE_atom_radius,
+    (freesasa_atom_class*) oons_PHE_atom_class,
+ {"PHE", 199.28, 35.20, 164.08, 30.08, 169.20, 0},
+};
+
+static const char *oons_PRO_atom_name[] = {"CD", "CG", "CB", };
+static double oons_PRO_atom_radius[] = {1.75, 1.75, 1.75, };
+static int oons_PRO_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_PRO_cfg = {
+    3,
+ "PRO",
+    (char**) oons_PRO_atom_name,
+    (double*) oons_PRO_atom_radius,
+    (freesasa_atom_class*) oons_PRO_atom_class,
+ {"PRO", 128.18, 31.08, 97.10, 13.95, 114.23, 0},
+};
+
+static const char *oons_PYL_atom_name[] = {"CD2", "CG2", "O2", "CA2", "CE2", "C2", "CG", "CD", "N2", "NZ", "CE", "CB2", };
+static double oons_PYL_atom_radius[] = {1.75, 1.75, 1.40, 1.75, 1.75, 1.55, 2.00, 2.00, 1.55, 1.55, 2.00, 2.00, };
+static int oons_PYL_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_PYL_cfg = {
+    12,
+ "PYL",
+    (char**) oons_PYL_atom_name,
+    (double*) oons_PYL_atom_radius,
+    (freesasa_atom_class*) oons_PYL_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *oons_SEC_atom_name[] = {"SE", };
+static double oons_SEC_atom_radius[] = {1.90, };
+static int oons_SEC_atom_class[] = {FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_SEC_cfg = {
+    1,
+ "SEC",
+    (char**) oons_SEC_atom_name,
+    (double*) oons_SEC_atom_radius,
+    (freesasa_atom_class*) oons_SEC_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *oons_SER_atom_name[] = {"OG", };
+static double oons_SER_atom_radius[] = {1.40, };
+static int oons_SER_atom_class[] = {FREESASA_ATOM_POLAR, };
+static struct classifier_residue oons_SER_cfg = {
+    1,
+ "SER",
+    (char**) oons_SER_atom_name,
+    (double*) oons_SER_atom_radius,
+    (freesasa_atom_class*) oons_SER_atom_class,
+ {"SER", 118.43, 40.20, 78.23, 60.41, 58.02, 0},
+};
+
+static const char *oons_THR_atom_name[] = {"OG1", "CG2", };
+static double oons_THR_atom_radius[] = {1.40, 2.00, };
+static int oons_THR_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_THR_cfg = {
+    2,
+ "THR",
+    (char**) oons_THR_atom_name,
+    (double*) oons_THR_atom_radius,
+    (freesasa_atom_class*) oons_THR_atom_class,
+ {"THR", 142.41, 38.32, 104.08, 56.42, 85.99, 0},
+};
+
+static const char *oons_TRP_atom_name[] = {"CD2", "CE3", "CE2", "CH2", "CD1", "CZ3", "CZ2", "NE1", "CG", };
+static double oons_TRP_atom_radius[] = {1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.55, 1.75, };
+static int oons_TRP_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_TRP_cfg = {
+    9,
+ "TRP",
+    (char**) oons_TRP_atom_name,
+    (double*) oons_TRP_atom_radius,
+    (freesasa_atom_class*) oons_TRP_atom_class,
+ {"TRP", 247.08, 39.43, 207.65, 52.90, 194.18, 0},
+};
+
+static const char *oons_TYR_atom_name[] = {"CG", "CD2", "CD1", "CZ", "CE1", "OH", "CE2", };
+static double oons_TYR_atom_radius[] = {1.75, 1.75, 1.75, 1.75, 1.75, 1.40, 1.75, };
+static int oons_TYR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_TYR_cfg = {
+    7,
+ "TYR",
+    (char**) oons_TYR_atom_name,
+    (double*) oons_TYR_atom_radius,
+    (freesasa_atom_class*) oons_TYR_atom_class,
+ {"TYR", 212.31, 35.20, 177.11, 72.41, 139.90, 0},
+};
+
+static const char *oons_VAL_atom_name[] = {"CG1", "CG2", };
+static double oons_VAL_atom_radius[] = {2.00, 2.00, };
+static int oons_VAL_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue oons_VAL_cfg = {
+    2,
+ "VAL",
+    (char**) oons_VAL_atom_name,
+    (double*) oons_VAL_atom_radius,
+    (freesasa_atom_class*) oons_VAL_atom_class,
+ {"VAL", 157.64, 37.96, 119.68, 31.70, 125.94, 0},
+};
+
+static struct classifier_residue *oons_residue_cfg[] = {
+    &oons_ACE_cfg, &oons_ANY_cfg, &oons_ARG_cfg, &oons_ASN_cfg, &oons_ASP_cfg, &oons_ASX_cfg, &oons_CSE_cfg, &oons_CYS_cfg, &oons_GLN_cfg, &oons_GLU_cfg, &oons_GLX_cfg, &oons_HIS_cfg, &oons_HOH_cfg, &oons_ILE_cfg, &oons_LEU_cfg, &oons_LYS_cfg, &oons_MET_cfg, &oons_MSE_cfg, &oons_NH2_cfg, &oons_PHE_cfg, &oons_PRO_cfg, &oons_PYL_cfg, &oons_SEC_cfg, &oons_SER_cfg, &oons_THR_cfg, &oons_TRP_cfg, &oons_TYR_cfg, &oons_VAL_cfg, };
+
+const freesasa_classifier freesasa_oons_classifier = {
+    28,    (char**) oons_residue_name,
+    "OONS",
+    (struct classifier_residue **) oons_residue_cfg,
+};
+

.venv_haddock/include/site/python3.12/freesasa/classifier_protor.c

@@ -0,0 +1,494 @@
+#include "classifier.h"
+
+/* Autogenerated code from the script config2c.pl */
+
+static const char *protor_residue_name[] = {"A", "ACE", "ALA", "ARG", "ASN", "ASP", "ASX", "C", "CYS", "DA", "DC", "DG", "DI", "DT", "DU", "G", "GLN", "GLU", "GLX", "GLY", "HIS", "HOH", "I", "ILE", "LEU", "LYS", "MET", "MSE", "NH2", "PHE", "PRO", "PYL", "SEC", "SER", "T", "THR", "TRP", "TYR", "U", "VAL", };
+static const char *protor_A_atom_name[] = {"C6", "O2'", "C2'", "OP1", "C5", "C4", "O3'", "OP3", "P", "C4'", "O4'", "C3'", "C8", "N6", "N9", "O5'", "N7", "OP2", "C5'", "N3", "C1'", "N1", "C2", };
+static double protor_A_atom_radius[] = {1.61, 1.46, 1.88, 1.42, 1.61, 1.61, 1.46, 1.46, 1.8, 1.88, 1.46, 1.88, 1.76, 1.64, 1.64, 1.46, 1.64, 1.46, 1.88, 1.64, 1.88, 1.64, 1.76, };
+static int protor_A_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_A_cfg = {
+    23,
+ "A",
+    (char**) protor_A_atom_name,
+    (double*) protor_A_atom_radius,
+    (freesasa_atom_class*) protor_A_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_ACE_atom_name[] = {"O", "CH3", "C", };
+static double protor_ACE_atom_radius[] = {1.42, 1.88, 1.76, };
+static int protor_ACE_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_ACE_cfg = {
+    3,
+ "ACE",
+    (char**) protor_ACE_atom_name,
+    (double*) protor_ACE_atom_radius,
+    (freesasa_atom_class*) protor_ACE_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_ALA_atom_name[] = {"N", "CB", "CA", "C", "O", "OXT", };
+static double protor_ALA_atom_radius[] = {1.64, 1.88, 1.88, 1.61, 1.42, 1.46, };
+static int protor_ALA_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_ALA_cfg = {
+    6,
+ "ALA",
+    (char**) protor_ALA_atom_name,
+    (double*) protor_ALA_atom_radius,
+    (freesasa_atom_class*) protor_ALA_atom_class,
+ {"ALA", 108.76, 43.96, 64.80, 37.75, 71.01, 0},
+};
+
+static const char *protor_ARG_atom_name[] = {"C", "CA", "CB", "NH1", "OXT", "CZ", "CG", "O", "NE", "CD", "N", "NH2", };
+static double protor_ARG_atom_radius[] = {1.61, 1.88, 1.88, 1.64, 1.46, 1.61, 1.88, 1.42, 1.64, 1.88, 1.64, 1.64, };
+static int protor_ARG_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_ARG_cfg = {
+    12,
+ "ARG",
+    (char**) protor_ARG_atom_name,
+    (double*) protor_ARG_atom_radius,
+    (freesasa_atom_class*) protor_ARG_atom_class,
+ {"ARG", 238.17, 42.00, 196.17, 165.00, 73.17, 0},
+};
+
+static const char *protor_ASN_atom_name[] = {"N", "CA", "CB", "C", "OD1", "O", "CG", "OXT", "ND2", };
+static double protor_ASN_atom_radius[] = {1.64, 1.88, 1.88, 1.61, 1.42, 1.42, 1.61, 1.46, 1.64, };
+static int protor_ASN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_ASN_cfg = {
+    9,
+ "ASN",
+    (char**) protor_ASN_atom_name,
+    (double*) protor_ASN_atom_radius,
+    (freesasa_atom_class*) protor_ASN_atom_class,
+ {"ASN", 145.01, 41.53, 103.48, 103.46, 41.55, 0},
+};
+
+static const char *protor_ASP_atom_name[] = {"OD2", "N", "CG", "O", "OXT", "CA", "CB", "C", "OD1", };
+static double protor_ASP_atom_radius[] = {1.46, 1.64, 1.61, 1.42, 1.46, 1.88, 1.88, 1.61, 1.42, };
+static int protor_ASP_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_ASP_cfg = {
+    9,
+ "ASP",
+    (char**) protor_ASP_atom_name,
+    (double*) protor_ASP_atom_radius,
+    (freesasa_atom_class*) protor_ASP_atom_class,
+ {"ASP", 142.76, 42.29, 100.47, 100.27, 42.49, 0},
+};
+
+static const char *protor_ASX_atom_name[] = {"XD2", "N", "O", "CG", "OXT", "CA", "CB", "XD1", "C", };
+static double protor_ASX_atom_radius[] = {1.5, 1.64, 1.42, 1.61, 1.46, 1.88, 1.88, 1.5, 1.61, };
+static int protor_ASX_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_ASX_cfg = {
+    9,
+ "ASX",
+    (char**) protor_ASX_atom_name,
+    (double*) protor_ASX_atom_radius,
+    (freesasa_atom_class*) protor_ASX_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_C_atom_name[] = {"C2", "N1", "N3", "C1'", "C5'", "OP2", "O5'", "C3'", "O4'", "P", "C4'", "O2", "N4", "OP3", "O3'", "C4", "C5", "OP1", "C2'", "O2'", "C6", };
+static double protor_C_atom_radius[] = {1.61, 1.64, 1.64, 1.88, 1.88, 1.46, 1.46, 1.88, 1.46, 1.8, 1.88, 1.42, 1.64, 1.46, 1.46, 1.61, 1.76, 1.42, 1.88, 1.46, 1.76, };
+static int protor_C_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_C_cfg = {
+    21,
+ "C",
+    (char**) protor_C_atom_name,
+    (double*) protor_C_atom_radius,
+    (freesasa_atom_class*) protor_C_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_CYS_atom_name[] = {"O", "OXT", "SG", "CA", "CB", "C", "N", };
+static double protor_CYS_atom_radius[] = {1.42, 1.46, 1.77, 1.88, 1.88, 1.61, 1.64, };
+static int protor_CYS_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_CYS_cfg = {
+    7,
+ "CYS",
+    (char**) protor_CYS_atom_name,
+    (double*) protor_CYS_atom_radius,
+    (freesasa_atom_class*) protor_CYS_atom_class,
+ {"CYS", 132.20, 42.55, 89.66, 92.74, 39.47, 0},
+};
+
+static const char *protor_DA_atom_name[] = {"OP2", "C5'", "C1'", "N3", "N1", "C2", "N6", "N9", "O5'", "N7", "C3'", "C8", "OP3", "C4'", "P", "O4'", "C4", "O3'", "C5", "OP1", "C6", "C2'", };
+static double protor_DA_atom_radius[] = {1.46, 1.88, 1.88, 1.64, 1.64, 1.76, 1.64, 1.64, 1.46, 1.64, 1.88, 1.76, 1.46, 1.88, 1.8, 1.46, 1.61, 1.46, 1.61, 1.42, 1.61, 1.88, };
+static int protor_DA_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_DA_cfg = {
+    22,
+ "DA",
+    (char**) protor_DA_atom_name,
+    (double*) protor_DA_atom_radius,
+    (freesasa_atom_class*) protor_DA_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_DC_atom_name[] = {"C5", "C4", "O3'", "C6", "C2'", "OP1", "O5'", "C5'", "OP2", "C2", "C1'", "N3", "N1", "C4'", "P", "N4", "O2", "OP3", "O4'", "C3'", };
+static double protor_DC_atom_radius[] = {1.76, 1.61, 1.46, 1.76, 1.88, 1.42, 1.46, 1.88, 1.46, 1.61, 1.88, 1.64, 1.64, 1.88, 1.8, 1.64, 1.42, 1.46, 1.46, 1.88, };
+static int protor_DC_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_DC_cfg = {
+    20,
+ "DC",
+    (char**) protor_DC_atom_name,
+    (double*) protor_DC_atom_radius,
+    (freesasa_atom_class*) protor_DC_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_DG_atom_name[] = {"C8", "C3'", "N2", "P", "C4'", "OP3", "O4'", "C5'", "OP2", "C2", "C1'", "N3", "N1", "O5'", "N9", "N7", "O6", "OP1", "C6", "C2'", "C4", "O3'", "C5", };
+static double protor_DG_atom_radius[] = {1.76, 1.88, 1.64, 1.8, 1.88, 1.46, 1.46, 1.88, 1.46, 1.61, 1.88, 1.64, 1.64, 1.46, 1.64, 1.64, 1.42, 1.42, 1.61, 1.88, 1.61, 1.46, 1.61, };
+static int protor_DG_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_DG_cfg = {
+    23,
+ "DG",
+    (char**) protor_DG_atom_name,
+    (double*) protor_DG_atom_radius,
+    (freesasa_atom_class*) protor_DG_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_DI_atom_name[] = {"N3", "N1", "C1'", "C2", "OP2", "C5'", "N7", "N9", "O5'", "C3'", "C8", "O4'", "OP3", "C4'", "P", "O3'", "C4", "C5", "OP1", "O6", "C2'", "C6", };
+static double protor_DI_atom_radius[] = {1.64, 1.64, 1.88, 1.76, 1.46, 1.88, 1.64, 1.64, 1.46, 1.88, 1.76, 1.46, 1.46, 1.88, 1.8, 1.46, 1.61, 1.61, 1.42, 1.42, 1.88, 1.61, };
+static int protor_DI_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_DI_cfg = {
+    22,
+ "DI",
+    (char**) protor_DI_atom_name,
+    (double*) protor_DI_atom_radius,
+    (freesasa_atom_class*) protor_DI_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_DT_atom_name[] = {"OP2", "C5'", "N3", "C1'", "N1", "C2", "O5'", "C3'", "O4", "OP3", "O2", "P", "C4'", "O4'", "C4", "O3'", "C5", "C7", "OP1", "C6", "C2'", };
+static double protor_DT_atom_radius[] = {1.46, 1.88, 1.64, 1.88, 1.64, 1.61, 1.46, 1.88, 1.42, 1.46, 1.42, 1.8, 1.88, 1.46, 1.61, 1.46, 1.61, 1.88, 1.42, 1.76, 1.88, };
+static int protor_DT_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_DT_cfg = {
+    21,
+ "DT",
+    (char**) protor_DT_atom_name,
+    (double*) protor_DT_atom_radius,
+    (freesasa_atom_class*) protor_DT_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_DU_atom_name[] = {"C5", "C4", "O3'", "C6", "C2'", "OP1", "O5'", "C5'", "OP2", "C2", "C1'", "N3", "N1", "C4'", "P", "OP3", "O2", "O4'", "C3'", "O4", };
+static double protor_DU_atom_radius[] = {1.76, 1.61, 1.46, 1.76, 1.88, 1.42, 1.46, 1.88, 1.46, 1.61, 1.88, 1.64, 1.64, 1.88, 1.8, 1.46, 1.42, 1.46, 1.88, 1.42, };
+static int protor_DU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_DU_cfg = {
+    20,
+ "DU",
+    (char**) protor_DU_atom_name,
+    (double*) protor_DU_atom_radius,
+    (freesasa_atom_class*) protor_DU_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_G_atom_name[] = {"O6", "OP1", "O2'", "C6", "C2'", "C4", "O3'", "C5", "C8", "C3'", "N2", "C4'", "P", "OP3", "O4'", "C5'", "OP2", "C2", "N1", "N3", "C1'", "N9", "O5'", "N7", };
+static double protor_G_atom_radius[] = {1.42, 1.42, 1.46, 1.61, 1.88, 1.61, 1.46, 1.61, 1.76, 1.88, 1.64, 1.88, 1.8, 1.46, 1.46, 1.88, 1.46, 1.61, 1.64, 1.64, 1.88, 1.64, 1.46, 1.64, };
+static int protor_G_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_G_cfg = {
+    24,
+ "G",
+    (char**) protor_G_atom_name,
+    (double*) protor_G_atom_radius,
+    (freesasa_atom_class*) protor_G_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_GLN_atom_name[] = {"OE1", "CD", "N", "CG", "O", "OXT", "CB", "CA", "C", "NE2", };
+static double protor_GLN_atom_radius[] = {1.42, 1.61, 1.64, 1.88, 1.42, 1.46, 1.88, 1.88, 1.61, 1.64, };
+static int protor_GLN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_GLN_cfg = {
+    10,
+ "GLN",
+    (char**) protor_GLN_atom_name,
+    (double*) protor_GLN_atom_radius,
+    (freesasa_atom_class*) protor_GLN_atom_class,
+ {"GLN", 178.83, 42.00, 136.83, 131.85, 46.98, 0},
+};
+
+static const char *protor_GLU_atom_name[] = {"O", "CG", "OXT", "OE2", "CA", "CB", "C", "N", "OE1", "CD", };
+static double protor_GLU_atom_radius[] = {1.42, 1.88, 1.46, 1.46, 1.88, 1.88, 1.61, 1.64, 1.42, 1.61, };
+static int protor_GLU_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_GLU_cfg = {
+    10,
+ "GLU",
+    (char**) protor_GLU_atom_name,
+    (double*) protor_GLU_atom_radius,
+    (freesasa_atom_class*) protor_GLU_atom_class,
+ {"GLU", 174.18, 42.00, 132.18, 122.48, 51.70, 0},
+};
+
+static const char *protor_GLX_atom_name[] = {"C", "CA", "CB", "XE1", "OXT", "O", "XE2", "CG", "CD", "N", };
+static double protor_GLX_atom_radius[] = {1.61, 1.88, 1.88, 1.5, 1.46, 1.42, 1.5, 1.88, 1.61, 1.64, };
+static int protor_GLX_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_GLX_cfg = {
+    10,
+ "GLX",
+    (char**) protor_GLX_atom_name,
+    (double*) protor_GLX_atom_radius,
+    (freesasa_atom_class*) protor_GLX_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_GLY_atom_name[] = {"OXT", "O", "C", "CA", "N", };
+static double protor_GLY_atom_radius[] = {1.46, 1.42, 1.61, 1.88, 1.64, };
+static int protor_GLY_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_GLY_cfg = {
+    5,
+ "GLY",
+    (char**) protor_GLY_atom_name,
+    (double*) protor_GLY_atom_radius,
+    (freesasa_atom_class*) protor_GLY_atom_class,
+ {"GLY", 81.09, 81.09, 0.00, 44.65, 36.44, 0},
+};
+
+static const char *protor_HIS_atom_name[] = {"ND1", "O", "CG", "OXT", "NE2", "CB", "CA", "C", "CD2", "N", "CE1", };
+static double protor_HIS_atom_radius[] = {1.64, 1.42, 1.61, 1.46, 1.64, 1.88, 1.88, 1.61, 1.76, 1.64, 1.76, };
+static int protor_HIS_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_HIS_cfg = {
+    11,
+ "HIS",
+    (char**) protor_HIS_atom_name,
+    (double*) protor_HIS_atom_radius,
+    (freesasa_atom_class*) protor_HIS_atom_class,
+ {"HIS", 182.97, 39.09, 143.87, 85.94, 97.03, 0},
+};
+
+static const char *protor_HOH_atom_name[] = {"O", };
+static double protor_HOH_atom_radius[] = {1.46, };
+static int protor_HOH_atom_class[] = {FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_HOH_cfg = {
+    1,
+ "HOH",
+    (char**) protor_HOH_atom_name,
+    (double*) protor_HOH_atom_radius,
+    (freesasa_atom_class*) protor_HOH_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_I_atom_name[] = {"O3'", "C4", "C5", "OP1", "O6", "C2'", "C6", "O2'", "N3", "N1", "C1'", "C2", "OP2", "C5'", "N7", "N9", "O5'", "C8", "C3'", "O4'", "OP3", "P", "C4'", };
+static double protor_I_atom_radius[] = {1.46, 1.61, 1.61, 1.42, 1.42, 1.88, 1.61, 1.46, 1.64, 1.64, 1.88, 1.76, 1.46, 1.88, 1.64, 1.64, 1.46, 1.76, 1.88, 1.46, 1.46, 1.8, 1.88, };
+static int protor_I_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_I_cfg = {
+    23,
+ "I",
+    (char**) protor_I_atom_name,
+    (double*) protor_I_atom_radius,
+    (freesasa_atom_class*) protor_I_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_ILE_atom_name[] = {"N", "OXT", "O", "CG1", "C", "CA", "CB", "CG2", "CD1", };
+static double protor_ILE_atom_radius[] = {1.64, 1.46, 1.42, 1.88, 1.61, 1.88, 1.88, 1.88, 1.88, };
+static int protor_ILE_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_ILE_cfg = {
+    9,
+ "ILE",
+    (char**) protor_ILE_atom_name,
+    (double*) protor_ILE_atom_radius,
+    (freesasa_atom_class*) protor_ILE_atom_class,
+ {"ILE", 175.73, 41.49, 134.23, 36.85, 138.87, 0},
+};
+
+static const char *protor_LEU_atom_name[] = {"CD2", "N", "OXT", "O", "CG", "C", "CA", "CB", "CD1", };
+static double protor_LEU_atom_radius[] = {1.88, 1.64, 1.46, 1.42, 1.88, 1.61, 1.88, 1.88, 1.88, };
+static int protor_LEU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_LEU_cfg = {
+    9,
+ "LEU",
+    (char**) protor_LEU_atom_name,
+    (double*) protor_LEU_atom_radius,
+    (freesasa_atom_class*) protor_LEU_atom_class,
+ {"LEU", 179.56, 39.78, 139.78, 37.16, 142.39, 0},
+};
+
+static const char *protor_LYS_atom_name[] = {"NZ", "N", "CD", "CA", "CB", "C", "CE", "O", "CG", "OXT", };
+static double protor_LYS_atom_radius[] = {1.64, 1.64, 1.88, 1.88, 1.88, 1.61, 1.88, 1.42, 1.88, 1.46, };
+static int protor_LYS_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_LYS_cfg = {
+    10,
+ "LYS",
+    (char**) protor_LYS_atom_name,
+    (double*) protor_LYS_atom_radius,
+    (freesasa_atom_class*) protor_LYS_atom_class,
+ {"LYS", 204.98, 42.00, 162.98, 93.88, 111.10, 0},
+};
+
+static const char *protor_MET_atom_name[] = {"N", "SD", "CA", "CB", "C", "O", "CG", "OXT", "CE", };
+static double protor_MET_atom_radius[] = {1.64, 1.77, 1.88, 1.88, 1.61, 1.42, 1.88, 1.46, 1.88, };
+static int protor_MET_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_MET_cfg = {
+    9,
+ "MET",
+    (char**) protor_MET_atom_name,
+    (double*) protor_MET_atom_radius,
+    (freesasa_atom_class*) protor_MET_atom_class,
+ {"MET", 193.10, 42.00, 151.10, 75.48, 117.62, 0},
+};
+
+static const char *protor_MSE_atom_name[] = {"SE", "N", "C", "CA", "CB", "OXT", "O", "CG", "CE", };
+static double protor_MSE_atom_radius[] = {1.9, 1.64, 1.61, 1.88, 1.88, 1.46, 1.42, 1.88, 1.88, };
+static int protor_MSE_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_MSE_cfg = {
+    9,
+ "MSE",
+    (char**) protor_MSE_atom_name,
+    (double*) protor_MSE_atom_radius,
+    (freesasa_atom_class*) protor_MSE_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_NH2_atom_name[] = {"N", };
+static double protor_NH2_atom_radius[] = {1.64, };
+static int protor_NH2_atom_class[] = {FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_NH2_cfg = {
+    1,
+ "NH2",
+    (char**) protor_NH2_atom_name,
+    (double*) protor_NH2_atom_radius,
+    (freesasa_atom_class*) protor_NH2_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_PHE_atom_name[] = {"CD1", "CA", "CB", "C", "CZ", "O", "CG", "OXT", "N", "CE1", "CE2", "CD2", };
+static double protor_PHE_atom_radius[] = {1.76, 1.88, 1.88, 1.61, 1.76, 1.42, 1.61, 1.46, 1.64, 1.76, 1.76, 1.76, };
+static int protor_PHE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_PHE_cfg = {
+    12,
+ "PHE",
+    (char**) protor_PHE_atom_name,
+    (double*) protor_PHE_atom_radius,
+    (freesasa_atom_class*) protor_PHE_atom_class,
+ {"PHE", 199.88, 38.43, 161.45, 34.94, 164.94, 0},
+};
+
+static const char *protor_PRO_atom_name[] = {"C", "CB", "CA", "OXT", "O", "CG", "CD", "N", };
+static double protor_PRO_atom_radius[] = {1.61, 1.88, 1.88, 1.46, 1.42, 1.88, 1.88, 1.64, };
+static int protor_PRO_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_PRO_cfg = {
+    8,
+ "PRO",
+    (char**) protor_PRO_atom_name,
+    (double*) protor_PRO_atom_radius,
+    (freesasa_atom_class*) protor_PRO_atom_class,
+ {"PRO", 137.21, 27.51, 109.70, 16.09, 121.12, 0},
+};
+
+static const char *protor_PYL_atom_name[] = {"N2", "N", "CD", "CD2", "O2", "CA2", "C2", "CB", "OXT", "O", "CG", "NZ", "CE2", "CG2", "C", "CA", "CE", "CB2", };
+static double protor_PYL_atom_radius[] = {1.64, 1.64, 1.88, 1.88, 1.42, 1.88, 1.61, 1.88, 1.46, 1.42, 1.88, 1.64, 1.76, 1.88, 1.61, 1.88, 1.88, 1.88, };
+static int protor_PYL_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_PYL_cfg = {
+    18,
+ "PYL",
+    (char**) protor_PYL_atom_name,
+    (double*) protor_PYL_atom_radius,
+    (freesasa_atom_class*) protor_PYL_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_SEC_atom_name[] = {"C", "SE", "CA", "CB", "N", "OXT", "O", };
+static double protor_SEC_atom_radius[] = {1.61, 1.9, 1.88, 1.88, 1.64, 1.46, 1.42, };
+static int protor_SEC_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_SEC_cfg = {
+    7,
+ "SEC",
+    (char**) protor_SEC_atom_name,
+    (double*) protor_SEC_atom_radius,
+    (freesasa_atom_class*) protor_SEC_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_SER_atom_name[] = {"C", "CA", "CB", "N", "OXT", "O", "OG", };
+static double protor_SER_atom_radius[] = {1.61, 1.88, 1.88, 1.64, 1.46, 1.42, 1.46, };
+static int protor_SER_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_SER_cfg = {
+    7,
+ "SER",
+    (char**) protor_SER_atom_name,
+    (double*) protor_SER_atom_radius,
+    (freesasa_atom_class*) protor_SER_atom_class,
+ {"SER", 118.34, 43.41, 74.93, 71.38, 46.96, 0},
+};
+
+static const char *protor_T_atom_name[] = {"O2", "OP3", "C4'", "P", "O4'", "C3'", "O4", "O5'", "OP2", "C5'", "N3", "C1'", "N1", "C2", "C6", "C2'", "OP1", "C5", "C7", "C4", "O3'", };
+static double protor_T_atom_radius[] = {1.42, 1.46, 1.88, 1.8, 1.46, 1.88, 1.42, 1.46, 1.46, 1.88, 1.64, 1.88, 1.64, 1.61, 1.76, 1.88, 1.42, 1.61, 1.88, 1.61, 1.46, };
+static int protor_T_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_T_cfg = {
+    21,
+ "T",
+    (char**) protor_T_atom_name,
+    (double*) protor_T_atom_radius,
+    (freesasa_atom_class*) protor_T_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_THR_atom_name[] = {"OXT", "O", "OG1", "C", "CA", "CB", "CG2", "N", };
+static double protor_THR_atom_radius[] = {1.46, 1.42, 1.46, 1.61, 1.88, 1.88, 1.88, 1.64, };
+static int protor_THR_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_THR_cfg = {
+    8,
+ "THR",
+    (char**) protor_THR_atom_name,
+    (double*) protor_THR_atom_radius,
+    (freesasa_atom_class*) protor_THR_atom_class,
+ {"THR", 140.60, 41.96, 98.64, 66.15, 74.45, 0},
+};
+
+static const char *protor_TRP_atom_name[] = {"CD1", "CA", "CB", "C", "CG", "O", "OXT", "CZ2", "N", "CZ3", "CE2", "NE1", "CD2", "CE3", "CH2", };
+static double protor_TRP_atom_radius[] = {1.76, 1.88, 1.88, 1.61, 1.61, 1.42, 1.46, 1.76, 1.64, 1.76, 1.61, 1.64, 1.61, 1.76, 1.76, };
+static int protor_TRP_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_TRP_cfg = {
+    15,
+ "TRP",
+    (char**) protor_TRP_atom_name,
+    (double*) protor_TRP_atom_radius,
+    (freesasa_atom_class*) protor_TRP_atom_class,
+ {"TRP", 249.19, 42.59, 206.60, 61.64, 187.55, 0},
+};
+
+static const char *protor_TYR_atom_name[] = {"CD2", "OH", "CE2", "N", "CE1", "OXT", "CZ", "CG", "O", "CD1", "C", "CA", "CB", };
+static double protor_TYR_atom_radius[] = {1.76, 1.46, 1.76, 1.64, 1.76, 1.46, 1.61, 1.61, 1.42, 1.76, 1.61, 1.88, 1.88, };
+static int protor_TYR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_TYR_cfg = {
+    13,
+ "TYR",
+    (char**) protor_TYR_atom_name,
+    (double*) protor_TYR_atom_radius,
+    (freesasa_atom_class*) protor_TYR_atom_class,
+ {"TYR", 214.19, 38.43, 175.76, 81.12, 133.07, 0},
+};
+
+static const char *protor_U_atom_name[] = {"O4", "C3'", "O4'", "C4'", "P", "OP3", "O2", "C2", "N3", "N1", "C1'", "C5'", "OP2", "O5'", "OP1", "C2'", "O2'", "C6", "O3'", "C4", "C5", };
+static double protor_U_atom_radius[] = {1.42, 1.88, 1.46, 1.88, 1.8, 1.46, 1.42, 1.61, 1.64, 1.64, 1.88, 1.88, 1.46, 1.46, 1.42, 1.88, 1.46, 1.76, 1.46, 1.61, 1.76, };
+static int protor_U_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, };
+static struct classifier_residue protor_U_cfg = {
+    21,
+ "U",
+    (char**) protor_U_atom_name,
+    (double*) protor_U_atom_radius,
+    (freesasa_atom_class*) protor_U_atom_class,
+ {NULL, 0, 0, 0, 0, 0},
+};
+
+static const char *protor_VAL_atom_name[] = {"CG2", "CB", "CA", "CG1", "C", "O", "OXT", "N", };
+static double protor_VAL_atom_radius[] = {1.88, 1.88, 1.88, 1.88, 1.61, 1.42, 1.46, 1.64, };
+static int protor_VAL_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, };
+static struct classifier_residue protor_VAL_cfg = {
+    8,
+ "VAL",
+    (char**) protor_VAL_atom_name,
+    (double*) protor_VAL_atom_radius,
+    (freesasa_atom_class*) protor_VAL_atom_class,
+ {"VAL", 151.97, 41.50, 110.46, 36.87, 115.09, 0},
+};
+
+static struct classifier_residue *protor_residue_cfg[] = {
+    &protor_A_cfg, &protor_ACE_cfg, &protor_ALA_cfg, &protor_ARG_cfg, &protor_ASN_cfg, &protor_ASP_cfg, &protor_ASX_cfg, &protor_C_cfg, &protor_CYS_cfg, &protor_DA_cfg, &protor_DC_cfg, &protor_DG_cfg, &protor_DI_cfg, &protor_DT_cfg, &protor_DU_cfg, &protor_G_cfg, &protor_GLN_cfg, &protor_GLU_cfg, &protor_GLX_cfg, &protor_GLY_cfg, &protor_HIS_cfg, &protor_HOH_cfg, &protor_I_cfg, &protor_ILE_cfg, &protor_LEU_cfg, &protor_LYS_cfg, &protor_MET_cfg, &protor_MSE_cfg, &protor_NH2_cfg, &protor_PHE_cfg, &protor_PRO_cfg, &protor_PYL_cfg, &protor_SEC_cfg, &protor_SER_cfg, &protor_T_cfg, &protor_THR_cfg, &protor_TRP_cfg, &protor_TYR_cfg, &protor_U_cfg, &protor_VAL_cfg, };
+
+const freesasa_classifier freesasa_protor_classifier = {
+    40,    (char**) protor_residue_name,
+    "ProtOr",
+    (struct classifier_residue **) protor_residue_cfg,
+};
+

.venv_haddock/include/site/python3.12/freesasa/coord.c

@@ -0,0 +1,342 @@
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+#include <assert.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "coord.h"
+#include "freesasa_internal.h"
+
+coord_t *
+freesasa_coord_new()
+{
+    coord_t *c = malloc(sizeof(coord_t));
+    if (c != NULL) {
+        c->xyz = NULL;
+        c->n = 0;
+        c->is_linked = 0;
+    } else {
+        mem_fail();
+    }
+    return c;
+}
+
+void freesasa_coord_free(coord_t *c)
+{
+    if (c) {
+        if (c->xyz && !c->is_linked) free(c->xyz);
+        free(c);
+    }
+}
+static void
+coord_clear(coord_t *c)
+{
+    assert(c);
+    assert(!c->is_linked);
+    if (c->xyz) {
+        free(c->xyz);
+        c->xyz = NULL;
+    }
+    c->n = 0;
+}
+
+coord_t *
+freesasa_coord_clone(const coord_t *src)
+{
+    coord_t *c = freesasa_coord_new();
+
+    assert(src);
+
+    if (c == NULL) {
+        mem_fail();
+        return NULL;
+    }
+
+    if (freesasa_coord_set_all(c, src->xyz, src->n) != FREESASA_SUCCESS) {
+        fail_msg("");
+        return NULL;
+    }
+
+    return c;
+}
+
+int freesasa_coord_copy(coord_t *target, const coord_t *src)
+{
+    if (src->n != target->n) return FREESASA_FAIL;
+    memcpy(target->xyz, src->xyz, sizeof(double) * src->n * 3);
+    return FREESASA_SUCCESS;
+}
+
+coord_t *
+freesasa_coord_new_linked(const double *xyz,
+                          int n)
+{
+    coord_t *c = freesasa_coord_new();
+
+    assert(xyz);
+    assert(n > 0);
+
+    if (c != NULL) {
+        c->xyz = (double *)xyz;
+        c->n = n;
+        c->is_linked = 1;
+    } else
+        mem_fail();
+    return c;
+}
+
+int freesasa_coord_append(coord_t *c,
+                          const double *xyz,
+                          int n)
+{
+    int n_old;
+    double *xyz_old;
+
+    assert(c);
+    assert(xyz);
+    assert(!c->is_linked);
+
+    n_old = c->n;
+    xyz_old = c->xyz;
+
+    if (n == 0) return FREESASA_SUCCESS;
+
+    c->xyz = (double *)realloc(c->xyz, sizeof(double) * 3 * (c->n + n));
+    if (c->xyz == NULL) {
+        free(xyz_old);
+        return mem_fail();
+    }
+    c->n += n;
+
+    memcpy(&(c->xyz[3 * n_old]), xyz, sizeof(double) * n * 3);
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_coord_append_xyz(coord_t *c,
+                              const double *x,
+                              const double *y,
+                              const double *z, int n)
+{
+    double *xyz;
+    int i;
+
+    assert(c);
+    assert(x);
+    assert(y);
+    assert(z);
+    assert(!c->is_linked);
+
+    if (n == 0) return FREESASA_SUCCESS;
+
+    xyz = malloc(sizeof(double) * n * 3);
+    if (xyz == NULL) return mem_fail();
+
+    for (i = 0; i < n; ++i) {
+        xyz[i * 3] = x[i];
+        xyz[i * 3 + 1] = y[i];
+        xyz[i * 3 + 2] = z[i];
+    }
+    if (freesasa_coord_append(c, xyz, n) == FREESASA_SUCCESS) {
+        free(xyz);
+        return FREESASA_SUCCESS;
+    }
+    return mem_fail();
+}
+
+void freesasa_coord_set_i(coord_t *c,
+                          int i,
+                          const double *xyz)
+{
+    assert(c);
+    assert(xyz);
+    assert(i < c->n && i >= 0);
+    assert(!c->is_linked);
+
+    memcpy(&c->xyz[i * 3], xyz, 3 * sizeof(double));
+}
+
+void freesasa_coord_set_i_xyz(coord_t *c,
+                              int i,
+                              double x,
+                              double y,
+                              double z)
+{
+    double *v_i;
+
+    assert(c);
+    assert(c->n > i);
+    assert(i >= 0);
+    assert(!c->is_linked);
+
+    v_i = &c->xyz[i * 3];
+
+    *(v_i++) = x;
+    *(v_i++) = y;
+    *v_i = z;
+}
+
+int freesasa_coord_set_all(coord_t *c,
+                           const double *xyz,
+                           int n)
+{
+    int result;
+
+    assert(c);
+    assert(xyz);
+
+    coord_clear(c);
+    result = freesasa_coord_append(c, xyz, n);
+
+    if (result != FREESASA_SUCCESS) {
+        fail_msg("");
+    }
+
+    return result;
+}
+
+int freesasa_coord_set_all_xyz(coord_t *c,
+                               const double *x,
+                               const double *y,
+                               const double *z,
+                               int n)
+{
+    assert(c);
+    assert(x);
+    assert(y);
+    assert(z);
+    coord_clear(c);
+    return freesasa_coord_append_xyz(c, x, y, z, n);
+}
+
+void freesasa_coord_set_length_i(coord_t *c,
+                                 int i,
+                                 double l)
+{
+    double x, y, z, r;
+
+    assert(c);
+    assert(c->xyz);
+    assert(!c->is_linked);
+    assert(i >= 0 && i < c->n);
+    assert(l >= 0);
+
+    x = c->xyz[3 * i];
+    y = c->xyz[3 * i + 1];
+    z = c->xyz[3 * i + 2];
+    r = sqrt(x * x + y * y + z * z);
+    c->xyz[3 * i] *= l / r;
+    c->xyz[3 * i + 1] *= l / r;
+    c->xyz[3 * i + 2] *= l / r;
+}
+
+void freesasa_coord_set_length_all(coord_t *c,
+                                   double l)
+{
+    int i;
+
+    assert(c);
+    assert(!c->is_linked);
+
+    for (i = 0; i < c->n; ++i)
+        freesasa_coord_set_length_i(c, i, l);
+}
+
+const double *
+freesasa_coord_i(const coord_t *c,
+                 int i)
+{
+    assert(c);
+    assert(i < c->n);
+    assert(i >= 0);
+    return &c->xyz[3 * i];
+}
+
+double
+freesasa_coord_dist(const coord_t *c,
+                    int i,
+                    int j)
+{
+    return sqrt(freesasa_coord_dist2(c, i, j));
+}
+
+static inline double
+dist2(const double *v1,
+      const double *v2)
+{
+    double dx = v1[0] - v2[0], dy = v1[1] - v2[1], dz = v1[2] - v2[2];
+    return dx * dx + dy * dy + dz * dz;
+}
+
+double
+freesasa_coord_dist2(const coord_t *c,
+                     int i,
+                     int j)
+{
+    double *v1 = &c->xyz[3 * i];
+    double *v2 = &c->xyz[3 * j];
+    return dist2(v1, v2);
+}
+
+double
+freesasa_coord_dist2_12(const coord_t *c1,
+                        const coord_t *c2,
+                        int i1,
+                        int i2)
+{
+    double *v1 = &c1->xyz[3 * i1];
+    double *v2 = &c2->xyz[3 * i2];
+    return dist2(v1, v2);
+}
+
+const double *
+freesasa_coord_all(const coord_t *c)
+{
+    assert(c);
+    return c->xyz;
+}
+
+int freesasa_coord_n(const coord_t *c)
+{
+    assert(c);
+    return c->n;
+}
+
+void freesasa_coord_translate(coord_t *c,
+                              const double *xyz)
+{
+    assert(!c->is_linked);
+    assert(xyz);
+    freesasa_coord_translate_xyz(c, xyz[0], xyz[1], xyz[2]);
+}
+
+void freesasa_coord_translate_xyz(coord_t *c,
+                                  double x,
+                                  double y,
+                                  double z)
+{
+    int i;
+
+    assert(c);
+    assert(!c->is_linked);
+
+    for (i = 0; i < c->n; ++i) {
+        c->xyz[3 * i] += x;
+        c->xyz[3 * i + 1] += y;
+        c->xyz[3 * i + 2] += z;
+    }
+}
+
+void freesasa_coord_scale(coord_t *c,
+                          double s)
+{
+    int i;
+
+    assert(c);
+    assert(!c->is_linked);
+
+    for (i = 0; i < c->n * 3; ++i) {
+        c->xyz[i] *= s;
+    }
+}

.venv_haddock/include/site/python3.12/freesasa/coord.h

@@ -0,0 +1,340 @@
+#ifndef FREESASA_COORD_H
+#define FREESASA_COORD_H
+
+#ifdef __GNUC__
+#define __attrib_pure__ __attribute__((pure))
+#else
+#define __attrib_pure__
+#endif
+
+/**
+    @file
+    @author Simon Mitternacht
+
+    This is only for interal use, error handling is done by asserts.
+    The header provides functions to store, copy and modify
+    coordinates through the type ::coord_t.
+
+    The distance calculation functions (freesasa_dist(),
+    freesasa_dist2() and freesasa_dist2_12()) are useful for code that
+    is not performance critical. When efficieny is a priority it is
+    better to use freesasa_coord_all() to obtain a pointer to the
+    array of coordinates and calculate directly using this..
+ */
+
+/** Store a set of 3-dimensional coordinates in a contiguous array */
+typedef struct coord_t {
+    /** number of 3-vectors */
+    int n;
+
+    /** If these coordinates are only a link to an externally stored
+        array this is 1, else 0. If it it is set, the coordinates can
+        not be changed and the array not freed. */
+    int is_linked;
+
+    /** array of all coordinates, dimension 3*n,
+        x_1,y_1,z_1,...,x_n,y_n,z_n. */
+    double *xyz;
+} coord_t;
+
+/**
+    Initialize new ::coord_t object.
+
+    Return value is dynamically allocated, should be freed with
+    freesasa_coord_free().
+
+    @return An empty ::coord_t object. Returns NULL if out of
+    memory.
+ */
+coord_t *
+freesasa_coord_new(void);
+
+/**
+   Free resources allocated by ::coord_t object.
+
+   Will not free the coordinate array itself if it was initialized by
+   freesasa_coord_new_linked().
+ */
+void freesasa_coord_free(coord_t *coord);
+
+/**
+   Clone coordinates.
+
+   Creates a new ::coord_t object that is a copy of the
+   argument `src`.
+
+   Return value is dynamically allocated, should be freed with
+   freesasa_coord_free().
+
+   @param src Coordinates to be copied.
+   @return Copy of coordinates. NULL if out of memory.
+ */
+coord_t *
+freesasa_coord_clone(const coord_t *src);
+
+/**
+   Copy coordinates
+
+   Copies value of source coordinates to target.
+
+   @param target Target coordinates
+   @param src Source coordinates
+   @return ::FREESASA_FAIL if size mismatch between src and target,
+     else ::FREESASA_SUCCESS
+ */
+int freesasa_coord_copy(coord_t *target, const coord_t *src);
+
+/**
+    Creates a `const` ::coord_t-object that is linked to an array of
+    coordinates owned by callee.
+
+    This allows repeated calculations on a changing object without
+    reinitialization. The returned ::coord_t-pointer is not
+    explicitly const, to allow it to be freed later, but objects
+    initiated through this interface will not change their
+    coordinates. It also allows ::coord_t to be used as a wrapper
+    for an array controlled by the caller.
+
+    Return value is dynamically allocated, should be freed with
+    freesasa_coord_free().
+
+    @param xyz Array of coordinates x1,y1,z1,x2,y2,z2,...
+    @param n Number of coordinates (array has size 3*n).
+    @return New linked ::coord_t object. NULL if out of memory.
+ */
+coord_t *
+freesasa_coord_new_linked(const double *xyz,
+                          int n);
+
+/**
+    Append coordinates to ::coord_t object from one array.
+
+    @param coord A ::coord_t object
+    @param xyz Array of coordinates x1,y1,z1,x2,y2,z2,...
+    @param n Number of coordinates (array has size 3*n).
+    @return FREESASA_SUCCESS if successful, FREESASA_FAIL if out of memory.
+ */
+int freesasa_coord_append(coord_t *coord,
+                          const double *xyz,
+                          int n);
+
+/**
+    Append coordinates to ::coord_t object from three
+    separate arrays.
+
+    @param coord A ::coord_t object
+    @param x Array of x-coordinates
+    @param y Array of x-coordinates
+    @param z Array of x-coordinates
+    @param n Size of arrays x, y and z.
+    @return FREESASA_SUCCESS if successful, FREESASA_FAIL if out of memory.
+ */
+int freesasa_coord_append_xyz(coord_t *coord,
+                              const double *x,
+                              const double *y,
+                              const double *z,
+                              int n);
+
+/**
+    Set given coordinate.
+
+    Bounds-checking of i is handled by asserts for efficiency,
+    i.e. only done in debug-mode.
+
+    @param coord A ::coord_t object
+    @param i Index
+    @param xyz Array with coordinates x,y,z.
+ */
+void freesasa_coord_set_i(coord_t *coord,
+                          int i,
+                          const double *xyz);
+
+/**
+    Set given coordinate.
+
+    Bounds-checking of i is handled by asserts for efficiency,
+    i.e. only done in debug-mode.
+
+    @param coord A ::coord_t object
+    @param i Index
+    @param x x-coordinate.
+    @param y y-coordinate.
+    @param z z-coordinate
+ */
+void freesasa_coord_set_i_xyz(coord_t *coord,
+                              int i,
+                              double x,
+                              double y,
+                              double z);
+
+/**
+    Reset everything.
+
+    Allocates memory to allow array of size n.
+
+    @param coord A ::coord_t object
+    @param xyz Array of coordinates x1,y1,z1,x2,y2,z2,...
+    @param n Number of coordinates (array has size 3*n).
+    @return FREESASA_SUCCESS if successful, FREESASA_FAIL if out of memory.
+ */
+int freesasa_coord_set_all(coord_t *coord,
+                           const double *xyz,
+                           int n);
+
+/**
+    Reset everything.
+
+    Allocates memory to allow array of size n.
+
+    @param coord A ::coord_t object
+    @param x Array of x-coordinates
+    @param y Array of x-coordinates
+    @param z Array of x-coordinates
+    @param n Size of arrays x, y and z.
+    @return FREESASA_SUCCESS if successful, FREESASA_FAIL if out of memory.
+ */
+int freesasa_coord_set_all_xyz(coord_t *coord,
+                               const double *x,
+                               const double *y,
+                               const double *z,
+                               int n);
+
+/**
+    Set length of a given coordinate vector. Useful for test-points in
+    S&R.
+
+    Bounds-checking of `i` and `length` is handled by asserts for
+    efficiency, i.e. only done in debug-mode.
+
+    @param coord A ::coord_t object
+    @param i Index
+    @param length Desired length (>= 0)
+ */
+void freesasa_coord_set_length_i(coord_t *coord,
+                                 int i,
+                                 double length);
+
+/**
+    Set length of all coordinate vectors to the same length.
+
+    This means all coordinates are on the same sphere.
+
+    Bounds-checking of length is handled by asserts for
+    efficiency, i.e. only done in debug-mode.
+
+    @param coord A ::coord_t object
+    @param length Desired length (>= 0)
+ */
+void freesasa_coord_set_length_all(coord_t *coord,
+                                   double length);
+
+/**
+    Coordinates for a given index.
+
+    Bounds-checking of `i` is handled by asserts for efficiency,
+    i.e. only done in debug-mode.
+
+    @param coord A ::coord_t object
+    @param i Index
+    @return Array with coordinates x,y,z
+ */
+const double *
+freesasa_coord_i(const coord_t *coord,
+                 int i);
+
+/**
+    Calculate distance between two coordinate vectors. For speed,
+    arguments aren't checked.
+
+    @param coord A ::coord_t object
+    @param i first index
+    @param j second index
+    @return Distance between coorsinate i and j.
+*/
+double freesasa_coord_dist(const coord_t *coord,
+                           int i,
+                           int j)
+    __attrib_pure__;
+
+/**
+    Calculate square distance between two coordinate vectors. For
+    speed, arguments aren't checked.
+
+    @param coord A ::coord_t object
+    @param i First index
+    @param j Second index
+    @return Square distance between coordinate i and j
+*/
+double
+freesasa_coord_dist2(const coord_t *coord,
+                     int i,
+                     int j)
+    __attrib_pure__;
+
+/**
+    Calculate square distance between two coordinate vectors in
+    separate coordinate sets. For speed, arguments aren't checked.
+
+    @param c1 First set of coordinates
+    @param c2 Second set of coordinates
+    @param i1 Index in first set
+    @param i2 Index in second set
+    @return Square distance between coordinates i1 and i2
+*/
+double freesasa_coord_dist2_12(const coord_t *c1,
+                               const coord_t *c2,
+                               int i1,
+                               int i2)
+    __attrib_pure__;
+
+/**
+    All coordinates as an array.
+
+    @param coord A ::coord_t object
+    @return Array of coordinates x1,y1,z1,x2,y2,z2,...
+ */
+const double *
+freesasa_coord_all(const coord_t *coord) __attrib_pure__;
+
+/**
+    Number of coordinates.
+
+    @param coord A ::coord_t object
+    @return Number of coordinates
+ */
+int freesasa_coord_n(const coord_t *coord) __attrib_pure__;
+
+/**
+    Translate all coordinates by same vector.
+
+    @param coord A ::coord_t object
+    @param xyz Array describing translation vector x,y,z.
+ */
+void freesasa_coord_translate(coord_t *coord,
+                              const double *xyz);
+
+/**
+    Translate all coordinates by same vector.
+
+    @param coord A ::coord_t object
+    @param x x-coordinate of translation vector
+    @param y y-coordinate of translation vector
+    @param z z-coordinate of translation vector
+ */
+void freesasa_coord_translate_xyz(coord_t *coord,
+                                  double x,
+                                  double y,
+                                  double z);
+
+/**
+    Scale all coordinates by given factor.
+
+    @param coord A ::coord_t object
+    @param a Factor to scale by
+ */
+void freesasa_coord_scale(coord_t *coord,
+                          double a);
+
+#undef __attrib_pure__
+
+#endif

.venv_haddock/include/site/python3.12/freesasa/freesasa.c

@@ -0,0 +1,266 @@
+/**
+ * This source file contains everything that is in freesasa.h
+ * interface and does not have a natural home in any of the other
+ * source files.
+ */
+
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+#include <assert.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "freesasa_internal.h"
+
+#ifdef PACKAGE_VERSION
+const char *freesasa_version = PACKAGE_VERSION;
+#else
+const char *freesasa_version = "";
+#endif
+
+#ifdef PACKAGE_STRING
+const char *freesasa_string = PACKAGE_STRING;
+#else
+const char *freesasa_string = "FreeSASA";
+#endif
+
+/* Allows compilation with different defaults
+   depending on USE_THREADS. but still exposing the value in a header
+   that doesn't depend on USE_THREADS */
+#if USE_THREADS
+#define DEF_NUMBER_THREADS 2
+#else
+#define DEF_NUMBER_THREADS 1
+#endif
+const int FREESASA_DEF_NUMBER_THREADS = DEF_NUMBER_THREADS;
+
+const freesasa_parameters freesasa_default_parameters = {
+    FREESASA_DEF_ALGORITHM,
+    FREESASA_DEF_PROBE_RADIUS,
+    FREESASA_DEF_SR_N,
+    FREESASA_DEF_LR_N,
+    DEF_NUMBER_THREADS};
+
+static freesasa_result *
+result_new(int n)
+{
+    freesasa_result *result = malloc(sizeof(freesasa_result));
+
+    if (result == NULL) {
+        mem_fail();
+        return NULL;
+    }
+
+    result->sasa = malloc(sizeof(double) * n);
+
+    if (result->sasa == NULL) {
+        mem_fail();
+        freesasa_result_free(result);
+        return NULL;
+    }
+
+    result->n_atoms = n;
+
+    return result;
+}
+
+void freesasa_result_free(freesasa_result *r)
+{
+    if (r) {
+        free(r->sasa);
+        free(r);
+    }
+}
+
+freesasa_result *
+freesasa_calc(const coord_t *c,
+              const double *radii,
+              const freesasa_parameters *parameters)
+
+{
+    freesasa_result *result;
+    int ret = FREESASA_SUCCESS, i;
+
+    assert(c);
+    assert(radii);
+
+    result = result_new(freesasa_coord_n(c));
+
+    if (result == NULL) {
+        fail_msg("");
+        return NULL;
+    }
+
+    if (parameters == NULL) parameters = &freesasa_default_parameters;
+
+    switch (parameters->alg) {
+    case FREESASA_SHRAKE_RUPLEY:
+        ret = freesasa_shrake_rupley(result->sasa, c, radii, parameters);
+        break;
+    case FREESASA_LEE_RICHARDS:
+        ret = freesasa_lee_richards(result->sasa, c, radii, parameters);
+        break;
+    default:
+        assert(0); /* should never get here */
+        break;
+    }
+    if (ret == FREESASA_FAIL) {
+        freesasa_result_free(result);
+        return NULL;
+    }
+
+    result->total = 0;
+    for (i = 0; i < freesasa_coord_n(c); ++i) {
+        result->total += result->sasa[i];
+    }
+    result->parameters = *parameters;
+
+    return result;
+}
+
+freesasa_result *
+freesasa_calc_coord(const double *xyz,
+                    const double *radii,
+                    int n,
+                    const freesasa_parameters *parameters)
+{
+    coord_t *coord = NULL;
+    freesasa_result *result = NULL;
+
+    assert(xyz);
+    assert(radii);
+    assert(n > 0);
+
+    coord = freesasa_coord_new_linked(xyz, n);
+    if (coord != NULL) result = freesasa_calc(coord, radii, parameters);
+    if (result == NULL) fail_msg("");
+
+    freesasa_coord_free(coord);
+
+    return result;
+}
+
+freesasa_result *
+freesasa_calc_structure(const freesasa_structure *structure,
+                        const freesasa_parameters *parameters)
+{
+    assert(structure);
+
+    return freesasa_calc(freesasa_structure_xyz(structure),
+                         freesasa_structure_radius(structure),
+                         parameters);
+}
+
+freesasa_node *
+freesasa_calc_tree(const freesasa_structure *structure,
+                   const freesasa_parameters *parameters,
+                   const char *name)
+{
+    freesasa_node *tree = NULL;
+    freesasa_result *result;
+
+    assert(structure);
+
+    result = freesasa_calc(freesasa_structure_xyz(structure),
+                           freesasa_structure_radius(structure),
+                           parameters);
+
+    if (result != NULL) {
+        tree = freesasa_tree_init(result, structure, name);
+    } else {
+        fail_msg("");
+    }
+
+    if (tree == NULL) {
+        fail_msg("");
+    }
+
+    freesasa_result_free(result);
+
+    return tree;
+}
+
+static inline void
+count_err(int return_value, int *n_err)
+{
+    if (return_value == FREESASA_FAIL) {
+        (*n_err)++;
+    }
+}
+
+int freesasa_tree_export(FILE *file,
+                         freesasa_node *root,
+                         int options)
+{
+    int n_err = 0;
+
+    assert(freesasa_node_type(root) == FREESASA_NODE_ROOT);
+
+    if (options & FREESASA_LOG) {
+        count_err(freesasa_write_log(file, root), &n_err);
+    }
+    if (options & FREESASA_RES) {
+        count_err(freesasa_write_res(file, root), &n_err);
+    }
+    if (options & FREESASA_SEQ) {
+        count_err(freesasa_write_seq(file, root), &n_err);
+    }
+    if (options & FREESASA_PDB) {
+        count_err(freesasa_write_pdb(file, root), &n_err);
+    }
+    if (options & FREESASA_RSA) {
+        count_err(freesasa_write_rsa(file, root, options), &n_err);
+    }
+    if (options & FREESASA_JSON) {
+#if USE_JSON
+        count_err(freesasa_write_json(file, root, options), &n_err);
+#else
+        return fail_msg("library was built without support for JSON output");
+#endif
+    }
+    if (options & FREESASA_XML) {
+#if USE_XML
+        count_err(freesasa_write_xml(file, root, options), &n_err);
+#else
+        return fail_msg("library was built without support for XML output");
+#endif
+    }
+    if (n_err > 0) {
+        return fail_msg("there were errors when writing output");
+    }
+    return FREESASA_SUCCESS;
+}
+
+freesasa_result *
+freesasa_result_clone(const freesasa_result *result)
+{
+    freesasa_result *clone = result_new(result->n_atoms);
+
+    if (clone == NULL) {
+        fail_msg("");
+        return NULL;
+    }
+
+    clone->n_atoms = result->n_atoms;
+    clone->total = result->total;
+    clone->parameters = result->parameters;
+    memcpy(clone->sasa, result->sasa, sizeof(double) * clone->n_atoms);
+
+    return clone;
+}
+
+const char *
+freesasa_alg_name(freesasa_algorithm alg)
+{
+    switch (alg) {
+    case FREESASA_SHRAKE_RUPLEY:
+        return "Shrake & Rupley";
+    case FREESASA_LEE_RICHARDS:
+        return "Lee & Richards";
+    default:
+        // This should never happen
+        assert(0 && "Illegal algorithm");
+        return "Unknown algorithm";
+    }
+}

.venv_haddock/include/site/python3.12/freesasa/freesasa_internal.h

@@ -0,0 +1,461 @@
+#ifndef FREESASA_INTERNAL_H
+#define FREESASA_INTERNAL_H
+
+#ifdef _MSC_VER
+#define _CRT_SECURE_NO_WARNINGS
+#endif
+
+/* These are included here so that the _CRT_SECURE_.. macro above will have the desired effect */
+#include <stdio.h>
+#include <string.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#include "coord.h"
+#include "freesasa.h"
+
+/** The name of the library, to be used in error messages and logging */
+extern const char *freesasa_name;
+
+/** The name of the package, to be used in regular output (includes version) */
+extern const char *freesasa_string;
+
+/** A ::freesasa_nodearea with `name == NULL` and all values 0 */
+extern const freesasa_nodearea freesasa_nodearea_null;
+
+/** Shortcut for memory error generation */
+#define mem_fail() freesasa_mem_fail(__FILE__, __LINE__)
+
+/** Shortcut for error message with position information, should be used by default */
+#define fail_msg(...) freesasa_fail_wloc(__FILE__, __LINE__, __VA_ARGS__)
+
+#ifdef _MSC_VER
+#define inline __inline
+#define strdup _strdup
+#define fmax(a, b) (((a) > (b)) ? (a) : (b))
+#define fmin(a, b) (((a) < (b)) ? (a) : (b))
+#include <float.h>
+#define isfinite _finite
+#endif
+
+#if defined(_MSC_VER) && !defined(__func__)
+#define __func__ __FUNCTION__
+#endif
+
+#if defined(_MSC_VER) && _MSC_VER >= 1400
+#define restrict __restrict
+#endif
+#if defined(_MSC_VER) && _MSC_VER < 1400
+#define restrict
+#endif
+
+/* The library is intended to be compiled with C99, but this macro
+   allows us to compile it with C89 too, to test MSC compatibility */
+#ifdef __STRICT_ANSI__
+#define restrict
+#define inline
+#endif
+
+/**
+    Calculate SASA using S&R algorithm.
+
+    @param sasa The results are written to this array, the user has to
+    make sure it is large enough.
+    @param c Coordinates of the object to calculate SASA for.
+    @param radii Array of radii for each sphere.
+    @param param Parameters specifying resolution, probe radius and
+    number of threads. If NULL :.freesasa_default_parameters is used.
+    @return ::FREESASA_SUCCESS on success, ::FREESASA_WARN if multiple
+    threads are requested when compiled in single-threaded mode (with
+    error message). ::FREESASA_FAIL if memory allocation failure.
+ */
+int freesasa_shrake_rupley(double *sasa,
+                           const coord_t *c,
+                           const double *radii,
+                           const freesasa_parameters *param);
+
+/**
+    Calculate SASA using L&R algorithm.
+
+    Solvent accessible surface area for each atom is written to the
+    array 'sasa'. The user is responsible for making sure this has the
+    right size. The argument grid sets the distance between grid
+    points in Å. Returns FREESASA_SUCCESS on success, FREESASA_WARN if
+    multiple threads are requested when compiled in single-threaded
+    mode (with error message).
+
+    @param sasa The results are written to this array, the user has to
+    make sure it is large enough.
+    @param c Coordinates of the object to calculate SASA for.
+    @param radii Array of radii for each sphere.
+    @param param Parameters specifying resolution, probe radius and
+    number of threads. If NULL :.freesasa_default_parameters is used.
+    @return ::FREESASA_SUCCESS on success, ::FREESASA_WARN if
+    multiple threads are requested when compiled in single-threaded
+    mode (with error message). ::FREESASA_FAIL if memory allocation
+    failure.
+ */
+int freesasa_lee_richards(double *sasa,
+                          const coord_t *c,
+                          const double *radii,
+                          const freesasa_parameters *param);
+
+/**
+    Calculate SASA based on a coordinate object, radii and parameters
+
+    Wrapper for freesasa_lee_richards() and freesasa_shrake_rupley()
+    that creates a result object.
+
+    Return value is dynamically allocated, should be freed with
+    freesasa_result_free().
+
+    @param c Coordinates
+    @param radii Atomi radii
+    @param parameters Parameters
+    @return Result of calculation, NULL if something went wrong.
+ */
+freesasa_result *
+freesasa_calc(const coord_t *c,
+              const double *radii,
+              const freesasa_parameters *parameters);
+
+int freesasa_write_log(FILE *log,
+                       freesasa_node *root);
+
+/**
+    Print RSA-file
+
+    @param output Output-file.
+    @param root A tree with stored results.
+    @param options Bitfield with option ::FREESASA_OUTPUT_SKIP_REL to specify
+      if REL column should be populated or not. If the classifier has no
+      reference values, it will be left empty either way.
+    @return ::FREESASA_SUCCESS on success, ::FREESASA_FAIL if problems
+      writing to file.
+ */
+int freesasa_write_rsa(FILE *output,
+                       freesasa_node *root,
+                       int options);
+
+/**
+    Export to JSON
+
+    Not thread-safe.
+
+    @param output Output-file.
+    @param root A tree with stored results.
+    @param parameters Parameters used in the calculation (NULL means
+      defaults are assumed).
+    @param options Bitfield with options ::FREESASA_OUTPUT_STRUCTURE,
+      ::FREESASA_OUTPUT_CHAIN and ::FREESASA_OUTPUT_RESIDUE, that specify
+      depth of the tree to output. If `options == 0` all levels are
+      written. The options ::FREESASA_OUTPUT_SKIP_REL specifies
+      if REL column should be populated or not. If the classifier has no
+      reference values, it will be left empty either way.
+    @return ::FREESASA_SUCCESS on success, ::FREESASA_FAIL if problems
+      writing to file.
+ */
+int freesasa_write_json(FILE *ouput,
+                        freesasa_node *root,
+                        int options);
+/**
+    Export to XML
+
+    @param output Output-file.
+    @param root A tree with stored results.
+    @param parameters Parameters used in the calculation (NULL means
+      defaults are assumed).
+    @param options Bitfield with options ::FREESASA_OUTPUT_STRUCTURE,
+      ::FREESASA_OUTPUT_CHAIN and ::FREESASA_OUTPUT_RESIDUE, that specify
+      depth of the tree to output. If `options == 0` all levels
+      written. The options ::FREESASA_OUTPUT_SKIP_REL specifies
+      if REL column should be populated or not. If the classifier has no
+      reference values, it will be left empty either way.
+    @return ::FREESASA_SUCCESS on success, ::FREESASA_FAIL if problems
+      writing to file.
+ */
+int freesasa_write_xml(FILE *ouput,
+                       freesasa_node *root,
+                       int options);
+
+/**
+    Write SASA values and atomic radii to new PDB-file.
+
+    Takes PDB information from the provided structure and writes a new
+    PDB-file to output, where the B-factors have been replaced with
+    the atom's SASA values in the results, and the occupancy
+    factors with the radii.
+
+    Will only work if the structure was initialized from a PDB-file, i.e.
+    using freesasa_structure_from_pdb() or freesasa_structure_array().
+
+    @param output Output-file
+    @param structure A ::freesasa_node of type ::FREESASA_NODE_STRUCTURE
+    @return ::FREESASA_SUCCESS if file written successfully.
+      ::FREESASA_FAIL if there is no previous PDB input to base output
+      on or if there were problems writing to the file.
+*/
+int freesasa_write_pdb(FILE *output,
+                       freesasa_node *structure);
+
+/**
+    Write per-residue-type output
+ */
+int freesasa_write_res(FILE *log,
+                       freesasa_node *root);
+
+/**
+    Write SASA per residue in sequence output
+ */
+int freesasa_write_seq(FILE *log,
+                       freesasa_node *root);
+
+/**
+    Write standard log message.
+ */
+int freesasa_write_log(FILE *log,
+                       freesasa_node *root);
+
+/**
+    Clone results object
+*/
+freesasa_result *
+freesasa_result_clone(const freesasa_result *result);
+
+/**
+    Clone selection object
+*/
+freesasa_selection *
+freesasa_selection_clone(const freesasa_selection *selection);
+
+/**
+    Get coordinates.
+
+    @param structure A structure.
+    @return The coordinates of the structure as a ::coord_t struct.
+ */
+const coord_t *
+freesasa_structure_xyz(const freesasa_structure *structure);
+
+/**
+    The class of an atom, in the classifier used to initialize the structure.
+
+    @param structure A structure.
+    @param i Atom index.
+    @return The class.
+ */
+freesasa_atom_class
+freesasa_structure_atom_class(const freesasa_structure *structure,
+                              int i);
+
+/**
+    The PDB line used to generate the atom.
+
+    @param structure A structure.
+    @param i Atom index.
+    @return The line, NULL if structure wasn't generated from a PDB file.
+ */
+const char *
+freesasa_structure_atom_pdb_line(const freesasa_structure *structure,
+                                 int i);
+
+/**
+    Add a reference number to the document used to generate the structure from a CIF file,
+    used when exporting to CIF file.
+
+    @param structure A structure.
+    @param ref Reference number for document. >= 1.
+    @param release_func A function that can be called when freeing the structure, to trigger
+        the destructor for the CIF document. This can be NULL if one wants another mode
+        of control over the CIF document.
+    @return ::FREESASA_SUCCESS if success.
+        ::FREESASA_FAIL if memory allocation error.
+*/
+void freesasa_structure_set_cif_ref(freesasa_structure *structure,
+                                    size_t ref,
+                                    void (*release_func)(size_t));
+
+/**
+    Retrieve the reference number for the CIF document used to generate the structure
+    from a CIF file.
+
+    @param structure A structure.
+    @return The reference number. 0 if structure is not from CIF file.
+*/
+size_t freesasa_structure_cif_ref(const freesasa_structure *structure);
+
+/**
+    Retrieve the reference number for the CIF document used to generate the structure
+    from a CIF file, in a structure node.
+
+    @param node A node of type ::FREESASA_NODE_STRUCTURE.
+    @return Reference to CIF document.
+
+    @ingroup node
+ */
+size_t
+freesasa_node_structure_cif_ref(const freesasa_node *node);
+
+const freesasa_nodearea *
+freesasa_structure_residue_reference(const freesasa_structure *structure,
+                                     int r_i);
+/**
+    Get the index of a chain.
+
+    @param structure A structure.
+    @param chain The chain label.
+    @return The index of `chain` in the structure. ::FREESASA_FAIL
+      if `chain` not found.
+ */
+int freesasa_structure_chain_index(const freesasa_structure *structure,
+                                   char chain);
+
+/**
+    Extract area to provided ::freesasa_nodearea object
+
+    Main-chain / side-chain atoms are defined by
+    ::freesasa_backbone_classifier.
+
+    @param area Area will be stored here
+    @param structure Structure to use for classification
+    @param result The areas to use
+    @param atom_index Index of atom in question
+    @return ::FREESASA_SUCCESS. ::FREESASA_FAIL if memory
+      allocation for name fails.
+ */
+int freesasa_atom_nodearea(freesasa_nodearea *area,
+                           const freesasa_structure *structure,
+                           const freesasa_result *result,
+                           int atom_index);
+
+/**
+    Adds all members of term to corresponding members of sum
+
+    @param sum Object to add to
+    @param term Object to add
+ */
+void freesasa_add_nodearea(freesasa_nodearea *sum,
+                           const freesasa_nodearea *term);
+
+/**
+    Compute nodearea for a range of atoms
+ */
+void freesasa_range_nodearea(freesasa_nodearea *area,
+                             const freesasa_structure *structure,
+                             const freesasa_result *result,
+                             int first_atom,
+                             int last_atom);
+
+/**
+    Calculate relative SASA values for a residue
+
+    If the array `ref_values` does not have an entry that has the same
+    `name` as `abs`, `rel->name` will be `NULL`.
+
+    @param rel Store results here, will have same name as `abs`
+    @param abs Absolute SASA for residue
+    @param reference Reference SASA for the residue
+ */
+void freesasa_residue_rel_nodearea(freesasa_nodearea *rel,
+                                   const freesasa_nodearea *abs,
+                                   const freesasa_nodearea *reference);
+
+/**
+    Is an atom a backbone atom
+
+    @param atom_name Name of atom
+    @return 1 if the atom_name equals CA, N, O or C after whitespace
+    is trimmed, 0 else. (i.e. does not check if it is an actual atom)
+ */
+int freesasa_atom_is_backbone(const char *atom_name);
+
+/**
+    Holds range in a file, to be initalized with ftell() and used
+    with fseek().
+ */
+struct file_range {
+    long begin; /**< Position of beginning of range */
+    long end;   /**< Position of end of range */
+};
+
+/**
+    For convenience, get a file range that covers a whole file.
+
+    @param file The file to study
+    @return the ::file_range.
+ */
+struct file_range
+freesasa_whole_file(FILE *file);
+
+/**
+    Algorithm name
+
+    @param algorithm The algorithm
+    @return Name
+ */
+const char *
+freesasa_alg_name(freesasa_algorithm algorithm);
+
+/**
+    Print failure message using format string and arguments.
+
+    Prefer using the macro fail_msg().
+
+    @param format Format string
+    @return ::FREESASA_FAIL
+*/
+int freesasa_fail(const char *format, ...);
+
+/**
+    Print warning message using format string and arguments.
+
+    @param format Format string
+    @return ::FREESASA_WARN
+ */
+int freesasa_warn(const char *format, ...);
+
+/**
+    Print warning message using function, file and line-number.
+
+    Usually used via the macro mem_fail().
+
+    @param func Name of the function that failed
+    @param file The file where the function is.
+    @param line Line number for the error.
+    @return ::FREESASA_FAIL
+ */
+int freesasa_mem_fail(const char *file,
+                      int line);
+
+/**
+    Returns string explaining return values of pthread_create() and
+    pthread_join().
+
+    @param error_code The error code
+    @return A string describing the error code.
+ */
+const char *
+freesasa_thread_error(int error_code);
+
+/**
+    Prints fail message with function name, file name, and line number.
+
+    Mainly intended to be used by the macros fail_msg() and mem_fail().
+
+    @param file The file name
+    @param line The line number
+    @param msg The error message
+    @return ::FREESASA_FAIL
+ */
+int freesasa_fail_wloc(const char *file,
+                       int line,
+                       const char *format,
+                       ...);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* FREESASA_INTERNAL_H */

.venv_haddock/include/site/python3.12/freesasa/lexer.c

@@ -0,0 +1,2129 @@
+#line 2 "lexer.c"
+
+#line 4 "lexer.c"
+
+#define  YY_INT_ALIGNED short int
+
+/* A lexical scanner generated by flex */
+
+#define FLEX_SCANNER
+#define YY_FLEX_MAJOR_VERSION 2
+#define YY_FLEX_MINOR_VERSION 6
+#define YY_FLEX_SUBMINOR_VERSION 1
+#if YY_FLEX_SUBMINOR_VERSION > 0
+#define FLEX_BETA
+#endif
+
+/* First, we deal with  platform-specific or compiler-specific issues. */
+
+/* begin standard C headers. */
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdlib.h>
+
+/* end standard C headers. */
+
+/* flex integer type definitions */
+
+#ifndef FLEXINT_H
+#define FLEXINT_H
+
+/* C99 systems have <inttypes.h>. Non-C99 systems may or may not. */
+
+#if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+
+/* C99 says to define __STDC_LIMIT_MACROS before including stdint.h,
+ * if you want the limit (max/min) macros for int types. 
+ */
+#ifndef __STDC_LIMIT_MACROS
+#define __STDC_LIMIT_MACROS 1
+#endif
+
+#include <inttypes.h>
+typedef int8_t flex_int8_t;
+typedef uint8_t flex_uint8_t;
+typedef int16_t flex_int16_t;
+typedef uint16_t flex_uint16_t;
+typedef int32_t flex_int32_t;
+typedef uint32_t flex_uint32_t;
+#else
+typedef signed char flex_int8_t;
+typedef short int flex_int16_t;
+typedef int flex_int32_t;
+typedef unsigned char flex_uint8_t; 
+typedef unsigned short int flex_uint16_t;
+typedef unsigned int flex_uint32_t;
+
+/* Limits of integral types. */
+#ifndef INT8_MIN
+#define INT8_MIN               (-128)
+#endif
+#ifndef INT16_MIN
+#define INT16_MIN              (-32767-1)
+#endif
+#ifndef INT32_MIN
+#define INT32_MIN              (-2147483647-1)
+#endif
+#ifndef INT8_MAX
+#define INT8_MAX               (127)
+#endif
+#ifndef INT16_MAX
+#define INT16_MAX              (32767)
+#endif
+#ifndef INT32_MAX
+#define INT32_MAX              (2147483647)
+#endif
+#ifndef UINT8_MAX
+#define UINT8_MAX              (255U)
+#endif
+#ifndef UINT16_MAX
+#define UINT16_MAX             (65535U)
+#endif
+#ifndef UINT32_MAX
+#define UINT32_MAX             (4294967295U)
+#endif
+
+#endif /* ! C99 */
+
+#endif /* ! FLEXINT_H */
+
+/* TODO: this is always defined, so inline it */
+#define yyconst const
+
+#if defined(__GNUC__) && __GNUC__ >= 3
+#define yynoreturn __attribute__((__noreturn__))
+#else
+#define yynoreturn
+#endif
+
+/* Returned upon end-of-file. */
+#define YY_NULL 0
+
+/* Promotes a possibly negative, possibly signed char to an unsigned
+ * integer for use as an array index.  If the signed char is negative,
+ * we want to instead treat it as an 8-bit unsigned char, hence the
+ * double cast.
+ */
+#define YY_SC_TO_UI(c) ((unsigned int) (unsigned char) c)
+
+/* An opaque pointer. */
+#ifndef YY_TYPEDEF_YY_SCANNER_T
+#define YY_TYPEDEF_YY_SCANNER_T
+typedef void* yyscan_t;
+#endif
+
+/* For convenience, these vars (plus the bison vars far below)
+   are macros in the reentrant scanner. */
+#define yyin yyg->yyin_r
+#define yyout yyg->yyout_r
+#define yyextra yyg->yyextra_r
+#define yyleng yyg->yyleng_r
+#define yytext yyg->yytext_r
+#define yylineno (YY_CURRENT_BUFFER_LVALUE->yy_bs_lineno)
+#define yycolumn (YY_CURRENT_BUFFER_LVALUE->yy_bs_column)
+#define yy_flex_debug yyg->yy_flex_debug_r
+
+/* Enter a start condition.  This macro really ought to take a parameter,
+ * but we do it the disgusting crufty way forced on us by the ()-less
+ * definition of BEGIN.
+ */
+#define BEGIN yyg->yy_start = 1 + 2 *
+
+/* Translate the current start state into a value that can be later handed
+ * to BEGIN to return to the state.  The YYSTATE alias is for lex
+ * compatibility.
+ */
+#define YY_START ((yyg->yy_start - 1) / 2)
+#define YYSTATE YY_START
+
+/* Action number for EOF rule of a given start state. */
+#define YY_STATE_EOF(state) (YY_END_OF_BUFFER + state + 1)
+
+/* Special action meaning "start processing a new file". */
+#define YY_NEW_FILE freesasa_yyrestart(yyin ,yyscanner )
+
+#define YY_END_OF_BUFFER_CHAR 0
+
+/* Size of default input buffer. */
+#ifndef YY_BUF_SIZE
+#ifdef __ia64__
+/* On IA-64, the buffer size is 16k, not 8k.
+ * Moreover, YY_BUF_SIZE is 2*YY_READ_BUF_SIZE in the general case.
+ * Ditto for the __ia64__ case accordingly.
+ */
+#define YY_BUF_SIZE 32768
+#else
+#define YY_BUF_SIZE 16384
+#endif /* __ia64__ */
+#endif
+
+/* The state buf must be large enough to hold one state per character in the main buffer.
+ */
+#define YY_STATE_BUF_SIZE   ((YY_BUF_SIZE + 2) * sizeof(yy_state_type))
+
+#ifndef YY_TYPEDEF_YY_BUFFER_STATE
+#define YY_TYPEDEF_YY_BUFFER_STATE
+typedef struct yy_buffer_state *YY_BUFFER_STATE;
+#endif
+
+#ifndef YY_TYPEDEF_YY_SIZE_T
+#define YY_TYPEDEF_YY_SIZE_T
+typedef size_t yy_size_t;
+#endif
+
+#define EOB_ACT_CONTINUE_SCAN 0
+#define EOB_ACT_END_OF_FILE 1
+#define EOB_ACT_LAST_MATCH 2
+
+    #define YY_LESS_LINENO(n)
+    #define YY_LINENO_REWIND_TO(ptr)
+    
+/* Return all but the first "n" matched characters back to the input stream. */
+#define yyless(n) \
+	do \
+		{ \
+		/* Undo effects of setting up yytext. */ \
+        int yyless_macro_arg = (n); \
+        YY_LESS_LINENO(yyless_macro_arg);\
+		*yy_cp = yyg->yy_hold_char; \
+		YY_RESTORE_YY_MORE_OFFSET \
+		yyg->yy_c_buf_p = yy_cp = yy_bp + yyless_macro_arg - YY_MORE_ADJ; \
+		YY_DO_BEFORE_ACTION; /* set up yytext again */ \
+		} \
+	while ( 0 )
+
+#define unput(c) yyunput( c, yyg->yytext_ptr , yyscanner )
+
+#ifndef YY_STRUCT_YY_BUFFER_STATE
+#define YY_STRUCT_YY_BUFFER_STATE
+struct yy_buffer_state
+	{
+	FILE *yy_input_file;
+
+	char *yy_ch_buf;		/* input buffer */
+	char *yy_buf_pos;		/* current position in input buffer */
+
+	/* Size of input buffer in bytes, not including room for EOB
+	 * characters.
+	 */
+	int yy_buf_size;
+
+	/* Number of characters read into yy_ch_buf, not including EOB
+	 * characters.
+	 */
+	int yy_n_chars;
+
+	/* Whether we "own" the buffer - i.e., we know we created it,
+	 * and can realloc() it to grow it, and should free() it to
+	 * delete it.
+	 */
+	int yy_is_our_buffer;
+
+	/* Whether this is an "interactive" input source; if so, and
+	 * if we're using stdio for input, then we want to use getc()
+	 * instead of fread(), to make sure we stop fetching input after
+	 * each newline.
+	 */
+	int yy_is_interactive;
+
+	/* Whether we're considered to be at the beginning of a line.
+	 * If so, '^' rules will be active on the next match, otherwise
+	 * not.
+	 */
+	int yy_at_bol;
+
+    int yy_bs_lineno; /**< The line count. */
+    int yy_bs_column; /**< The column count. */
+    
+	/* Whether to try to fill the input buffer when we reach the
+	 * end of it.
+	 */
+	int yy_fill_buffer;
+
+	int yy_buffer_status;
+
+#define YY_BUFFER_NEW 0
+#define YY_BUFFER_NORMAL 1
+	/* When an EOF's been seen but there's still some text to process
+	 * then we mark the buffer as YY_EOF_PENDING, to indicate that we
+	 * shouldn't try reading from the input source any more.  We might
+	 * still have a bunch of tokens to match, though, because of
+	 * possible backing-up.
+	 *
+	 * When we actually see the EOF, we change the status to "new"
+	 * (via freesasa_yyrestart()), so that the user can continue scanning by
+	 * just pointing yyin at a new input file.
+	 */
+#define YY_BUFFER_EOF_PENDING 2
+
+	};
+#endif /* !YY_STRUCT_YY_BUFFER_STATE */
+
+/* We provide macros for accessing buffer states in case in the
+ * future we want to put the buffer states in a more general
+ * "scanner state".
+ *
+ * Returns the top of the stack, or NULL.
+ */
+#define YY_CURRENT_BUFFER ( yyg->yy_buffer_stack \
+                          ? yyg->yy_buffer_stack[yyg->yy_buffer_stack_top] \
+                          : NULL)
+
+/* Same as previous macro, but useful when we know that the buffer stack is not
+ * NULL or when we need an lvalue. For internal use only.
+ */
+#define YY_CURRENT_BUFFER_LVALUE yyg->yy_buffer_stack[yyg->yy_buffer_stack_top]
+
+void freesasa_yyrestart (FILE *input_file ,yyscan_t yyscanner );
+void freesasa_yy_switch_to_buffer (YY_BUFFER_STATE new_buffer ,yyscan_t yyscanner );
+YY_BUFFER_STATE freesasa_yy_create_buffer (FILE *file,int size ,yyscan_t yyscanner );
+void freesasa_yy_delete_buffer (YY_BUFFER_STATE b ,yyscan_t yyscanner );
+void freesasa_yy_flush_buffer (YY_BUFFER_STATE b ,yyscan_t yyscanner );
+void freesasa_yypush_buffer_state (YY_BUFFER_STATE new_buffer ,yyscan_t yyscanner );
+void freesasa_yypop_buffer_state (yyscan_t yyscanner );
+
+static void freesasa_yyensure_buffer_stack (yyscan_t yyscanner );
+static void freesasa_yy_load_buffer_state (yyscan_t yyscanner );
+static void freesasa_yy_init_buffer (YY_BUFFER_STATE b,FILE *file ,yyscan_t yyscanner );
+
+#define YY_FLUSH_BUFFER freesasa_yy_flush_buffer(YY_CURRENT_BUFFER ,yyscanner)
+
+YY_BUFFER_STATE freesasa_yy_scan_buffer (char *base,yy_size_t size ,yyscan_t yyscanner );
+YY_BUFFER_STATE freesasa_yy_scan_string (yyconst char *yy_str ,yyscan_t yyscanner );
+YY_BUFFER_STATE freesasa_yy_scan_bytes (yyconst char *bytes,int len ,yyscan_t yyscanner );
+
+void *freesasa_yyalloc (yy_size_t ,yyscan_t yyscanner );
+void *freesasa_yyrealloc (void *,yy_size_t ,yyscan_t yyscanner );
+void freesasa_yyfree (void * ,yyscan_t yyscanner );
+
+#define yy_new_buffer freesasa_yy_create_buffer
+
+#define yy_set_interactive(is_interactive) \
+	{ \
+	if ( ! YY_CURRENT_BUFFER ){ \
+        freesasa_yyensure_buffer_stack (yyscanner); \
+		YY_CURRENT_BUFFER_LVALUE =    \
+            freesasa_yy_create_buffer(yyin,YY_BUF_SIZE ,yyscanner); \
+	} \
+	YY_CURRENT_BUFFER_LVALUE->yy_is_interactive = is_interactive; \
+	}
+
+#define yy_set_bol(at_bol) \
+	{ \
+	if ( ! YY_CURRENT_BUFFER ){\
+        freesasa_yyensure_buffer_stack (yyscanner); \
+		YY_CURRENT_BUFFER_LVALUE =    \
+            freesasa_yy_create_buffer(yyin,YY_BUF_SIZE ,yyscanner); \
+	} \
+	YY_CURRENT_BUFFER_LVALUE->yy_at_bol = at_bol; \
+	}
+
+#define YY_AT_BOL() (YY_CURRENT_BUFFER_LVALUE->yy_at_bol)
+
+#define freesasa_yywrap(yyscanner) (/*CONSTCOND*/1)
+#define YY_SKIP_YYWRAP
+
+typedef unsigned char YY_CHAR;
+
+typedef int yy_state_type;
+
+#define yytext_ptr yytext_r
+
+static yy_state_type yy_get_previous_state (yyscan_t yyscanner );
+static yy_state_type yy_try_NUL_trans (yy_state_type current_state  ,yyscan_t yyscanner);
+static int yy_get_next_buffer (yyscan_t yyscanner );
+static void yynoreturn yy_fatal_error (yyconst char* msg ,yyscan_t yyscanner );
+
+/* Done after the current pattern has been matched and before the
+ * corresponding action - sets up yytext.
+ */
+#define YY_DO_BEFORE_ACTION \
+	yyg->yytext_ptr = yy_bp; \
+	yyleng = (int) (yy_cp - yy_bp); \
+	yyg->yy_hold_char = *yy_cp; \
+	*yy_cp = '\0'; \
+	yyg->yy_c_buf_p = yy_cp;
+
+#define YY_NUM_RULES 19
+#define YY_END_OF_BUFFER 20
+/* This struct is not used in this scanner,
+   but its presence is necessary. */
+struct yy_trans_info
+	{
+	flex_int32_t yy_verify;
+	flex_int32_t yy_nxt;
+	};
+static yyconst flex_int16_t yy_accept[52] =
+    {   0,
+       15,   15,   20,   19,   15,   13,   11,    4,    5,    3,
+        1,    2,   16,   17,   17,   17,   17,   17,   17,   17,
+       19,   12,   15,    0,   18,   17,   16,   17,   17,   17,
+       17,   17,   12,   17,   17,   14,   11,   17,   17,   13,
+       17,   17,   17,    9,    7,    6,   17,   10,   17,    8,
+        0
+    } ;
+
+static yyconst YY_CHAR yy_ec[256] =
+    {   0,
+        1,    1,    1,    1,    1,    1,    1,    1,    2,    2,
+        1,    1,    2,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    2,    3,    1,    1,    1,    1,    4,    5,    6,
+        7,    1,    8,    9,   10,    1,    1,   11,   11,   11,
+       11,   11,   11,   11,   11,   11,   11,    1,    1,    1,
+        1,    1,    1,    1,   12,   13,   14,   15,   16,   17,
+       17,   18,   19,   17,   17,   20,   21,   22,   23,   17,
+       17,   24,   25,   26,   17,   17,   17,   17,   27,   17,
+        1,   28,    1,    1,   17,    1,   29,   30,   31,   32,
+
+       33,   17,   17,   34,   35,   17,   17,   36,   37,   38,
+       39,   17,   17,   40,   41,   42,   17,   17,   17,   17,
+       43,   17,    1,   44,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1
+    } ;
+
+static yyconst YY_CHAR yy_meta[45] =
+    {   0,
+        1,    1,    1,    1,    2,    1,    1,    3,    3,    3,
+        3,    3,    3,    3,    3,    3,    3,    3,    3,    3,
+        3,    3,    3,    3,    3,    3,    3,    1,    3,    3,
+        3,    3,    3,    3,    3,    3,    3,    3,    3,    3,
+        3,    3,    3,    1
+    } ;
+
+static yyconst flex_uint16_t yy_base[54] =
+    {   0,
+        0,    0,   68,  281,   64,  281,  281,  281,  281,   56,
+      281,   51,   40,   47,   53,   62,   92,   68,   74,  101,
+       49,  281,   52,   44,  281,   42,  108,  115,  124,   52,
+      114,  126,  118,  138,  152,  281,  147,  159,  180,  172,
+      208,  187,  183,  203,  210,  214,  185,  211,  239,  232,
+      281,   43,  277
+    } ;
+
+static yyconst flex_int16_t yy_def[54] =
+    {   0,
+       51,    1,   51,   51,   51,   51,   51,   51,   51,   52,
+       51,   52,   53,   53,   53,   53,   53,   53,   53,   53,
+       51,   51,   51,   52,   51,   51,   53,   53,   53,   17,
+       17,   17,   17,   17,   17,   51,   17,   17,   17,   17,
+       17,   17,   41,   41,   41,   41,   17,   17,   17,   17,
+        0,   51,   51
+    } ;
+
+static yyconst flex_uint16_t yy_nxt[326] =
+    {   0,
+        4,    5,    6,    7,    4,    8,    9,   10,   11,   12,
+       13,   14,   15,   16,   15,   15,   15,   15,   15,   15,
+       15,   17,   18,   19,   20,   15,   15,   21,   14,   15,
+       16,   15,   15,   15,   15,   15,   15,   17,   18,   19,
+       20,   15,   15,   22,   26,   24,   26,   24,   25,   24,
+       27,   26,   25,   23,   24,   25,   24,   26,   36,   25,
+       24,   25,   24,   38,   25,   23,   26,   51,   29,   24,
+       25,   24,   26,   51,   28,   24,   25,   24,   26,   30,
+       38,   24,   25,   24,   29,   51,   51,   51,   51,   34,
+       28,   33,   51,   51,   51,   30,   26,   51,   51,   24,
+
+       25,   24,   51,   31,   51,   26,   34,   33,   24,   25,
+       24,   51,   26,   51,   32,   24,   25,   24,   27,   26,
+       31,   51,   24,   25,   24,   28,   51,   35,   26,   28,
+       32,   24,   25,   24,   39,   51,   28,   28,   37,   51,
+       28,   51,   28,   35,   51,   51,   28,   51,   28,   28,
+       39,   40,   28,   51,   28,   37,   28,   51,   28,   51,
+       28,   51,   41,   28,   28,   51,   28,   40,   51,   28,
+       28,   51,   42,   51,   28,   28,   28,   43,   41,   51,
+       28,   28,   51,   28,   51,   28,   51,   28,   42,   51,
+       28,   28,   51,   43,   28,   44,   28,   28,   28,   47,
+
+       28,   28,   28,   51,   48,   51,   51,   49,   28,   28,
+       28,   51,   44,   28,   51,   28,   47,   28,   28,   28,
+       48,   28,   28,   49,   28,   28,   45,   51,   28,   46,
+       28,   28,   28,   28,   51,   28,   28,   28,   51,   28,
+       28,   51,   45,   28,   28,   46,   28,   28,   28,   28,
+       28,   28,   51,   51,   28,   51,   51,   51,   50,   51,
+       28,   28,   51,   51,   51,   51,   51,   28,   51,   51,
+       28,   51,   51,   51,   50,   51,   51,   28,   28,   28,
+        3,   51,   51,   51,   51,   51,   51,   51,   51,   51,
+       51,   51,   51,   51,   51,   51,   51,   51,   51,   51,
+
+       51,   51,   51,   51,   51,   51,   51,   51,   51,   51,
+       51,   51,   51,   51,   51,   51,   51,   51,   51,   51,
+       51,   51,   51,   51,   51
+    } ;
+
+static yyconst flex_int16_t yy_chk[326] =
+    {   0,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
+        1,    1,    1,    1,   13,   52,   26,   13,   13,   13,
+       13,   14,   24,   23,   14,   14,   14,   15,   21,   12,
+       15,   15,   15,   30,   10,    5,   16,    3,   14,   16,
+       16,   16,   18,    0,   30,   18,   18,   18,   19,   16,
+       30,   19,   19,   19,   14,    0,    0,    0,    0,   19,
+       30,   18,    0,    0,    0,   16,   17,    0,    0,   17,
+
+       17,   17,    0,   17,    0,   20,   19,   18,   20,   20,
+       20,    0,   27,    0,   17,   27,   27,   27,   27,   28,
+       17,    0,   28,   28,   28,   31,    0,   20,   29,   33,
+       17,   29,   29,   29,   31,    0,   31,   32,   29,    0,
+       33,    0,   31,   20,    0,    0,   33,    0,   32,   34,
+       31,   32,   31,    0,   32,   29,   33,    0,   37,    0,
+       34,    0,   34,   35,   32,    0,   34,   32,    0,   37,
+       38,    0,   35,    0,   35,   37,   34,   38,   34,    0,
+       35,   38,    0,   40,    0,   37,    0,   38,   35,    0,
+       35,   39,    0,   38,   40,   39,   47,   38,   42,   42,
+
+       40,   43,   39,    0,   43,    0,    0,   47,   39,   42,
+       40,    0,   39,   47,    0,   42,   42,   43,   39,   41,
+       43,   44,   48,   47,   44,   42,   41,    0,   45,   41,
+       41,   45,   46,   48,    0,   46,   41,   44,    0,   48,
+       44,    0,   41,   50,   45,   41,   41,   45,   46,   48,
+       49,   46,    0,    0,   50,    0,    0,    0,   49,    0,
+       50,   49,    0,    0,    0,    0,    0,   49,    0,    0,
+       50,    0,    0,    0,   49,    0,    0,   49,   53,   53,
+       51,   51,   51,   51,   51,   51,   51,   51,   51,   51,
+       51,   51,   51,   51,   51,   51,   51,   51,   51,   51,
+
+       51,   51,   51,   51,   51,   51,   51,   51,   51,   51,
+       51,   51,   51,   51,   51,   51,   51,   51,   51,   51,
+       51,   51,   51,   51,   51
+    } ;
+
+/* The intent behind this definition is that it'll catch
+ * any uses of REJECT which flex missed.
+ */
+#define REJECT reject_used_but_not_detected
+#define yymore() yymore_used_but_not_detected
+#define YY_MORE_ADJ 0
+#define YY_RESTORE_YY_MORE_OFFSET
+#line 1 "lexer.l"
+#line 2 "lexer.l"
+
+#include "selection.h"
+#include "parser.h"
+#include "freesasa_internal.h"
+
+#include <stdio.h>
+
+#define YY_NO_UNISTD_H 1
+#line 526 "lexer.c"
+
+#define INITIAL 0
+
+#ifndef YY_EXTRA_TYPE
+#define YY_EXTRA_TYPE void *
+#endif
+
+/* Holds the entire state of the reentrant scanner. */
+struct yyguts_t
+    {
+
+    /* User-defined. Not touched by flex. */
+    YY_EXTRA_TYPE yyextra_r;
+
+    /* The rest are the same as the globals declared in the non-reentrant scanner. */
+    FILE *yyin_r, *yyout_r;
+    size_t yy_buffer_stack_top; /**< index of top of stack. */
+    size_t yy_buffer_stack_max; /**< capacity of stack. */
+    YY_BUFFER_STATE * yy_buffer_stack; /**< Stack as an array. */
+    char yy_hold_char;
+    int yy_n_chars;
+    int yyleng_r;
+    char *yy_c_buf_p;
+    int yy_init;
+    int yy_start;
+    int yy_did_buffer_switch_on_eof;
+    int yy_start_stack_ptr;
+    int yy_start_stack_depth;
+    int *yy_start_stack;
+    yy_state_type yy_last_accepting_state;
+    char* yy_last_accepting_cpos;
+
+    int yylineno_r;
+    int yy_flex_debug_r;
+
+    char *yytext_r;
+    int yy_more_flag;
+    int yy_more_len;
+
+    YYSTYPE * yylval_r;
+
+    }; /* end struct yyguts_t */
+
+static int yy_init_globals (yyscan_t yyscanner );
+
+    /* This must go here because YYSTYPE and YYLTYPE are included
+     * from bison output in section 1.*/
+    #    define yylval yyg->yylval_r
+    
+int freesasa_yylex_init (yyscan_t* scanner);
+
+int freesasa_yylex_init_extra (YY_EXTRA_TYPE user_defined,yyscan_t* scanner);
+
+/* Accessor methods to globals.
+   These are made visible to non-reentrant scanners for convenience. */
+
+int freesasa_yylex_destroy (yyscan_t yyscanner );
+
+int freesasa_yyget_debug (yyscan_t yyscanner );
+
+void freesasa_yyset_debug (int debug_flag ,yyscan_t yyscanner );
+
+YY_EXTRA_TYPE freesasa_yyget_extra (yyscan_t yyscanner );
+
+void freesasa_yyset_extra (YY_EXTRA_TYPE user_defined ,yyscan_t yyscanner );
+
+FILE *freesasa_yyget_in (yyscan_t yyscanner );
+
+void freesasa_yyset_in  (FILE * _in_str ,yyscan_t yyscanner );
+
+FILE *freesasa_yyget_out (yyscan_t yyscanner );
+
+void freesasa_yyset_out  (FILE * _out_str ,yyscan_t yyscanner );
+
+			int freesasa_yyget_leng (yyscan_t yyscanner );
+
+char *freesasa_yyget_text (yyscan_t yyscanner );
+
+int freesasa_yyget_lineno (yyscan_t yyscanner );
+
+void freesasa_yyset_lineno (int _line_number ,yyscan_t yyscanner );
+
+int freesasa_yyget_column  (yyscan_t yyscanner );
+
+void freesasa_yyset_column (int _column_no ,yyscan_t yyscanner );
+
+YYSTYPE * freesasa_yyget_lval (yyscan_t yyscanner );
+
+void freesasa_yyset_lval (YYSTYPE * yylval_param ,yyscan_t yyscanner );
+
+/* Macros after this point can all be overridden by user definitions in
+ * section 1.
+ */
+
+#ifndef YY_SKIP_YYWRAP
+#ifdef __cplusplus
+extern "C" int freesasa_yywrap (yyscan_t yyscanner );
+#else
+extern int freesasa_yywrap (yyscan_t yyscanner );
+#endif
+#endif
+
+#ifndef YY_NO_UNPUT
+    
+    static void yyunput (int c,char *buf_ptr  ,yyscan_t yyscanner);
+    
+#endif
+
+#ifndef yytext_ptr
+static void yy_flex_strncpy (char *,yyconst char *,int ,yyscan_t yyscanner);
+#endif
+
+#ifdef YY_NEED_STRLEN
+static int yy_flex_strlen (yyconst char * ,yyscan_t yyscanner);
+#endif
+
+#ifndef YY_NO_INPUT
+
+#ifdef __cplusplus
+static int yyinput (yyscan_t yyscanner );
+#else
+static int input (yyscan_t yyscanner );
+#endif
+
+#endif
+
+/* Amount of stuff to slurp up with each read. */
+#ifndef YY_READ_BUF_SIZE
+#ifdef __ia64__
+/* On IA-64, the buffer size is 16k, not 8k */
+#define YY_READ_BUF_SIZE 16384
+#else
+#define YY_READ_BUF_SIZE 8192
+#endif /* __ia64__ */
+#endif
+
+/* Copy whatever the last rule matched to the standard output. */
+#ifndef ECHO
+/* This used to be an fputs(), but since the string might contain NUL's,
+ * we now use fwrite().
+ */
+#define ECHO do { if (fwrite( yytext, (size_t) yyleng, 1, yyout )) {} } while (0)
+#endif
+
+/* Gets input and stuffs it into "buf".  number of characters read, or YY_NULL,
+ * is returned in "result".
+ */
+#ifndef YY_INPUT
+#define YY_INPUT(buf,result,max_size) \
+	if ( YY_CURRENT_BUFFER_LVALUE->yy_is_interactive ) \
+		{ \
+		int c = '*'; \
+		size_t n; \
+		for ( n = 0; n < max_size && \
+			     (c = getc( yyin )) != EOF && c != '\n'; ++n ) \
+			buf[n] = (char) c; \
+		if ( c == '\n' ) \
+			buf[n++] = (char) c; \
+		if ( c == EOF && ferror( yyin ) ) \
+			YY_FATAL_ERROR( "input in flex scanner failed" ); \
+		result = n; \
+		} \
+	else \
+		{ \
+		errno=0; \
+		while ( (result = (int) fread(buf, 1, max_size, yyin))==0 && ferror(yyin)) \
+			{ \
+			if( errno != EINTR) \
+				{ \
+				YY_FATAL_ERROR( "input in flex scanner failed" ); \
+				break; \
+				} \
+			errno=0; \
+			clearerr(yyin); \
+			} \
+		}\
+\
+
+#endif
+
+/* No semi-colon after return; correct usage is to write "yyterminate();" -
+ * we don't want an extra ';' after the "return" because that will cause
+ * some compilers to complain about unreachable statements.
+ */
+#ifndef yyterminate
+#define yyterminate() return YY_NULL
+#endif
+
+/* Number of entries by which start-condition stack grows. */
+#ifndef YY_START_STACK_INCR
+#define YY_START_STACK_INCR 25
+#endif
+
+/* Report a fatal error. */
+#ifndef YY_FATAL_ERROR
+#define YY_FATAL_ERROR(msg) yy_fatal_error( msg , yyscanner)
+#endif
+
+/* end tables serialization structures and prototypes */
+
+/* Default declaration of generated scanner - a define so the user can
+ * easily add parameters.
+ */
+#ifndef YY_DECL
+#define YY_DECL_IS_OURS 1
+
+extern int freesasa_yylex \
+               (YYSTYPE * yylval_param ,yyscan_t yyscanner);
+
+#define YY_DECL int freesasa_yylex \
+               (YYSTYPE * yylval_param , yyscan_t yyscanner)
+#endif /* !YY_DECL */
+
+/* Code executed at the beginning of each rule, after yytext and yyleng
+ * have been set up.
+ */
+#ifndef YY_USER_ACTION
+#define YY_USER_ACTION
+#endif
+
+/* Code executed at the end of each rule. */
+#ifndef YY_BREAK
+#define YY_BREAK /*LINTED*/break;
+#endif
+
+#define YY_RULE_SETUP \
+	YY_USER_ACTION
+
+/** The main scanner function which does all the work.
+ */
+YY_DECL
+{
+	yy_state_type yy_current_state;
+	char *yy_cp, *yy_bp;
+	int yy_act;
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+    yylval = yylval_param;
+
+	if ( !yyg->yy_init )
+		{
+		yyg->yy_init = 1;
+
+#ifdef YY_USER_INIT
+		YY_USER_INIT;
+#endif
+
+		if ( ! yyg->yy_start )
+			yyg->yy_start = 1;	/* first start state */
+
+		if ( ! yyin )
+			yyin = stdin;
+
+		if ( ! yyout )
+			yyout = stdout;
+
+		if ( ! YY_CURRENT_BUFFER ) {
+			freesasa_yyensure_buffer_stack (yyscanner);
+			YY_CURRENT_BUFFER_LVALUE =
+				freesasa_yy_create_buffer(yyin,YY_BUF_SIZE ,yyscanner);
+		}
+
+		freesasa_yy_load_buffer_state(yyscanner );
+		}
+
+	{
+#line 32 "lexer.l"
+
+
+#line 796 "lexer.c"
+
+	while ( /*CONSTCOND*/1 )		/* loops until end-of-file is reached */
+		{
+		yy_cp = yyg->yy_c_buf_p;
+
+		/* Support of yytext. */
+		*yy_cp = yyg->yy_hold_char;
+
+		/* yy_bp points to the position in yy_ch_buf of the start of
+		 * the current run.
+		 */
+		yy_bp = yy_cp;
+
+		yy_current_state = yyg->yy_start;
+yy_match:
+		do
+			{
+			YY_CHAR yy_c = yy_ec[YY_SC_TO_UI(*yy_cp)] ;
+			if ( yy_accept[yy_current_state] )
+				{
+				yyg->yy_last_accepting_state = yy_current_state;
+				yyg->yy_last_accepting_cpos = yy_cp;
+				}
+			while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state )
+				{
+				yy_current_state = (int) yy_def[yy_current_state];
+				if ( yy_current_state >= 52 )
+					yy_c = yy_meta[(unsigned int) yy_c];
+				}
+			yy_current_state = yy_nxt[yy_base[yy_current_state] + (flex_int16_t) yy_c];
+			++yy_cp;
+			}
+		while ( yy_current_state != 51 );
+		yy_cp = yyg->yy_last_accepting_cpos;
+		yy_current_state = yyg->yy_last_accepting_state;
+
+yy_find_action:
+		yy_act = yy_accept[yy_current_state];
+
+		YY_DO_BEFORE_ACTION;
+
+do_action:	/* This label is used only to access EOF actions. */
+
+		switch ( yy_act )
+	{ /* beginning of action switch */
+			case 0: /* must back up */
+			/* undo the effects of YY_DO_BEFORE_ACTION */
+			*yy_cp = yyg->yy_hold_char;
+			yy_cp = yyg->yy_last_accepting_cpos;
+			yy_current_state = yyg->yy_last_accepting_state;
+			goto yy_find_action;
+
+case 1:
+YY_RULE_SETUP
+#line 34 "lexer.l"
+{ return ','; }
+	YY_BREAK
+case 2:
+YY_RULE_SETUP
+#line 35 "lexer.l"
+{ return '-'; }
+	YY_BREAK
+case 3:
+YY_RULE_SETUP
+#line 36 "lexer.l"
+{ return '+'; }
+	YY_BREAK
+case 4:
+YY_RULE_SETUP
+#line 37 "lexer.l"
+{ return '('; }
+	YY_BREAK
+case 5:
+YY_RULE_SETUP
+#line 38 "lexer.l"
+{ return ')'; }
+	YY_BREAK
+case 6:
+YY_RULE_SETUP
+#line 40 "lexer.l"
+{ return T_RESN; }
+	YY_BREAK
+case 7:
+YY_RULE_SETUP
+#line 41 "lexer.l"
+{ return T_RESI; }
+	YY_BREAK
+case 8:
+YY_RULE_SETUP
+#line 42 "lexer.l"
+{ return T_SYMBOL; }
+	YY_BREAK
+case 9:
+YY_RULE_SETUP
+#line 43 "lexer.l"
+{ return T_NAME; }
+	YY_BREAK
+case 10:
+YY_RULE_SETUP
+#line 44 "lexer.l"
+{ return T_CHAIN; }
+	YY_BREAK
+case 11:
+YY_RULE_SETUP
+#line 46 "lexer.l"
+{ return T_AND; }
+	YY_BREAK
+case 12:
+YY_RULE_SETUP
+#line 47 "lexer.l"
+{ return T_OR; }
+	YY_BREAK
+case 13:
+YY_RULE_SETUP
+#line 48 "lexer.l"
+{ return T_NOT; }
+	YY_BREAK
+case 14:
+YY_RULE_SETUP
+#line 49 "lexer.l"
+{ return T_MINUS; }
+	YY_BREAK
+case 15:
+/* rule 15 can match eol */
+YY_RULE_SETUP
+#line 51 "lexer.l"
+{}
+	YY_BREAK
+case 16:
+YY_RULE_SETUP
+#line 52 "lexer.l"
+{ yylval->value = strdup(yytext); return T_NUMBER; }
+	YY_BREAK
+case 17:
+YY_RULE_SETUP
+#line 53 "lexer.l"
+{ yylval->value = strdup(yytext); return T_ID; }
+	YY_BREAK
+case 18:
+*yy_cp = yyg->yy_hold_char; /* undo effects of setting up yytext */
+yyg->yy_c_buf_p = yy_cp -= 1;
+YY_DO_BEFORE_ACTION; /* set up yytext again */
+YY_RULE_SETUP
+#line 54 "lexer.l"
+{ yylval->value = strdup(yytext); return T_SELID; }
+	YY_BREAK
+case 19:
+YY_RULE_SETUP
+#line 55 "lexer.l"
+ECHO;
+	YY_BREAK
+#line 948 "lexer.c"
+case YY_STATE_EOF(INITIAL):
+	yyterminate();
+
+	case YY_END_OF_BUFFER:
+		{
+		/* Amount of text matched not including the EOB char. */
+		int yy_amount_of_matched_text = (int) (yy_cp - yyg->yytext_ptr) - 1;
+
+		/* Undo the effects of YY_DO_BEFORE_ACTION. */
+		*yy_cp = yyg->yy_hold_char;
+		YY_RESTORE_YY_MORE_OFFSET
+
+		if ( YY_CURRENT_BUFFER_LVALUE->yy_buffer_status == YY_BUFFER_NEW )
+			{
+			/* We're scanning a new file or input source.  It's
+			 * possible that this happened because the user
+			 * just pointed yyin at a new source and called
+			 * freesasa_yylex().  If so, then we have to assure
+			 * consistency between YY_CURRENT_BUFFER and our
+			 * globals.  Here is the right place to do so, because
+			 * this is the first action (other than possibly a
+			 * back-up) that will match for the new input source.
+			 */
+			yyg->yy_n_chars = YY_CURRENT_BUFFER_LVALUE->yy_n_chars;
+			YY_CURRENT_BUFFER_LVALUE->yy_input_file = yyin;
+			YY_CURRENT_BUFFER_LVALUE->yy_buffer_status = YY_BUFFER_NORMAL;
+			}
+
+		/* Note that here we test for yy_c_buf_p "<=" to the position
+		 * of the first EOB in the buffer, since yy_c_buf_p will
+		 * already have been incremented past the NUL character
+		 * (since all states make transitions on EOB to the
+		 * end-of-buffer state).  Contrast this with the test
+		 * in input().
+		 */
+		if ( yyg->yy_c_buf_p <= &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[yyg->yy_n_chars] )
+			{ /* This was really a NUL. */
+			yy_state_type yy_next_state;
+
+			yyg->yy_c_buf_p = yyg->yytext_ptr + yy_amount_of_matched_text;
+
+			yy_current_state = yy_get_previous_state( yyscanner );
+
+			/* Okay, we're now positioned to make the NUL
+			 * transition.  We couldn't have
+			 * yy_get_previous_state() go ahead and do it
+			 * for us because it doesn't know how to deal
+			 * with the possibility of jamming (and we don't
+			 * want to build jamming into it because then it
+			 * will run more slowly).
+			 */
+
+			yy_next_state = yy_try_NUL_trans( yy_current_state , yyscanner);
+
+			yy_bp = yyg->yytext_ptr + YY_MORE_ADJ;
+
+			if ( yy_next_state )
+				{
+				/* Consume the NUL. */
+				yy_cp = ++yyg->yy_c_buf_p;
+				yy_current_state = yy_next_state;
+				goto yy_match;
+				}
+
+			else
+				{
+				yy_cp = yyg->yy_last_accepting_cpos;
+				yy_current_state = yyg->yy_last_accepting_state;
+				goto yy_find_action;
+				}
+			}
+
+		else switch ( yy_get_next_buffer( yyscanner ) )
+			{
+			case EOB_ACT_END_OF_FILE:
+				{
+				yyg->yy_did_buffer_switch_on_eof = 0;
+
+				if ( freesasa_yywrap(yyscanner ) )
+					{
+					/* Note: because we've taken care in
+					 * yy_get_next_buffer() to have set up
+					 * yytext, we can now set up
+					 * yy_c_buf_p so that if some total
+					 * hoser (like flex itself) wants to
+					 * call the scanner after we return the
+					 * YY_NULL, it'll still work - another
+					 * YY_NULL will get returned.
+					 */
+					yyg->yy_c_buf_p = yyg->yytext_ptr + YY_MORE_ADJ;
+
+					yy_act = YY_STATE_EOF(YY_START);
+					goto do_action;
+					}
+
+				else
+					{
+					if ( ! yyg->yy_did_buffer_switch_on_eof )
+						YY_NEW_FILE;
+					}
+				break;
+				}
+
+			case EOB_ACT_CONTINUE_SCAN:
+				yyg->yy_c_buf_p =
+					yyg->yytext_ptr + yy_amount_of_matched_text;
+
+				yy_current_state = yy_get_previous_state( yyscanner );
+
+				yy_cp = yyg->yy_c_buf_p;
+				yy_bp = yyg->yytext_ptr + YY_MORE_ADJ;
+				goto yy_match;
+
+			case EOB_ACT_LAST_MATCH:
+				yyg->yy_c_buf_p =
+				&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[yyg->yy_n_chars];
+
+				yy_current_state = yy_get_previous_state( yyscanner );
+
+				yy_cp = yyg->yy_c_buf_p;
+				yy_bp = yyg->yytext_ptr + YY_MORE_ADJ;
+				goto yy_find_action;
+			}
+		break;
+		}
+
+	default:
+		YY_FATAL_ERROR(
+			"fatal flex scanner internal error--no action found" );
+	} /* end of action switch */
+		} /* end of scanning one token */
+	} /* end of user's declarations */
+} /* end of freesasa_yylex */
+
+/* yy_get_next_buffer - try to read in a new buffer
+ *
+ * Returns a code representing an action:
+ *	EOB_ACT_LAST_MATCH -
+ *	EOB_ACT_CONTINUE_SCAN - continue scanning from current position
+ *	EOB_ACT_END_OF_FILE - end of file
+ */
+static int yy_get_next_buffer (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+	char *dest = YY_CURRENT_BUFFER_LVALUE->yy_ch_buf;
+	char *source = yyg->yytext_ptr;
+	yy_size_t number_to_move, i;
+	int ret_val;
+
+	if ( yyg->yy_c_buf_p > &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[yyg->yy_n_chars + 1] )
+		YY_FATAL_ERROR(
+		"fatal flex scanner internal error--end of buffer missed" );
+
+	if ( YY_CURRENT_BUFFER_LVALUE->yy_fill_buffer == 0 )
+		{ /* Don't try to fill the buffer, so this is an EOF. */
+		if ( yyg->yy_c_buf_p - yyg->yytext_ptr - YY_MORE_ADJ == 1 )
+			{
+			/* We matched a single character, the EOB, so
+			 * treat this as a final EOF.
+			 */
+			return EOB_ACT_END_OF_FILE;
+			}
+
+		else
+			{
+			/* We matched some text prior to the EOB, first
+			 * process it.
+			 */
+			return EOB_ACT_LAST_MATCH;
+			}
+		}
+
+	/* Try to read more data. */
+
+	/* First move last chars to start of buffer. */
+	number_to_move = (yy_size_t) (yyg->yy_c_buf_p - yyg->yytext_ptr) - 1;
+
+	for ( i = 0; i < number_to_move; ++i )
+		*(dest++) = *(source++);
+
+	if ( YY_CURRENT_BUFFER_LVALUE->yy_buffer_status == YY_BUFFER_EOF_PENDING )
+		/* don't do the read, it's not guaranteed to return an EOF,
+		 * just force an EOF
+		 */
+		YY_CURRENT_BUFFER_LVALUE->yy_n_chars = yyg->yy_n_chars = 0;
+
+	else
+		{
+			int num_to_read =
+			YY_CURRENT_BUFFER_LVALUE->yy_buf_size - number_to_move - 1;
+
+		while ( num_to_read <= 0 )
+			{ /* Not enough room in the buffer - grow it. */
+
+			/* just a shorter name for the current buffer */
+			YY_BUFFER_STATE b = YY_CURRENT_BUFFER_LVALUE;
+
+			int yy_c_buf_p_offset =
+				(int) (yyg->yy_c_buf_p - b->yy_ch_buf);
+
+			if ( b->yy_is_our_buffer )
+				{
+				int new_size = b->yy_buf_size * 2;
+
+				if ( new_size <= 0 )
+					b->yy_buf_size += b->yy_buf_size / 8;
+				else
+					b->yy_buf_size *= 2;
+
+				b->yy_ch_buf = (char *)
+					/* Include room in for 2 EOB chars. */
+					freesasa_yyrealloc((void *) b->yy_ch_buf,b->yy_buf_size + 2 ,yyscanner );
+				}
+			else
+				/* Can't grow it, we don't own it. */
+				b->yy_ch_buf = NULL;
+
+			if ( ! b->yy_ch_buf )
+				YY_FATAL_ERROR(
+				"fatal error - scanner input buffer overflow" );
+
+			yyg->yy_c_buf_p = &b->yy_ch_buf[yy_c_buf_p_offset];
+
+			num_to_read = YY_CURRENT_BUFFER_LVALUE->yy_buf_size -
+						number_to_move - 1;
+
+			}
+
+		if ( num_to_read > YY_READ_BUF_SIZE )
+			num_to_read = YY_READ_BUF_SIZE;
+
+		/* Read in more data. */
+		YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]),
+			yyg->yy_n_chars, num_to_read );
+
+		YY_CURRENT_BUFFER_LVALUE->yy_n_chars = yyg->yy_n_chars;
+		}
+
+	if ( yyg->yy_n_chars == 0 )
+		{
+		if ( number_to_move == YY_MORE_ADJ )
+			{
+			ret_val = EOB_ACT_END_OF_FILE;
+			freesasa_yyrestart(yyin  ,yyscanner);
+			}
+
+		else
+			{
+			ret_val = EOB_ACT_LAST_MATCH;
+			YY_CURRENT_BUFFER_LVALUE->yy_buffer_status =
+				YY_BUFFER_EOF_PENDING;
+			}
+		}
+
+	else
+		ret_val = EOB_ACT_CONTINUE_SCAN;
+
+	if ((int) (yyg->yy_n_chars + number_to_move) > YY_CURRENT_BUFFER_LVALUE->yy_buf_size) {
+		/* Extend the array by 50%, plus the number we really need. */
+		int new_size = yyg->yy_n_chars + number_to_move + (yyg->yy_n_chars >> 1);
+		YY_CURRENT_BUFFER_LVALUE->yy_ch_buf = (char *) freesasa_yyrealloc((void *) YY_CURRENT_BUFFER_LVALUE->yy_ch_buf,new_size ,yyscanner );
+		if ( ! YY_CURRENT_BUFFER_LVALUE->yy_ch_buf )
+			YY_FATAL_ERROR( "out of dynamic memory in yy_get_next_buffer()" );
+	}
+
+	yyg->yy_n_chars += number_to_move;
+	YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[yyg->yy_n_chars] = YY_END_OF_BUFFER_CHAR;
+	YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[yyg->yy_n_chars + 1] = YY_END_OF_BUFFER_CHAR;
+
+	yyg->yytext_ptr = &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[0];
+
+	return ret_val;
+}
+
+/* yy_get_previous_state - get the state just before the EOB char was reached */
+
+    static yy_state_type yy_get_previous_state (yyscan_t yyscanner)
+{
+	yy_state_type yy_current_state;
+	char *yy_cp;
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+	yy_current_state = yyg->yy_start;
+
+	for ( yy_cp = yyg->yytext_ptr + YY_MORE_ADJ; yy_cp < yyg->yy_c_buf_p; ++yy_cp )
+		{
+		YY_CHAR yy_c = (*yy_cp ? yy_ec[YY_SC_TO_UI(*yy_cp)] : 1);
+		if ( yy_accept[yy_current_state] )
+			{
+			yyg->yy_last_accepting_state = yy_current_state;
+			yyg->yy_last_accepting_cpos = yy_cp;
+			}
+		while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state )
+			{
+			yy_current_state = (int) yy_def[yy_current_state];
+			if ( yy_current_state >= 52 )
+				yy_c = yy_meta[(unsigned int) yy_c];
+			}
+		yy_current_state = yy_nxt[yy_base[yy_current_state] + (flex_int16_t) yy_c];
+		}
+
+	return yy_current_state;
+}
+
+/* yy_try_NUL_trans - try to make a transition on the NUL character
+ *
+ * synopsis
+ *	next_state = yy_try_NUL_trans( current_state );
+ */
+    static yy_state_type yy_try_NUL_trans  (yy_state_type yy_current_state , yyscan_t yyscanner)
+{
+	int yy_is_jam;
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner; /* This var may be unused depending upon options. */
+	char *yy_cp = yyg->yy_c_buf_p;
+
+	YY_CHAR yy_c = 1;
+	if ( yy_accept[yy_current_state] )
+		{
+		yyg->yy_last_accepting_state = yy_current_state;
+		yyg->yy_last_accepting_cpos = yy_cp;
+		}
+	while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state )
+		{
+		yy_current_state = (int) yy_def[yy_current_state];
+		if ( yy_current_state >= 52 )
+			yy_c = yy_meta[(unsigned int) yy_c];
+		}
+	yy_current_state = yy_nxt[yy_base[yy_current_state] + (flex_int16_t) yy_c];
+	yy_is_jam = (yy_current_state == 51);
+
+	(void)yyg;
+	return yy_is_jam ? 0 : yy_current_state;
+}
+
+#ifndef YY_NO_UNPUT
+
+    static void yyunput (int c, char * yy_bp , yyscan_t yyscanner)
+{
+	char *yy_cp;
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+    yy_cp = yyg->yy_c_buf_p;
+
+	/* undo effects of setting up yytext */
+	*yy_cp = yyg->yy_hold_char;
+
+	if ( yy_cp < YY_CURRENT_BUFFER_LVALUE->yy_ch_buf + 2 )
+		{ /* need to shift things up to make room */
+		/* +2 for EOB chars. */
+		int number_to_move = yyg->yy_n_chars + 2;
+		char *dest = &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[
+					YY_CURRENT_BUFFER_LVALUE->yy_buf_size + 2];
+		char *source =
+				&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move];
+
+		while ( source > YY_CURRENT_BUFFER_LVALUE->yy_ch_buf )
+			*--dest = *--source;
+
+		yy_cp += (int) (dest - source);
+		yy_bp += (int) (dest - source);
+		YY_CURRENT_BUFFER_LVALUE->yy_n_chars =
+			yyg->yy_n_chars = (int) YY_CURRENT_BUFFER_LVALUE->yy_buf_size;
+
+		if ( yy_cp < YY_CURRENT_BUFFER_LVALUE->yy_ch_buf + 2 )
+			YY_FATAL_ERROR( "flex scanner push-back overflow" );
+		}
+
+	*--yy_cp = (char) c;
+
+	yyg->yytext_ptr = yy_bp;
+	yyg->yy_hold_char = *yy_cp;
+	yyg->yy_c_buf_p = yy_cp;
+}
+
+#endif
+
+#ifndef YY_NO_INPUT
+#ifdef __cplusplus
+    static int yyinput (yyscan_t yyscanner)
+#else
+    static int input  (yyscan_t yyscanner)
+#endif
+
+{
+	int c;
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+	*yyg->yy_c_buf_p = yyg->yy_hold_char;
+
+	if ( *yyg->yy_c_buf_p == YY_END_OF_BUFFER_CHAR )
+		{
+		/* yy_c_buf_p now points to the character we want to return.
+		 * If this occurs *before* the EOB characters, then it's a
+		 * valid NUL; if not, then we've hit the end of the buffer.
+		 */
+		if ( yyg->yy_c_buf_p < &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[yyg->yy_n_chars] )
+			/* This was really a NUL. */
+			*yyg->yy_c_buf_p = '\0';
+
+		else
+			{ /* need more input */
+			int offset = yyg->yy_c_buf_p - yyg->yytext_ptr;
+			++yyg->yy_c_buf_p;
+
+			switch ( yy_get_next_buffer( yyscanner ) )
+				{
+				case EOB_ACT_LAST_MATCH:
+					/* This happens because yy_g_n_b()
+					 * sees that we've accumulated a
+					 * token and flags that we need to
+					 * try matching the token before
+					 * proceeding.  But for input(),
+					 * there's no matching to consider.
+					 * So convert the EOB_ACT_LAST_MATCH
+					 * to EOB_ACT_END_OF_FILE.
+					 */
+
+					/* Reset buffer status. */
+					freesasa_yyrestart(yyin ,yyscanner);
+
+					/*FALLTHROUGH*/
+
+				case EOB_ACT_END_OF_FILE:
+					{
+					if ( freesasa_yywrap(yyscanner ) )
+						return 0;
+
+					if ( ! yyg->yy_did_buffer_switch_on_eof )
+						YY_NEW_FILE;
+#ifdef __cplusplus
+					return yyinput(yyscanner);
+#else
+					return input(yyscanner);
+#endif
+					}
+
+				case EOB_ACT_CONTINUE_SCAN:
+					yyg->yy_c_buf_p = yyg->yytext_ptr + offset;
+					break;
+				}
+			}
+		}
+
+	c = *(unsigned char *) yyg->yy_c_buf_p;	/* cast for 8-bit char's */
+	*yyg->yy_c_buf_p = '\0';	/* preserve yytext */
+	yyg->yy_hold_char = *++yyg->yy_c_buf_p;
+
+	return c;
+}
+#endif	/* ifndef YY_NO_INPUT */
+
+/** Immediately switch to a different input stream.
+ * @param input_file A readable stream.
+ * @param yyscanner The scanner object.
+ * @note This function does not reset the start condition to @c INITIAL .
+ */
+    void freesasa_yyrestart  (FILE * input_file , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+	if ( ! YY_CURRENT_BUFFER ){
+        freesasa_yyensure_buffer_stack (yyscanner);
+		YY_CURRENT_BUFFER_LVALUE =
+            freesasa_yy_create_buffer(yyin,YY_BUF_SIZE ,yyscanner);
+	}
+
+	freesasa_yy_init_buffer(YY_CURRENT_BUFFER,input_file ,yyscanner);
+	freesasa_yy_load_buffer_state(yyscanner );
+}
+
+/** Switch to a different input buffer.
+ * @param new_buffer The new input buffer.
+ * @param yyscanner The scanner object.
+ */
+    void freesasa_yy_switch_to_buffer  (YY_BUFFER_STATE  new_buffer , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+	/* TODO. We should be able to replace this entire function body
+	 * with
+	 *		freesasa_yypop_buffer_state();
+	 *		freesasa_yypush_buffer_state(new_buffer);
+     */
+	freesasa_yyensure_buffer_stack (yyscanner);
+	if ( YY_CURRENT_BUFFER == new_buffer )
+		return;
+
+	if ( YY_CURRENT_BUFFER )
+		{
+		/* Flush out information for old buffer. */
+		*yyg->yy_c_buf_p = yyg->yy_hold_char;
+		YY_CURRENT_BUFFER_LVALUE->yy_buf_pos = yyg->yy_c_buf_p;
+		YY_CURRENT_BUFFER_LVALUE->yy_n_chars = yyg->yy_n_chars;
+		}
+
+	YY_CURRENT_BUFFER_LVALUE = new_buffer;
+	freesasa_yy_load_buffer_state(yyscanner );
+
+	/* We don't actually know whether we did this switch during
+	 * EOF (freesasa_yywrap()) processing, but the only time this flag
+	 * is looked at is after freesasa_yywrap() is called, so it's safe
+	 * to go ahead and always set it.
+	 */
+	yyg->yy_did_buffer_switch_on_eof = 1;
+}
+
+static void freesasa_yy_load_buffer_state  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+	yyg->yy_n_chars = YY_CURRENT_BUFFER_LVALUE->yy_n_chars;
+	yyg->yytext_ptr = yyg->yy_c_buf_p = YY_CURRENT_BUFFER_LVALUE->yy_buf_pos;
+	yyin = YY_CURRENT_BUFFER_LVALUE->yy_input_file;
+	yyg->yy_hold_char = *yyg->yy_c_buf_p;
+}
+
+/** Allocate and initialize an input buffer state.
+ * @param file A readable stream.
+ * @param size The character buffer size in bytes. When in doubt, use @c YY_BUF_SIZE.
+ * @param yyscanner The scanner object.
+ * @return the allocated buffer state.
+ */
+    YY_BUFFER_STATE freesasa_yy_create_buffer  (FILE * file, int  size , yyscan_t yyscanner)
+{
+	YY_BUFFER_STATE b;
+    
+	b = (YY_BUFFER_STATE) freesasa_yyalloc(sizeof( struct yy_buffer_state ) ,yyscanner );
+	if ( ! b )
+		YY_FATAL_ERROR( "out of dynamic memory in freesasa_yy_create_buffer()" );
+
+	b->yy_buf_size = (yy_size_t)size;
+
+	/* yy_ch_buf has to be 2 characters longer than the size given because
+	 * we need to put in 2 end-of-buffer characters.
+	 */
+	b->yy_ch_buf = (char *) freesasa_yyalloc(b->yy_buf_size + 2 ,yyscanner );
+	if ( ! b->yy_ch_buf )
+		YY_FATAL_ERROR( "out of dynamic memory in freesasa_yy_create_buffer()" );
+
+	b->yy_is_our_buffer = 1;
+
+	freesasa_yy_init_buffer(b,file ,yyscanner);
+
+	return b;
+}
+
+/** Destroy the buffer.
+ * @param b a buffer created with freesasa_yy_create_buffer()
+ * @param yyscanner The scanner object.
+ */
+    void freesasa_yy_delete_buffer (YY_BUFFER_STATE  b , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+	if ( ! b )
+		return;
+
+	if ( b == YY_CURRENT_BUFFER ) /* Not sure if we should pop here. */
+		YY_CURRENT_BUFFER_LVALUE = (YY_BUFFER_STATE) 0;
+
+	if ( b->yy_is_our_buffer )
+		freesasa_yyfree((void *) b->yy_ch_buf ,yyscanner );
+
+	freesasa_yyfree((void *) b ,yyscanner );
+}
+
+/* Initializes or reinitializes a buffer.
+ * This function is sometimes called more than once on the same buffer,
+ * such as during a freesasa_yyrestart() or at EOF.
+ */
+    static void freesasa_yy_init_buffer  (YY_BUFFER_STATE  b, FILE * file , yyscan_t yyscanner)
+
+{
+	int oerrno = errno;
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+	freesasa_yy_flush_buffer(b ,yyscanner);
+
+	b->yy_input_file = file;
+	b->yy_fill_buffer = 1;
+
+    /* If b is the current buffer, then freesasa_yy_init_buffer was _probably_
+     * called from freesasa_yyrestart() or through yy_get_next_buffer.
+     * In that case, we don't want to reset the lineno or column.
+     */
+    if (b != YY_CURRENT_BUFFER){
+        b->yy_bs_lineno = 1;
+        b->yy_bs_column = 0;
+    }
+
+        b->yy_is_interactive = 0;
+    
+	errno = oerrno;
+}
+
+/** Discard all buffered characters. On the next scan, YY_INPUT will be called.
+ * @param b the buffer state to be flushed, usually @c YY_CURRENT_BUFFER.
+ * @param yyscanner The scanner object.
+ */
+    void freesasa_yy_flush_buffer (YY_BUFFER_STATE  b , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+	if ( ! b )
+		return;
+
+	b->yy_n_chars = 0;
+
+	/* We always need two end-of-buffer characters.  The first causes
+	 * a transition to the end-of-buffer state.  The second causes
+	 * a jam in that state.
+	 */
+	b->yy_ch_buf[0] = YY_END_OF_BUFFER_CHAR;
+	b->yy_ch_buf[1] = YY_END_OF_BUFFER_CHAR;
+
+	b->yy_buf_pos = &b->yy_ch_buf[0];
+
+	b->yy_at_bol = 1;
+	b->yy_buffer_status = YY_BUFFER_NEW;
+
+	if ( b == YY_CURRENT_BUFFER )
+		freesasa_yy_load_buffer_state(yyscanner );
+}
+
+/** Pushes the new state onto the stack. The new state becomes
+ *  the current state. This function will allocate the stack
+ *  if necessary.
+ *  @param new_buffer The new state.
+ *  @param yyscanner The scanner object.
+ */
+void freesasa_yypush_buffer_state (YY_BUFFER_STATE new_buffer , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+	if (new_buffer == NULL)
+		return;
+
+	freesasa_yyensure_buffer_stack(yyscanner);
+
+	/* This block is copied from freesasa_yy_switch_to_buffer. */
+	if ( YY_CURRENT_BUFFER )
+		{
+		/* Flush out information for old buffer. */
+		*yyg->yy_c_buf_p = yyg->yy_hold_char;
+		YY_CURRENT_BUFFER_LVALUE->yy_buf_pos = yyg->yy_c_buf_p;
+		YY_CURRENT_BUFFER_LVALUE->yy_n_chars = yyg->yy_n_chars;
+		}
+
+	/* Only push if top exists. Otherwise, replace top. */
+	if (YY_CURRENT_BUFFER)
+		yyg->yy_buffer_stack_top++;
+	YY_CURRENT_BUFFER_LVALUE = new_buffer;
+
+	/* copied from freesasa_yy_switch_to_buffer. */
+	freesasa_yy_load_buffer_state(yyscanner );
+	yyg->yy_did_buffer_switch_on_eof = 1;
+}
+
+/** Removes and deletes the top of the stack, if present.
+ *  The next element becomes the new top.
+ *  @param yyscanner The scanner object.
+ */
+void freesasa_yypop_buffer_state (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+	if (!YY_CURRENT_BUFFER)
+		return;
+
+	freesasa_yy_delete_buffer(YY_CURRENT_BUFFER ,yyscanner);
+	YY_CURRENT_BUFFER_LVALUE = NULL;
+	if (yyg->yy_buffer_stack_top > 0)
+		--yyg->yy_buffer_stack_top;
+
+	if (YY_CURRENT_BUFFER) {
+		freesasa_yy_load_buffer_state(yyscanner );
+		yyg->yy_did_buffer_switch_on_eof = 1;
+	}
+}
+
+/* Allocates the stack if it does not exist.
+ *  Guarantees space for at least one push.
+ */
+static void freesasa_yyensure_buffer_stack (yyscan_t yyscanner)
+{
+	int num_to_alloc;
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+	if (!yyg->yy_buffer_stack) {
+
+		/* First allocation is just for 2 elements, since we don't know if this
+		 * scanner will even need a stack. We use 2 instead of 1 to avoid an
+		 * immediate realloc on the next call.
+         */
+      num_to_alloc = 1; /* After all that talk, this was set to 1 anyways... */
+		yyg->yy_buffer_stack = (struct yy_buffer_state**)freesasa_yyalloc
+								(num_to_alloc * sizeof(struct yy_buffer_state*)
+								, yyscanner);
+		if ( ! yyg->yy_buffer_stack )
+			YY_FATAL_ERROR( "out of dynamic memory in freesasa_yyensure_buffer_stack()" );
+								  
+		memset(yyg->yy_buffer_stack, 0, num_to_alloc * sizeof(struct yy_buffer_state*));
+				
+		yyg->yy_buffer_stack_max = num_to_alloc;
+		yyg->yy_buffer_stack_top = 0;
+		return;
+	}
+
+	if (yyg->yy_buffer_stack_top >= (yyg->yy_buffer_stack_max) - 1){
+
+		/* Increase the buffer to prepare for a possible push. */
+		yy_size_t grow_size = 8 /* arbitrary grow size */;
+
+		num_to_alloc = yyg->yy_buffer_stack_max + grow_size;
+		yyg->yy_buffer_stack = (struct yy_buffer_state**)freesasa_yyrealloc
+								(yyg->yy_buffer_stack,
+								num_to_alloc * sizeof(struct yy_buffer_state*)
+								, yyscanner);
+		if ( ! yyg->yy_buffer_stack )
+			YY_FATAL_ERROR( "out of dynamic memory in freesasa_yyensure_buffer_stack()" );
+
+		/* zero only the new slots.*/
+		memset(yyg->yy_buffer_stack + yyg->yy_buffer_stack_max, 0, grow_size * sizeof(struct yy_buffer_state*));
+		yyg->yy_buffer_stack_max = num_to_alloc;
+	}
+}
+
+/** Setup the input buffer state to scan directly from a user-specified character buffer.
+ * @param base the character buffer
+ * @param size the size in bytes of the character buffer
+ * @param yyscanner The scanner object.
+ * @return the newly allocated buffer state object. 
+ */
+YY_BUFFER_STATE freesasa_yy_scan_buffer  (char * base, yy_size_t  size , yyscan_t yyscanner)
+{
+	YY_BUFFER_STATE b;
+    
+	if ( size < 2 ||
+	     base[size-2] != YY_END_OF_BUFFER_CHAR ||
+	     base[size-1] != YY_END_OF_BUFFER_CHAR )
+		/* They forgot to leave room for the EOB's. */
+		return NULL;
+
+	b = (YY_BUFFER_STATE) freesasa_yyalloc(sizeof( struct yy_buffer_state ) ,yyscanner );
+	if ( ! b )
+		YY_FATAL_ERROR( "out of dynamic memory in freesasa_yy_scan_buffer()" );
+
+	b->yy_buf_size = size - 2;	/* "- 2" to take care of EOB's */
+	b->yy_buf_pos = b->yy_ch_buf = base;
+	b->yy_is_our_buffer = 0;
+	b->yy_input_file = NULL;
+	b->yy_n_chars = b->yy_buf_size;
+	b->yy_is_interactive = 0;
+	b->yy_at_bol = 1;
+	b->yy_fill_buffer = 0;
+	b->yy_buffer_status = YY_BUFFER_NEW;
+
+	freesasa_yy_switch_to_buffer(b ,yyscanner );
+
+	return b;
+}
+
+/** Setup the input buffer state to scan a string. The next call to freesasa_yylex() will
+ * scan from a @e copy of @a str.
+ * @param yystr a NUL-terminated string to scan
+ * @param yyscanner The scanner object.
+ * @return the newly allocated buffer state object.
+ * @note If you want to scan bytes that may contain NUL values, then use
+ *       freesasa_yy_scan_bytes() instead.
+ */
+YY_BUFFER_STATE freesasa_yy_scan_string (yyconst char * yystr , yyscan_t yyscanner)
+{
+    
+	return freesasa_yy_scan_bytes(yystr,(int) strlen(yystr) ,yyscanner);
+}
+
+/** Setup the input buffer state to scan the given bytes. The next call to freesasa_yylex() will
+ * scan from a @e copy of @a bytes.
+ * @param yybytes the byte buffer to scan
+ * @param _yybytes_len the number of bytes in the buffer pointed to by @a bytes.
+ * @param yyscanner The scanner object.
+ * @return the newly allocated buffer state object.
+ */
+YY_BUFFER_STATE freesasa_yy_scan_bytes  (yyconst char * yybytes, int  _yybytes_len , yyscan_t yyscanner)
+{
+	YY_BUFFER_STATE b;
+	char *buf;
+	yy_size_t n;
+	yy_size_t i;
+    
+	/* Get memory for full buffer, including space for trailing EOB's. */
+	n = (yy_size_t) _yybytes_len + 2;
+	buf = (char *) freesasa_yyalloc(n ,yyscanner );
+	if ( ! buf )
+		YY_FATAL_ERROR( "out of dynamic memory in freesasa_yy_scan_bytes()" );
+
+	for ( i = 0; i < _yybytes_len; ++i )
+		buf[i] = yybytes[i];
+
+	buf[_yybytes_len] = buf[_yybytes_len+1] = YY_END_OF_BUFFER_CHAR;
+
+	b = freesasa_yy_scan_buffer(buf,n ,yyscanner);
+	if ( ! b )
+		YY_FATAL_ERROR( "bad buffer in freesasa_yy_scan_bytes()" );
+
+	/* It's okay to grow etc. this buffer, and we should throw it
+	 * away when we're done.
+	 */
+	b->yy_is_our_buffer = 1;
+
+	return b;
+}
+
+#ifndef YY_EXIT_FAILURE
+#define YY_EXIT_FAILURE 2
+#endif
+
+static void yynoreturn yy_fatal_error (yyconst char* msg , yyscan_t yyscanner)
+{
+	struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+	(void)yyg;
+	(void) fprintf( stderr, "%s\n", msg );
+	exit( YY_EXIT_FAILURE );
+}
+
+/* Redefine yyless() so it works in section 3 code. */
+
+#undef yyless
+#define yyless(n) \
+	do \
+		{ \
+		/* Undo effects of setting up yytext. */ \
+        int yyless_macro_arg = (n); \
+        YY_LESS_LINENO(yyless_macro_arg);\
+		yytext[yyleng] = yyg->yy_hold_char; \
+		yyg->yy_c_buf_p = yytext + yyless_macro_arg; \
+		yyg->yy_hold_char = *yyg->yy_c_buf_p; \
+		*yyg->yy_c_buf_p = '\0'; \
+		yyleng = yyless_macro_arg; \
+		} \
+	while ( 0 )
+
+/* Accessor  methods (get/set functions) to struct members. */
+
+/** Get the user-defined data for this scanner.
+ * @param yyscanner The scanner object.
+ */
+YY_EXTRA_TYPE freesasa_yyget_extra  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    return yyextra;
+}
+
+/** Get the current line number.
+ * @param yyscanner The scanner object.
+ */
+int freesasa_yyget_lineno  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    
+        if (! YY_CURRENT_BUFFER)
+            return 0;
+    
+    return yylineno;
+}
+
+/** Get the current column number.
+ * @param yyscanner The scanner object.
+ */
+int freesasa_yyget_column  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    
+        if (! YY_CURRENT_BUFFER)
+            return 0;
+    
+    return yycolumn;
+}
+
+/** Get the input stream.
+ * @param yyscanner The scanner object.
+ */
+FILE *freesasa_yyget_in  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    return yyin;
+}
+
+/** Get the output stream.
+ * @param yyscanner The scanner object.
+ */
+FILE *freesasa_yyget_out  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    return yyout;
+}
+
+/** Get the length of the current token.
+ * @param yyscanner The scanner object.
+ */
+int freesasa_yyget_leng  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    return yyleng;
+}
+
+/** Get the current token.
+ * @param yyscanner The scanner object.
+ */
+
+char *freesasa_yyget_text  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    return yytext;
+}
+
+/** Set the user-defined data. This data is never touched by the scanner.
+ * @param user_defined The data to be associated with this scanner.
+ * @param yyscanner The scanner object.
+ */
+void freesasa_yyset_extra (YY_EXTRA_TYPE  user_defined , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    yyextra = user_defined ;
+}
+
+/** Set the current line number.
+ * @param _line_number line number
+ * @param yyscanner The scanner object.
+ */
+void freesasa_yyset_lineno (int  _line_number , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+        /* lineno is only valid if an input buffer exists. */
+        if (! YY_CURRENT_BUFFER )
+           YY_FATAL_ERROR( "freesasa_yyset_lineno called with no buffer" );
+    
+    yylineno = _line_number;
+}
+
+/** Set the current column.
+ * @param _column_no column number
+ * @param yyscanner The scanner object.
+ */
+void freesasa_yyset_column (int  _column_no , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+        /* column is only valid if an input buffer exists. */
+        if (! YY_CURRENT_BUFFER )
+           YY_FATAL_ERROR( "freesasa_yyset_column called with no buffer" );
+    
+    yycolumn = _column_no;
+}
+
+/** Set the input stream. This does not discard the current
+ * input buffer.
+ * @param _in_str A readable stream.
+ * @param yyscanner The scanner object.
+ * @see freesasa_yy_switch_to_buffer
+ */
+void freesasa_yyset_in (FILE *  _in_str , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    yyin = _in_str ;
+}
+
+void freesasa_yyset_out (FILE *  _out_str , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    yyout = _out_str ;
+}
+
+int freesasa_yyget_debug  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    return yy_flex_debug;
+}
+
+void freesasa_yyset_debug (int  _bdebug , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    yy_flex_debug = _bdebug ;
+}
+
+/* Accessor methods for yylval and yylloc */
+
+YYSTYPE * freesasa_yyget_lval  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    return yylval;
+}
+
+void freesasa_yyset_lval (YYSTYPE *  yylval_param , yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    yylval = yylval_param;
+}
+
+/* User-visible API */
+
+/* freesasa_yylex_init is special because it creates the scanner itself, so it is
+ * the ONLY reentrant function that doesn't take the scanner as the last argument.
+ * That's why we explicitly handle the declaration, instead of using our macros.
+ */
+
+int freesasa_yylex_init(yyscan_t* ptr_yy_globals)
+
+{
+    if (ptr_yy_globals == NULL){
+        errno = EINVAL;
+        return 1;
+    }
+
+    *ptr_yy_globals = (yyscan_t) freesasa_yyalloc ( sizeof( struct yyguts_t ), NULL );
+
+    if (*ptr_yy_globals == NULL){
+        errno = ENOMEM;
+        return 1;
+    }
+
+    /* By setting to 0xAA, we expose bugs in yy_init_globals. Leave at 0x00 for releases. */
+    memset(*ptr_yy_globals,0x00,sizeof(struct yyguts_t));
+
+    return yy_init_globals ( *ptr_yy_globals );
+}
+
+/* freesasa_yylex_init_extra has the same functionality as freesasa_yylex_init, but follows the
+ * convention of taking the scanner as the last argument. Note however, that
+ * this is a *pointer* to a scanner, as it will be allocated by this call (and
+ * is the reason, too, why this function also must handle its own declaration).
+ * The user defined value in the first argument will be available to freesasa_yyalloc in
+ * the yyextra field.
+ */
+
+int freesasa_yylex_init_extra(YY_EXTRA_TYPE yy_user_defined,yyscan_t* ptr_yy_globals )
+
+{
+    struct yyguts_t dummy_yyguts;
+
+    freesasa_yyset_extra (yy_user_defined, &dummy_yyguts);
+
+    if (ptr_yy_globals == NULL){
+        errno = EINVAL;
+        return 1;
+    }
+	
+    *ptr_yy_globals = (yyscan_t) freesasa_yyalloc ( sizeof( struct yyguts_t ), &dummy_yyguts );
+	
+    if (*ptr_yy_globals == NULL){
+        errno = ENOMEM;
+        return 1;
+    }
+    
+    /* By setting to 0xAA, we expose bugs in
+    yy_init_globals. Leave at 0x00 for releases. */
+    memset(*ptr_yy_globals,0x00,sizeof(struct yyguts_t));
+    
+    freesasa_yyset_extra (yy_user_defined, *ptr_yy_globals);
+    
+    return yy_init_globals ( *ptr_yy_globals );
+}
+
+static int yy_init_globals (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+    /* Initialization is the same as for the non-reentrant scanner.
+     * This function is called from freesasa_yylex_destroy(), so don't allocate here.
+     */
+
+    yyg->yy_buffer_stack = NULL;
+    yyg->yy_buffer_stack_top = 0;
+    yyg->yy_buffer_stack_max = 0;
+    yyg->yy_c_buf_p = NULL;
+    yyg->yy_init = 0;
+    yyg->yy_start = 0;
+
+    yyg->yy_start_stack_ptr = 0;
+    yyg->yy_start_stack_depth = 0;
+    yyg->yy_start_stack =  NULL;
+
+/* Defined in main.c */
+#ifdef YY_STDINIT
+    yyin = stdin;
+    yyout = stdout;
+#else
+    yyin = NULL;
+    yyout = NULL;
+#endif
+
+    /* For future reference: Set errno on error, since we are called by
+     * freesasa_yylex_init()
+     */
+    return 0;
+}
+
+/* freesasa_yylex_destroy is for both reentrant and non-reentrant scanners. */
+int freesasa_yylex_destroy  (yyscan_t yyscanner)
+{
+    struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+
+    /* Pop the buffer stack, destroying each element. */
+	while(YY_CURRENT_BUFFER){
+		freesasa_yy_delete_buffer(YY_CURRENT_BUFFER ,yyscanner );
+		YY_CURRENT_BUFFER_LVALUE = NULL;
+		freesasa_yypop_buffer_state(yyscanner);
+	}
+
+	/* Destroy the stack itself. */
+	freesasa_yyfree(yyg->yy_buffer_stack ,yyscanner);
+	yyg->yy_buffer_stack = NULL;
+
+    /* Destroy the start condition stack. */
+        freesasa_yyfree(yyg->yy_start_stack ,yyscanner );
+        yyg->yy_start_stack = NULL;
+
+    /* Reset the globals. This is important in a non-reentrant scanner so the next time
+     * freesasa_yylex() is called, initialization will occur. */
+    yy_init_globals( yyscanner);
+
+    /* Destroy the main struct (reentrant only). */
+    freesasa_yyfree ( yyscanner , yyscanner );
+    yyscanner = NULL;
+    return 0;
+}
+
+/*
+ * Internal utility routines.
+ */
+
+#ifndef yytext_ptr
+static void yy_flex_strncpy (char* s1, yyconst char * s2, int n , yyscan_t yyscanner)
+{
+	struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+	(void)yyg;
+
+	int i;
+	for ( i = 0; i < n; ++i )
+		s1[i] = s2[i];
+}
+#endif
+
+#ifdef YY_NEED_STRLEN
+static int yy_flex_strlen (yyconst char * s , yyscan_t yyscanner)
+{
+	int n;
+	for ( n = 0; s[n]; ++n )
+		;
+
+	return n;
+}
+#endif
+
+void *freesasa_yyalloc (yy_size_t  size , yyscan_t yyscanner)
+{
+	struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+	(void)yyg;
+	return malloc(size);
+}
+
+void *freesasa_yyrealloc  (void * ptr, yy_size_t  size , yyscan_t yyscanner)
+{
+	struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+	(void)yyg;
+
+	/* The cast to (char *) in the following accommodates both
+	 * implementations that use char* generic pointers, and those
+	 * that use void* generic pointers.  It works with the latter
+	 * because both ANSI C and C++ allow castless assignment from
+	 * any pointer type to void*, and deal with argument conversions
+	 * as though doing an assignment.
+	 */
+	return realloc(ptr, size);
+}
+
+void freesasa_yyfree (void * ptr , yyscan_t yyscanner)
+{
+	struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
+	(void)yyg;
+	free( (char *) ptr );	/* see freesasa_yyrealloc() for (char *) cast */
+}
+
+#define YYTABLES_NAME "yytables"
+
+#line 55 "lexer.l"

.venv_haddock/include/site/python3.12/freesasa/lexer.h

@@ -0,0 +1,336 @@
+#ifndef freesasa_yyHEADER_H
+#define freesasa_yyHEADER_H 1
+#define freesasa_yyIN_HEADER 1
+
+#line 6 "lexer.h"
+
+#line 8 "lexer.h"
+
+#define  YY_INT_ALIGNED short int
+
+/* A lexical scanner generated by flex */
+
+#define FLEX_SCANNER
+#define YY_FLEX_MAJOR_VERSION 2
+#define YY_FLEX_MINOR_VERSION 6
+#define YY_FLEX_SUBMINOR_VERSION 1
+#if YY_FLEX_SUBMINOR_VERSION > 0
+#define FLEX_BETA
+#endif
+
+/* First, we deal with  platform-specific or compiler-specific issues. */
+
+/* begin standard C headers. */
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdlib.h>
+
+/* end standard C headers. */
+
+/* flex integer type definitions */
+
+#ifndef FLEXINT_H
+#define FLEXINT_H
+
+/* C99 systems have <inttypes.h>. Non-C99 systems may or may not. */
+
+#if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+
+/* C99 says to define __STDC_LIMIT_MACROS before including stdint.h,
+ * if you want the limit (max/min) macros for int types. 
+ */
+#ifndef __STDC_LIMIT_MACROS
+#define __STDC_LIMIT_MACROS 1
+#endif
+
+#include <inttypes.h>
+typedef int8_t flex_int8_t;
+typedef uint8_t flex_uint8_t;
+typedef int16_t flex_int16_t;
+typedef uint16_t flex_uint16_t;
+typedef int32_t flex_int32_t;
+typedef uint32_t flex_uint32_t;
+#else
+typedef signed char flex_int8_t;
+typedef short int flex_int16_t;
+typedef int flex_int32_t;
+typedef unsigned char flex_uint8_t; 
+typedef unsigned short int flex_uint16_t;
+typedef unsigned int flex_uint32_t;
+
+/* Limits of integral types. */
+#ifndef INT8_MIN
+#define INT8_MIN               (-128)
+#endif
+#ifndef INT16_MIN
+#define INT16_MIN              (-32767-1)
+#endif
+#ifndef INT32_MIN
+#define INT32_MIN              (-2147483647-1)
+#endif
+#ifndef INT8_MAX
+#define INT8_MAX               (127)
+#endif
+#ifndef INT16_MAX
+#define INT16_MAX              (32767)
+#endif
+#ifndef INT32_MAX
+#define INT32_MAX              (2147483647)
+#endif
+#ifndef UINT8_MAX
+#define UINT8_MAX              (255U)
+#endif
+#ifndef UINT16_MAX
+#define UINT16_MAX             (65535U)
+#endif
+#ifndef UINT32_MAX
+#define UINT32_MAX             (4294967295U)
+#endif
+
+#endif /* ! C99 */
+
+#endif /* ! FLEXINT_H */
+
+/* TODO: this is always defined, so inline it */
+#define yyconst const
+
+#if defined(__GNUC__) && __GNUC__ >= 3
+#define yynoreturn __attribute__((__noreturn__))
+#else
+#define yynoreturn
+#endif
+
+/* An opaque pointer. */
+#ifndef YY_TYPEDEF_YY_SCANNER_T
+#define YY_TYPEDEF_YY_SCANNER_T
+typedef void* yyscan_t;
+#endif
+
+/* For convenience, these vars (plus the bison vars far below)
+   are macros in the reentrant scanner. */
+#define yyin yyg->yyin_r
+#define yyout yyg->yyout_r
+#define yyextra yyg->yyextra_r
+#define yyleng yyg->yyleng_r
+#define yytext yyg->yytext_r
+#define yylineno (YY_CURRENT_BUFFER_LVALUE->yy_bs_lineno)
+#define yycolumn (YY_CURRENT_BUFFER_LVALUE->yy_bs_column)
+#define yy_flex_debug yyg->yy_flex_debug_r
+
+/* Size of default input buffer. */
+#ifndef YY_BUF_SIZE
+#ifdef __ia64__
+/* On IA-64, the buffer size is 16k, not 8k.
+ * Moreover, YY_BUF_SIZE is 2*YY_READ_BUF_SIZE in the general case.
+ * Ditto for the __ia64__ case accordingly.
+ */
+#define YY_BUF_SIZE 32768
+#else
+#define YY_BUF_SIZE 16384
+#endif /* __ia64__ */
+#endif
+
+#ifndef YY_TYPEDEF_YY_BUFFER_STATE
+#define YY_TYPEDEF_YY_BUFFER_STATE
+typedef struct yy_buffer_state *YY_BUFFER_STATE;
+#endif
+
+#ifndef YY_TYPEDEF_YY_SIZE_T
+#define YY_TYPEDEF_YY_SIZE_T
+typedef size_t yy_size_t;
+#endif
+
+#ifndef YY_STRUCT_YY_BUFFER_STATE
+#define YY_STRUCT_YY_BUFFER_STATE
+struct yy_buffer_state
+	{
+	FILE *yy_input_file;
+
+	char *yy_ch_buf;		/* input buffer */
+	char *yy_buf_pos;		/* current position in input buffer */
+
+	/* Size of input buffer in bytes, not including room for EOB
+	 * characters.
+	 */
+	int yy_buf_size;
+
+	/* Number of characters read into yy_ch_buf, not including EOB
+	 * characters.
+	 */
+	int yy_n_chars;
+
+	/* Whether we "own" the buffer - i.e., we know we created it,
+	 * and can realloc() it to grow it, and should free() it to
+	 * delete it.
+	 */
+	int yy_is_our_buffer;
+
+	/* Whether this is an "interactive" input source; if so, and
+	 * if we're using stdio for input, then we want to use getc()
+	 * instead of fread(), to make sure we stop fetching input after
+	 * each newline.
+	 */
+	int yy_is_interactive;
+
+	/* Whether we're considered to be at the beginning of a line.
+	 * If so, '^' rules will be active on the next match, otherwise
+	 * not.
+	 */
+	int yy_at_bol;
+
+    int yy_bs_lineno; /**< The line count. */
+    int yy_bs_column; /**< The column count. */
+    
+	/* Whether to try to fill the input buffer when we reach the
+	 * end of it.
+	 */
+	int yy_fill_buffer;
+
+	int yy_buffer_status;
+
+	};
+#endif /* !YY_STRUCT_YY_BUFFER_STATE */
+
+void freesasa_yyrestart (FILE *input_file ,yyscan_t yyscanner );
+void freesasa_yy_switch_to_buffer (YY_BUFFER_STATE new_buffer ,yyscan_t yyscanner );
+YY_BUFFER_STATE freesasa_yy_create_buffer (FILE *file,int size ,yyscan_t yyscanner );
+void freesasa_yy_delete_buffer (YY_BUFFER_STATE b ,yyscan_t yyscanner );
+void freesasa_yy_flush_buffer (YY_BUFFER_STATE b ,yyscan_t yyscanner );
+void freesasa_yypush_buffer_state (YY_BUFFER_STATE new_buffer ,yyscan_t yyscanner );
+void freesasa_yypop_buffer_state (yyscan_t yyscanner );
+
+YY_BUFFER_STATE freesasa_yy_scan_buffer (char *base,yy_size_t size ,yyscan_t yyscanner );
+YY_BUFFER_STATE freesasa_yy_scan_string (yyconst char *yy_str ,yyscan_t yyscanner );
+YY_BUFFER_STATE freesasa_yy_scan_bytes (yyconst char *bytes,int len ,yyscan_t yyscanner );
+
+void *freesasa_yyalloc (yy_size_t ,yyscan_t yyscanner );
+void *freesasa_yyrealloc (void *,yy_size_t ,yyscan_t yyscanner );
+void freesasa_yyfree (void * ,yyscan_t yyscanner );
+
+#define freesasa_yywrap(yyscanner) (/*CONSTCOND*/1)
+#define YY_SKIP_YYWRAP
+
+#define yytext_ptr yytext_r
+
+#ifdef YY_HEADER_EXPORT_START_CONDITIONS
+#define INITIAL 0
+
+#endif
+
+#ifndef YY_EXTRA_TYPE
+#define YY_EXTRA_TYPE void *
+#endif
+
+int freesasa_yylex_init (yyscan_t* scanner);
+
+int freesasa_yylex_init_extra (YY_EXTRA_TYPE user_defined,yyscan_t* scanner);
+
+/* Accessor methods to globals.
+   These are made visible to non-reentrant scanners for convenience. */
+
+int freesasa_yylex_destroy (yyscan_t yyscanner );
+
+int freesasa_yyget_debug (yyscan_t yyscanner );
+
+void freesasa_yyset_debug (int debug_flag ,yyscan_t yyscanner );
+
+YY_EXTRA_TYPE freesasa_yyget_extra (yyscan_t yyscanner );
+
+void freesasa_yyset_extra (YY_EXTRA_TYPE user_defined ,yyscan_t yyscanner );
+
+FILE *freesasa_yyget_in (yyscan_t yyscanner );
+
+void freesasa_yyset_in  (FILE * _in_str ,yyscan_t yyscanner );
+
+FILE *freesasa_yyget_out (yyscan_t yyscanner );
+
+void freesasa_yyset_out  (FILE * _out_str ,yyscan_t yyscanner );
+
+			int freesasa_yyget_leng (yyscan_t yyscanner );
+
+char *freesasa_yyget_text (yyscan_t yyscanner );
+
+int freesasa_yyget_lineno (yyscan_t yyscanner );
+
+void freesasa_yyset_lineno (int _line_number ,yyscan_t yyscanner );
+
+int freesasa_yyget_column  (yyscan_t yyscanner );
+
+void freesasa_yyset_column (int _column_no ,yyscan_t yyscanner );
+
+YYSTYPE * freesasa_yyget_lval (yyscan_t yyscanner );
+
+void freesasa_yyset_lval (YYSTYPE * yylval_param ,yyscan_t yyscanner );
+
+/* Macros after this point can all be overridden by user definitions in
+ * section 1.
+ */
+
+#ifndef YY_SKIP_YYWRAP
+#ifdef __cplusplus
+extern "C" int freesasa_yywrap (yyscan_t yyscanner );
+#else
+extern int freesasa_yywrap (yyscan_t yyscanner );
+#endif
+#endif
+
+#ifndef yytext_ptr
+static void yy_flex_strncpy (char *,yyconst char *,int ,yyscan_t yyscanner);
+#endif
+
+#ifdef YY_NEED_STRLEN
+static int yy_flex_strlen (yyconst char * ,yyscan_t yyscanner);
+#endif
+
+#ifndef YY_NO_INPUT
+
+#endif
+
+/* Amount of stuff to slurp up with each read. */
+#ifndef YY_READ_BUF_SIZE
+#ifdef __ia64__
+/* On IA-64, the buffer size is 16k, not 8k */
+#define YY_READ_BUF_SIZE 16384
+#else
+#define YY_READ_BUF_SIZE 8192
+#endif /* __ia64__ */
+#endif
+
+/* Number of entries by which start-condition stack grows. */
+#ifndef YY_START_STACK_INCR
+#define YY_START_STACK_INCR 25
+#endif
+
+/* Default declaration of generated scanner - a define so the user can
+ * easily add parameters.
+ */
+#ifndef YY_DECL
+#define YY_DECL_IS_OURS 1
+
+extern int freesasa_yylex \
+               (YYSTYPE * yylval_param ,yyscan_t yyscanner);
+
+#define YY_DECL int freesasa_yylex \
+               (YYSTYPE * yylval_param , yyscan_t yyscanner)
+#endif /* !YY_DECL */
+
+/* yy_get_previous_state - get the state just before the EOB char was reached */
+
+#undef YY_NEW_FILE
+#undef YY_FLUSH_BUFFER
+#undef yy_set_bol
+#undef yy_new_buffer
+#undef yy_set_interactive
+#undef YY_DO_BEFORE_ACTION
+
+#ifdef YY_DECL_IS_OURS
+#undef YY_DECL_IS_OURS
+#undef YY_DECL
+#endif
+
+#line 55 "lexer.l"
+
+#line 335 "lexer.h"
+#undef freesasa_yyIN_HEADER
+#endif /* freesasa_yyHEADER_H */

.venv_haddock/include/site/python3.12/freesasa/log.c

@@ -0,0 +1,270 @@
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <assert.h>
+#include <errno.h>
+#include <stdlib.h>
+
+#include "classifier.h"
+#include "freesasa_internal.h"
+
+/** to control error messages (used for debugging and testing) */
+static freesasa_verbosity verbosity;
+
+int freesasa_set_verbosity(freesasa_verbosity s)
+{
+    if (s == FREESASA_V_NORMAL ||
+        s == FREESASA_V_NOWARNINGS ||
+        s == FREESASA_V_SILENT ||
+        s == FREESASA_V_DEBUG) {
+        verbosity = s;
+        return FREESASA_SUCCESS;
+    }
+    return FREESASA_WARN;
+}
+
+freesasa_verbosity
+freesasa_get_verbosity(void)
+{
+    return verbosity;
+}
+
+static int
+write_result(FILE *log,
+             freesasa_node *result)
+{
+    const char *name = NULL;
+    freesasa_node *structure = NULL, *chain = NULL;
+    const freesasa_nodearea *area = NULL;
+
+    assert(log);
+    assert(freesasa_node_type(result) == FREESASA_NODE_RESULT);
+
+    name = freesasa_node_name(result);
+    structure = freesasa_node_children(result);
+    assert(structure);
+    area = freesasa_node_area(structure);
+    assert(area);
+
+    fprintf(log, "\nINPUT\n");
+    if (name == NULL)
+        fprintf(log, "source  : unknown\n");
+    else
+        fprintf(log, "source  : %s\n", name);
+    fprintf(log, "chains  : %s\n", freesasa_node_structure_chain_labels(structure));
+    fprintf(log, "model   : %d\n", freesasa_node_structure_model(structure));
+    fprintf(log, "atoms   : %d\n", freesasa_node_structure_n_atoms(structure));
+
+    fprintf(log, "\nRESULTS (A^2)\n");
+    fprintf(log, "Total   : %10.2f\n", area->total);
+    fprintf(log, "Apolar  : %10.2f\n", area->apolar);
+    fprintf(log, "Polar   : %10.2f\n", area->polar);
+    if (area->unknown > 0) {
+        fprintf(log, "Unknown : %10.2f\n", area->unknown);
+    }
+
+    chain = freesasa_node_children(structure);
+    while (chain) {
+        area = freesasa_node_area(chain);
+        assert(area);
+        fprintf(log, "CHAIN %s : %10.2f\n", freesasa_node_name(chain), area->total);
+        chain = freesasa_node_next(chain);
+    }
+
+    fflush(log);
+    if (ferror(log)) {
+        return fail_msg(strerror(errno));
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+static int
+write_selections(FILE *log,
+                 freesasa_node *result)
+{
+    freesasa_node *structure = freesasa_node_children(result);
+    const freesasa_selection **selection;
+
+    while (structure) {
+        selection = freesasa_node_structure_selections(structure);
+        if (selection && *selection) {
+            fprintf(log, "\nSELECTIONS\n");
+            while (*selection) {
+                fprintf(log, "%s : %10.2f\n",
+                        freesasa_selection_name(*selection),
+                        freesasa_selection_area(*selection));
+                ++selection;
+            }
+        }
+        structure = freesasa_node_next(structure);
+    }
+
+    fflush(log);
+    if (ferror(log)) {
+        return fail_msg(strerror(errno));
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+static int
+write_parameters(FILE *log,
+                 const freesasa_parameters *parameters)
+{
+    const freesasa_parameters *p = parameters;
+
+    assert(log);
+
+    if (p == NULL) p = &freesasa_default_parameters;
+
+    fprintf(log, "\nPARAMETERS\n");
+
+    fprintf(log, "algorithm    : %s\n", freesasa_alg_name(p->alg));
+    fprintf(log, "probe-radius : %.3f\n", p->probe_radius);
+#if USE_THREADS
+    fprintf(log, "threads      : %d\n", p->n_threads);
+#endif
+
+    switch (p->alg) {
+    case FREESASA_SHRAKE_RUPLEY:
+        fprintf(log, "testpoints   : %d\n", p->shrake_rupley_n_points);
+        break;
+    case FREESASA_LEE_RICHARDS:
+        fprintf(log, "slices       : %d\n", p->lee_richards_n_slices);
+        break;
+    default:
+        assert(0);
+        break;
+    }
+
+    fflush(log);
+    if (ferror(log)) {
+        return fail_msg(strerror(errno));
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_write_res(FILE *log,
+                       freesasa_node *root)
+{
+    freesasa_node *result, *structure, *chain, *residue;
+    int n_res = freesasa_classify_n_residue_types() + 1, i_res, i;
+    double *residue_area = malloc(sizeof(double) * n_res);
+
+    assert(log);
+    assert(root);
+    assert(freesasa_node_type(root) == FREESASA_NODE_ROOT);
+
+    if (residue_area == NULL) return mem_fail();
+
+    result = freesasa_node_children(root);
+    while (result) {
+        for (i = 0; i < n_res; ++i)
+            residue_area[i] = 0;
+        structure = freesasa_node_children(result);
+        while (structure) {
+            chain = freesasa_node_children(structure);
+            while (chain) {
+                residue = freesasa_node_children(chain);
+                while (residue) {
+                    assert(freesasa_node_type(residue) == FREESASA_NODE_RESIDUE);
+                    i_res = freesasa_classify_residue(freesasa_node_name(residue));
+                    residue_area[i_res] += freesasa_node_area(residue)->total;
+                    residue = freesasa_node_next(residue);
+                }
+                chain = freesasa_node_next(chain);
+            }
+            structure = freesasa_node_next(structure);
+        }
+
+        fprintf(log, "# Residue types in %s\n", freesasa_node_name(result));
+        for (i_res = 0; i_res < n_res; ++i_res) {
+            double sasa = residue_area[i_res];
+            if (i_res < 20 || sasa > 0) {
+                fprintf(log, "RES %s : %10.2f\n",
+                        freesasa_classify_residue_name(i_res),
+                        sasa);
+            }
+        }
+        fprintf(log, "\n");
+
+        result = freesasa_node_next(result);
+    }
+
+    fflush(log);
+    if (ferror(log)) {
+        return fail_msg(strerror(errno));
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_write_seq(FILE *log,
+                       freesasa_node *root)
+{
+    freesasa_node *result, *structure, *chain, *residue;
+
+    assert(log);
+    assert(root);
+    assert(freesasa_node_type(root) == FREESASA_NODE_ROOT);
+
+    result = freesasa_node_children(root);
+
+    while (result) {
+        structure = freesasa_node_children(result);
+        fprintf(log, "# Residues in %s\n", freesasa_node_name(result));
+        while (structure) {
+            chain = freesasa_node_children(structure);
+            while (chain) {
+                residue = freesasa_node_children(chain);
+                while (residue) {
+                    assert(freesasa_node_type(residue) == FREESASA_NODE_RESIDUE);
+                    fprintf(log, "SEQ %s %s %s : %7.2f\n",
+                            freesasa_node_name(chain),
+                            freesasa_node_residue_number(residue),
+                            freesasa_node_name(residue),
+                            freesasa_node_area(residue)->total);
+                    residue = freesasa_node_next(residue);
+                }
+                chain = freesasa_node_next(chain);
+            }
+            structure = freesasa_node_next(structure);
+        }
+        fprintf(log, "\n");
+        result = freesasa_node_next(result);
+    }
+
+    fflush(log);
+    if (ferror(log)) {
+        return fail_msg(strerror(errno));
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_write_log(FILE *log,
+                       freesasa_node *root)
+{
+    freesasa_node *result = freesasa_node_children(root);
+    int several = (freesasa_node_next(result) != NULL); /* are there more than one result */
+    int err = 0;
+
+    assert(log);
+    assert(freesasa_node_type(root) == FREESASA_NODE_ROOT);
+
+    if (write_parameters(log, freesasa_node_result_parameters(result)) == FREESASA_FAIL)
+        ++err;
+
+    while (result) {
+        if (several) fprintf(log, "\n\n####################\n");
+        if (write_result(log, result) == FREESASA_FAIL) ++err;
+        if (write_selections(log, result) == FREESASA_FAIL) ++err;
+        result = freesasa_node_next(result);
+    }
+    if (err) return FREESASA_FAIL;
+
+    return FREESASA_SUCCESS;
+}

.venv_haddock/include/site/python3.12/freesasa/nb.c

@@ -0,0 +1,642 @@
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+#include <assert.h>
+#include <math.h>
+#include <stdlib.h>
+
+#include "freesasa_internal.h"
+#include "nb.h"
+
+#ifndef FREESASA_NB_CHUNK
+#define FREESASA_NB_CHUNK 128
+#endif
+
+typedef struct cell cell;
+struct cell {
+    cell *nb[17]; /** includes self, only forward neighbors */
+    int *atom;    /** indices of the atoms/coordinates in a cell */
+    int n_nb;     /** number of neighbors to cell */
+    int n_atoms;  /** number of atoms in cell */
+};
+
+static cell empty_cell = {{NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL,
+                           NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL},
+                          NULL,
+                          0,
+                          0};
+
+/** cell lists, divide space into boxes */
+typedef struct cell_list {
+    cell *cell;     /** the cells */
+    int n;          /** number of cells */
+    int nx, ny, nz; /** number of cells along each axis */
+    double d;       /** cell size */
+    double x_max, x_min;
+    double y_max, y_min;
+    double z_max, z_min;
+} cell_list;
+
+static struct cell_list empty_cell_list = {NULL, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
+
+/** Finds the bounds of the cell list and writes them to the provided cell list */
+static void
+cell_list_bounds(cell_list *c,
+                 const coord_t *coord)
+{
+    const int n = freesasa_coord_n(coord);
+    int i;
+    double d = c->d;
+    const double *restrict v = freesasa_coord_i(coord, 0);
+    double x = v[0], X = v[0], y = v[1], Y = v[1], z = v[2], Z = v[2];
+
+    for (i = 1; i < n; ++i) {
+        v = freesasa_coord_i(coord, i);
+        x = fmin(v[0], x);
+        X = fmax(v[0], X);
+        y = fmin(v[1], y);
+        Y = fmax(v[1], Y);
+        z = fmin(v[2], z);
+        Z = fmax(v[2], Z);
+    }
+    c->x_min = x - d / 2.;
+    c->x_max = X + d / 2.;
+    c->y_min = y - d / 2.;
+    c->y_max = Y + d / 2.;
+    c->z_min = z - d / 2.;
+    c->z_max = Z + d / 2.;
+    c->nx = (int)ceil((c->x_max - c->x_min) / d);
+    c->ny = (int)ceil((c->y_max - c->y_min) / d);
+    c->nz = (int)ceil((c->z_max - c->z_min) / d);
+    c->n = c->nx * c->ny * c->nz;
+}
+
+static inline int
+cell_index(const cell_list *c,
+           int ix,
+           int iy,
+           int iz)
+{
+    assert(ix >= 0 && ix < c->nx);
+    assert(iy >= 0 && iy < c->ny);
+    return ix + c->nx * (iy + c->ny * iz);
+}
+
+/** Fill the neighbor list for a given cell, only "forward" neighbors considered */
+static void
+fill_nb(cell_list *c,
+        int ix,
+        int iy,
+        int iz)
+{
+    cell *cell = &c->cell[cell_index(c, ix, iy, iz)];
+    int n = 0, i, j, k;
+    int xmin = ix > 0 ? ix - 1 : 0;
+    int xmax = ix < c->nx - 1 ? ix + 1 : ix;
+    int ymin = iy > 0 ? iy - 1 : 0;
+    int ymax = iy < c->ny - 1 ? iy + 1 : iy;
+    int zmin = iz > 0 ? iz - 1 : 0;
+    int zmax = iz < c->nz - 1 ? iz + 1 : iz;
+    for (i = xmin; i <= xmax; ++i) {
+        for (j = ymin; j <= ymax; ++j) {
+            for (k = zmin; k <= zmax; ++k) {
+                /* Scalar product between (i-ix,j-iy,k-iz) and (1,1,1) should
+                   be non-negative. Using only forward neighbors means
+                   there's no double counting when comparing cells */
+                if (i - ix + j - iy + k - iz >= 0) {
+                    cell->nb[n] = &c->cell[cell_index(c, i, j, k)];
+                    ++n;
+                }
+            }
+        }
+    }
+    cell->n_nb = n;
+    assert(n > 0);
+}
+
+/** find neighbors to all cells */
+static void
+get_nb(cell_list *c)
+{
+    int ix, iy, iz;
+
+    for (ix = 0; ix < c->nx; ++ix) {
+        for (iy = 0; iy < c->ny; ++iy) {
+            for (iz = 0; iz < c->nz; ++iz) {
+                fill_nb(c, ix, iy, iz);
+            }
+        }
+    }
+}
+
+/** Get the cell index of a given atom */
+static int
+coord2cell_index(const cell_list *c,
+                 const double *restrict xyz)
+{
+    double d = c->d;
+    int ix = (int)((xyz[0] - c->x_min) / d);
+    int iy = (int)((xyz[1] - c->y_min) / d);
+    int iz = (int)((xyz[2] - c->z_min) / d);
+
+    return cell_index(c, ix, iy, iz);
+}
+
+/**
+   Assigns cells to each coordinate. Returns FREESASA_FAIL if realloc
+   fails, FREESASA_SUCCESS else.
+ */
+static int
+fill_cells(cell_list *c,
+           const coord_t *coord)
+{
+    int i;
+    cell *cell;
+    int *a;
+    const double *restrict v;
+
+    for (i = 0; i < c->n; ++i) {
+        c->cell[i].n_atoms = 0;
+    }
+
+    for (i = 0; i < freesasa_coord_n(coord); ++i) {
+        v = freesasa_coord_i(coord, i);
+        cell = &c->cell[coord2cell_index(c, v)];
+        ++cell->n_atoms;
+        a = cell->atom;
+        cell->atom = realloc(cell->atom, sizeof(int) * cell->n_atoms);
+        if (!cell->atom) {
+            cell->atom = a;
+            return mem_fail();
+        }
+        cell->atom[cell->n_atoms - 1] = i;
+    }
+    return FREESASA_SUCCESS;
+}
+
+/** Frees an object created by cell_list_new(). */
+static void
+cell_list_free(cell_list *c)
+{
+    int i;
+
+    if (c) {
+        if (c->cell) {
+            for (i = 0; i < c->n; ++i)
+                free(c->cell[i].atom);
+        }
+        free(c->cell);
+        free(c);
+    }
+}
+
+/**
+    Creates a cell list with provided cell-size assigning cells to
+    each of the provided coordinates. The created cell list should be
+    freed using cell_list_free().
+
+    Returns NULL if there are malloc fails.
+ */
+static cell_list *
+cell_list_new(double cell_size,
+              const coord_t *coord)
+{
+    int i;
+    cell_list *c;
+
+    assert(cell_size > 0);
+    assert(coord);
+
+    c = malloc(sizeof(cell_list));
+    if (!c) {
+        mem_fail();
+        return NULL;
+    }
+
+    *c = empty_cell_list;
+
+    c->d = cell_size;
+    cell_list_bounds(c, coord);
+
+    c->cell = malloc(sizeof(cell) * c->n);
+    if (!c->cell) {
+        cell_list_free(c);
+        mem_fail();
+        return NULL;
+    }
+
+    for (i = 0; i < c->n; ++i)
+        c->cell[i] = empty_cell;
+
+    if (fill_cells(c, coord)) {
+        cell_list_free(c);
+        mem_fail();
+        return NULL;
+    }
+
+    get_nb(c);
+    return c;
+}
+
+/** assumes max value in a is positive */
+static double
+max_array(const double *a,
+          int n)
+{
+    int i;
+    double max = 0;
+
+    for (i = 0; i < n; ++i) {
+        max = fmax(a[i], max);
+    }
+
+    return max;
+}
+
+/**
+    Allocate memory for ::nb_list object. Tries to free everything
+    and returns NULL if malloc somewhere along the way.
+ */
+static nb_list *
+freesasa_nb_alloc(int n)
+{
+    int i;
+    nb_list *nb;
+
+    assert(n > 0);
+
+    nb = malloc(sizeof(nb_list));
+    if (!nb) {
+        mem_fail();
+        return NULL;
+    }
+
+    nb->n = n;
+
+    /* in case the mallocs break, we can clean up in a safer way */
+    nb->nn = NULL;
+    nb->nb = NULL;
+    nb->capacity = NULL;
+    nb->xyd = nb->xd = nb->yd = NULL;
+
+    nb->nn = malloc(sizeof(int) * n);
+    nb->nb = malloc(sizeof(int *) * n);
+    nb->xyd = malloc(sizeof(double *) * n);
+    nb->xd = malloc(sizeof(double *) * n);
+    nb->yd = malloc(sizeof(double *) * n);
+    nb->capacity = malloc(sizeof(int) * n);
+
+    if (!nb->nn || !nb->nb || !nb->xyd ||
+        !nb->xd || !nb->yd || !nb->capacity) {
+        free(nb->nn);
+        free(nb->nb);
+        free(nb->xyd);
+        free(nb->xd);
+        free(nb->yd);
+        free(nb->capacity);
+        free(nb);
+        mem_fail();
+        return NULL;
+    }
+
+    for (i = 0; i < n; ++i) {
+        nb->nn[i] = 0;
+        nb->capacity[i] = FREESASA_NB_CHUNK;
+        /* again prepare for a potential cleanup */
+        nb->nb[i] = NULL;
+        nb->xyd[i] = nb->xd[i] = nb->yd[i] = NULL;
+    }
+    for (i = 0; i < n; ++i) {
+        nb->nb[i] = malloc(sizeof(int) * FREESASA_NB_CHUNK);
+        nb->xyd[i] = malloc(sizeof(double) * FREESASA_NB_CHUNK);
+        nb->xd[i] = malloc(sizeof(double) * FREESASA_NB_CHUNK);
+        nb->yd[i] = malloc(sizeof(double) * FREESASA_NB_CHUNK);
+        if (!nb->nb[i] || !nb->xyd[i] || !nb->xd[i] || !nb->yd[i]) {
+            freesasa_nb_free(nb);
+            mem_fail();
+            return NULL;
+        }
+    }
+    return nb;
+}
+
+void freesasa_nb_free(nb_list *nb)
+{
+    int n, i;
+
+    if (nb != NULL) {
+        n = nb->n;
+        if (nb->nb)
+            for (i = 0; i < n; ++i)
+                free(nb->nb[i]);
+        if (nb->xyd)
+            for (i = 0; i < n; ++i)
+                free(nb->xyd[i]);
+        if (nb->xd)
+            for (i = 0; i < n; ++i)
+                free(nb->xd[i]);
+        if (nb->yd)
+            for (i = 0; i < n; ++i)
+                free(nb->yd[i]);
+        free(nb->nb);
+        free(nb->nn);
+        free(nb->capacity);
+        free(nb->xyd);
+        free(nb->xd);
+        free(nb->yd);
+        free(nb);
+    }
+}
+
+/**
+    Increases sizes of arrays when they cross a threshold. Returns
+    FREESASA_FAIL if realloc fails, FREESASA_SUCCESS else
+ */
+static int
+chunk_up(nb_list *nb_list,
+         int i)
+{
+    int nni = nb_list->nn[i];
+    int **nbi, *nbi_b, new_cap;
+    double **xydi, **xdi, **ydi, *xydi_b, *xdi_b, *ydi_b;
+
+    if (nni > nb_list->capacity[i]) {
+        nbi = &nb_list->nb[i];
+        nbi_b = *nbi;
+        xydi = &nb_list->xyd[i];
+        xdi = &nb_list->xd[i];
+        ydi = &nb_list->yd[i];
+        xydi_b = *xydi;
+        xdi_b = *xdi;
+        ydi_b = *ydi;
+        new_cap = (nb_list->capacity[i] += FREESASA_NB_CHUNK);
+
+        *nbi = realloc(*nbi, sizeof(int) * new_cap);
+        if (*nbi == NULL) {
+            nb_list->nb[i] = nbi_b;
+            return mem_fail();
+        }
+
+        *xydi = realloc(*xydi, sizeof(double) * new_cap);
+        if (*xydi == NULL) {
+            nb_list->xyd[i] = xydi_b;
+            return mem_fail();
+        }
+
+        *xdi = realloc(*xdi, sizeof(double) * new_cap);
+        if (*xdi == NULL) {
+            nb_list->xd[i] = xdi_b;
+            return mem_fail();
+        }
+
+        *ydi = realloc(*ydi, sizeof(double) * new_cap);
+        if (*ydi == NULL) {
+            nb_list->yd[i] = ydi_b;
+            return mem_fail();
+        }
+    }
+    return FREESASA_SUCCESS;
+}
+
+/**
+    Assumes the coordinates i and j have been determined to be
+    neighbors and adds them both to the provided nb lists,
+    symmetrically.
+
+    Returns FREESASA_FAIL if can't allocate memory. FREESASA_SUCCESS
+    else.
+*/
+static int
+nb_add_pair(nb_list *nb_list,
+            int i,
+            int j,
+            double dx,
+            double dy)
+{
+    int **nb;
+    int *nn = nb_list->nn;
+    int nni, nnj;
+    double **xyd;
+    double **xd;
+    double **yd;
+    double d;
+
+    assert(i != j);
+
+    nni = nn[i]++;
+    nnj = nn[j]++;
+
+    if (chunk_up(nb_list, i)) return mem_fail();
+    if (chunk_up(nb_list, j)) return mem_fail();
+
+    nb = nb_list->nb;
+    xyd = nb_list->xyd;
+    xd = nb_list->xd;
+    yd = nb_list->yd;
+
+    nb[i][nni] = j;
+    nb[j][nnj] = i;
+
+    d = sqrt(dx * dx + dy * dy);
+
+    xyd[i][nni] = d;
+    xyd[j][nnj] = d;
+
+    xd[i][nni] = dx;
+    xd[j][nnj] = -dx;
+    yd[i][nni] = dy;
+    yd[j][nnj] = -dy;
+
+    return FREESASA_SUCCESS;
+}
+
+/**
+    Fills the nb list for all contacts between coordinates
+    belonging to the cells ci and cj. Handles the case ci == cj
+    correctly.
+*/
+static int
+nb_calc_cell_pair(nb_list *nb_list,
+                  const coord_t *coord,
+                  const double *radii,
+                  const cell *ci,
+                  const cell *cj)
+{
+    const double *restrict v = freesasa_coord_all(coord);
+    double ri, rj, xi, yi, zi, xj, yj, zj,
+        dx, dy, dz, cut2;
+    int i, j, ia, ja;
+
+    for (i = 0; i < ci->n_atoms; ++i) {
+        ia = ci->atom[i];
+        ri = radii[ia];
+        xi = v[ia * 3];
+        yi = v[ia * 3 + 1];
+        zi = v[ia * 3 + 2];
+        if (ci == cj)
+            j = i + 1;
+        else
+            j = 0;
+        /** the following loop is performance critical */
+        for (; j < cj->n_atoms; ++j) {
+            ja = cj->atom[j];
+            rj = radii[ja];
+            xj = v[ja * 3];
+            yj = v[ja * 3 + 1];
+            zj = v[ja * 3 + 2];
+            cut2 = (ri + rj) * (ri + rj);
+            dx = xj - xi;
+            dy = yj - yi;
+            dz = zj - zi;
+            if (dx * dx + dy * dy + dz * dz < cut2) {
+                if (nb_add_pair(nb_list, ia, ja, dx, dy))
+                    return mem_fail();
+            }
+        }
+    }
+    return FREESASA_SUCCESS;
+}
+
+/**
+    Iterates through the cells and records all contacts in the
+    provided nb list
+ */
+static int
+nb_fill_list(nb_list *nb_list,
+             cell_list *c,
+             const coord_t *coord,
+             const double *radii)
+{
+    int nc = c->n, ic, jc;
+    cell *ci, *cj;
+
+    for (ic = 0; ic < nc; ++ic) {
+        ci = &c->cell[ic];
+        for (jc = 0; jc < ci->n_nb; ++jc) {
+            cj = ci->nb[jc];
+            if (nb_calc_cell_pair(nb_list, coord, radii, ci, cj))
+                return mem_fail();
+        }
+    }
+    return FREESASA_SUCCESS;
+}
+
+nb_list *
+freesasa_nb_new(const coord_t *coord,
+                const double *radii)
+{
+    double cell_size;
+    cell_list *c;
+    int n;
+    nb_list *nb;
+
+    if (coord == NULL || radii == NULL) return NULL;
+
+    n = freesasa_coord_n(coord);
+    nb = freesasa_nb_alloc(n);
+
+    if (!nb) {
+        mem_fail();
+        return NULL;
+    }
+
+    cell_size = 2 * max_array(radii, n);
+    assert(cell_size > 0);
+    c = cell_list_new(cell_size, coord);
+    if (c == NULL ||
+        nb_fill_list(nb, c, coord, radii)) {
+        mem_fail();
+        freesasa_nb_free(nb);
+        nb = NULL;
+    }
+
+    /* the cell lists are only a tool to generate the neighbor lists */
+    cell_list_free(c);
+
+    return nb;
+}
+
+int freesasa_nb_contact(const nb_list *nb,
+                        int i,
+                        int j)
+{
+    int k;
+    assert(nb != NULL);
+    assert(i < nb->n && i >= 0);
+    assert(j < nb->n && j >= 0);
+
+    for (k = 0; k < nb->nn[i]; ++k) {
+        if (nb->nb[i][k] == j) return 1;
+    }
+
+    return 0;
+}
+
+#if USE_CHECK
+#include <check.h>
+#include <math.h>
+
+START_TEST(test_cell)
+{
+    int na, i;
+    const int n_atoms = 6;
+    static const double v[] = {0, 0, 0, 1, 1, 1, -1, 1, -1, 2, 0, -2, 2, 2, 0, -5, 5, 5};
+    static const double r[] = {4, 2, 2, 2, 2, 2};
+    double r_max;
+    cell_list *c;
+    coord_t *coord = freesasa_coord_new();
+    cell ci;
+
+    freesasa_coord_append(coord, v, n_atoms);
+    r_max = max_array(r, n_atoms);
+    ck_assert(fabs(r_max - 4) < 1e-10);
+    c = cell_list_new(r_max, coord);
+    ck_assert(c != NULL);
+    ck_assert(c->cell != NULL);
+    ck_assert(fabs(c->d - r_max) < 1e-10);
+
+    /* check bounds */
+    ck_assert(c->x_min < -5);
+    ck_assert(c->x_max > 2);
+    ck_assert(c->y_min < 0);
+    ck_assert(c->y_max > 5);
+    ck_assert(c->z_min < -2);
+    ck_assert(c->z_max > 5);
+
+    /* check number of cells */
+    ck_assert(c->nx * c->d >= 7);
+    ck_assert(c->nx <= ceil(7 / r_max) + 1);
+    ck_assert(c->ny * c->d >= 5);
+    ck_assert(c->ny <= ceil(5 / r_max) + 1);
+    ck_assert(c->nz * c->d >= 7);
+    ck_assert(c->nz <= ceil(7 / r_max) + 1);
+    ck_assert_int_eq(c->n, c->nx * c->ny * c->nz);
+
+    /* check the individual cells */
+    na = 0;
+    ck_assert_int_eq(c->cell[0].n_nb, 8);
+    ck_assert_int_eq(c->cell[c->n - 1].n_nb, 1);
+    for (i = 0; i < c->n; ++i) {
+        ci = c->cell[i];
+        ck_assert(ci.n_atoms >= 0);
+        if (ci.n_atoms > 0) ck_assert(ci.atom != NULL);
+        ck_assert_int_ge(ci.n_nb, 1);
+        ck_assert_int_le(ci.n_nb, 17);
+        na += ci.n_atoms;
+    }
+    ck_assert_int_eq(na, n_atoms);
+    cell_list_free(c);
+    freesasa_coord_free(coord);
+}
+END_TEST
+
+TCase *
+test_nb_static()
+{
+    TCase *tc = tcase_create("nb.c static");
+    tcase_add_test(tc, test_cell);
+
+    return tc;
+}
+
+#endif /* USE_CHECK */

.venv_haddock/include/site/python3.12/freesasa/nb.h

@@ -0,0 +1,67 @@
+#ifndef FREESASA_NB_H
+#define FREESASA_NB_H
+
+#include <stdlib.h>
+
+#include "coord.h"
+
+/**
+   @file
+   @author Simon Mitternacht
+
+   Functions to compute neighbor lists. The function
+   freesasa_nb_contact() is mainly intended for checking consistency,
+   in performance-critical code it is advisible to use the struct (as
+   demonstrated in sasa_lr.c and sasa_sr.c).
+ */
+
+/** Neighbor list */
+typedef struct {
+    int n;         /**< number of elements */
+    int **nb;      /**< neighbors to each element */
+    int *nn;       /**< number of neighbors to each element */
+    double **xyd;  /**< distance between neighbors in xy-plane */
+    double **xd;   /**< signed distance between neighbors along x-axis */
+    double **yd;   /**< signed distance between neighbors along y-axis */
+    int *capacity; /**< keeps track of memory chunks (don't change this) */
+} nb_list;
+
+/**
+    Creates a neigbor list based on a set of coordinates with
+    corresponding sphere radii.
+
+    Implemented using cell lists, giving O(N) performance. Should be
+    freed with freesasa_nb_free(). For efficient calculations
+    using this list the members of the returned struct should be used
+    directly and not freesasa_nb_contact().
+
+    @param coord a set of coordinates
+    @param radii radii for the coordinates
+    @return a neigbor list. Returns NULL if either argument is null or
+      if there were any problems constructing the list (see error
+      messages).
+ */
+nb_list *
+freesasa_nb_new(const coord_t *coord,
+                const double *radii);
+
+/**
+    Frees a neigbor list created by freesasa_nb_new().
+
+    @param nb The neigbor list to free
+ */
+void freesasa_nb_free(nb_list *nb);
+
+/**
+    Checks if two atoms are in contact. Only included for reference.
+
+    @param nb The neigbor list
+    @param i Index of first coordinate
+    @param j Index of second coordinate
+    @return 1 if contact, 0 else.
+ */
+int freesasa_nb_contact(const nb_list *nb,
+                        int i,
+                        int j);
+
+#endif /* FREESASA_NB_H */

.venv_haddock/include/site/python3.12/freesasa/parser.c

@@ -0,0 +1,1639 @@
+/* A Bison parser, made by GNU Bison 3.0.4.  */
+
+/* Bison implementation for Yacc-like parsers in C
+
+   Copyright (C) 1984, 1989-1990, 2000-2015 Free Software Foundation, Inc.
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.  */
+
+/* As a special exception, you may create a larger work that contains
+   part or all of the Bison parser skeleton and distribute that work
+   under terms of your choice, so long as that work isn't itself a
+   parser generator using the skeleton or a modified version thereof
+   as a parser skeleton.  Alternatively, if you modify or redistribute
+   the parser skeleton itself, you may (at your option) remove this
+   special exception, which will cause the skeleton and the resulting
+   Bison output files to be licensed under the GNU General Public
+   License without this special exception.
+
+   This special exception was added by the Free Software Foundation in
+   version 2.2 of Bison.  */
+
+/* C LALR(1) parser skeleton written by Richard Stallman, by
+   simplifying the original so-called "semantic" parser.  */
+
+/* All symbols defined below should begin with yy or YY, to avoid
+   infringing on user name space.  This should be done even for local
+   variables, as they might otherwise be expanded by user macros.
+   There are some unavoidable exceptions within include files to
+   define necessary library symbols; they are noted "INFRINGES ON
+   USER NAME SPACE" below.  */
+
+/* Identify Bison output.  */
+#define YYBISON 1
+
+/* Bison version.  */
+#define YYBISON_VERSION "3.0.4"
+
+/* Skeleton name.  */
+#define YYSKELETON_NAME "yacc.c"
+
+/* Pure parsers.  */
+#define YYPURE 2
+
+/* Push parsers.  */
+#define YYPUSH 0
+
+/* Pull parsers.  */
+#define YYPULL 1
+
+
+/* Substitute the variable and function names.  */
+#define yyparse         freesasa_yyparse
+#define yylex           freesasa_yylex
+#define yyerror         freesasa_yyerror
+#define yydebug         freesasa_yydebug
+#define yynerrs         freesasa_yynerrs
+
+
+/* Copy the first part of user declarations.  */
+#line 1 "parser.y" /* yacc.c:339  */
+
+
+#include "selection.h"
+#include "parser.h"
+#include "lexer.h"
+    extern int freesasa_selection_parse_error(expression *e, yyscan_t scanner, const char *msg);
+    int freesasa_yyerror(expression **expression, yyscan_t scanner, const char *msg) {
+        return freesasa_selection_parse_error(*expression,scanner,msg);
+    }
+
+
+#line 84 "parser.c" /* yacc.c:339  */
+
+# ifndef YY_NULLPTR
+#  if defined __cplusplus && 201103L <= __cplusplus
+#   define YY_NULLPTR nullptr
+#  else
+#   define YY_NULLPTR 0
+#  endif
+# endif
+
+/* Enabling verbose error messages.  */
+#ifdef YYERROR_VERBOSE
+# undef YYERROR_VERBOSE
+# define YYERROR_VERBOSE 1
+#else
+# define YYERROR_VERBOSE 0
+#endif
+
+/* In a future release of Bison, this section will be replaced
+   by #include "parser.h".  */
+#ifndef YY_FREESASA_YY_PARSER_H_INCLUDED
+# define YY_FREESASA_YY_PARSER_H_INCLUDED
+/* Debug traces.  */
+#ifndef YYDEBUG
+# define YYDEBUG 0
+#endif
+#if YYDEBUG
+extern int freesasa_yydebug;
+#endif
+/* "%code requires" blocks.  */
+#line 13 "parser.y" /* yacc.c:355  */
+
+
+#ifndef FREESASA_TYPEDEF_YY_SCANNER_T
+#define FREESASA_TYPEDEF_YY_SCANNER_T
+    typedef void* freesasa_yyscan_t;
+#endif
+
+
+#line 123 "parser.c" /* yacc.c:355  */
+
+/* Token type.  */
+#ifndef YYTOKENTYPE
+# define YYTOKENTYPE
+  enum yytokentype
+  {
+    T_NUMBER = 258,
+    T_ID = 259,
+    T_SELID = 260,
+    T_AND = 261,
+    T_OR = 262,
+    T_NOT = 263,
+    T_RESN = 264,
+    T_RESI = 265,
+    T_SYMBOL = 266,
+    T_NAME = 267,
+    T_CHAIN = 268,
+    T_MINUS = 269,
+    ATOM = 270
+  };
+#endif
+
+/* Value type.  */
+#if ! defined YYSTYPE && ! defined YYSTYPE_IS_DECLARED
+
+union YYSTYPE
+{
+#line 30 "parser.y" /* yacc.c:355  */
+
+    const char *value;
+    expression *expression;
+
+#line 156 "parser.c" /* yacc.c:355  */
+};
+
+typedef union YYSTYPE YYSTYPE;
+# define YYSTYPE_IS_TRIVIAL 1
+# define YYSTYPE_IS_DECLARED 1
+#endif
+
+
+
+int freesasa_yyparse (expression **expression, freesasa_yyscan_t scanner);
+
+#endif /* !YY_FREESASA_YY_PARSER_H_INCLUDED  */
+
+/* Copy the second part of user declarations.  */
+
+#line 172 "parser.c" /* yacc.c:358  */
+
+#ifdef short
+# undef short
+#endif
+
+#ifdef YYTYPE_UINT8
+typedef YYTYPE_UINT8 yytype_uint8;
+#else
+typedef unsigned char yytype_uint8;
+#endif
+
+#ifdef YYTYPE_INT8
+typedef YYTYPE_INT8 yytype_int8;
+#else
+typedef signed char yytype_int8;
+#endif
+
+#ifdef YYTYPE_UINT16
+typedef YYTYPE_UINT16 yytype_uint16;
+#else
+typedef unsigned short int yytype_uint16;
+#endif
+
+#ifdef YYTYPE_INT16
+typedef YYTYPE_INT16 yytype_int16;
+#else
+typedef short int yytype_int16;
+#endif
+
+#ifndef YYSIZE_T
+# ifdef __SIZE_TYPE__
+#  define YYSIZE_T __SIZE_TYPE__
+# elif defined size_t
+#  define YYSIZE_T size_t
+# elif ! defined YYSIZE_T
+#  include <stddef.h> /* INFRINGES ON USER NAME SPACE */
+#  define YYSIZE_T size_t
+# else
+#  define YYSIZE_T unsigned int
+# endif
+#endif
+
+#define YYSIZE_MAXIMUM ((YYSIZE_T) -1)
+
+#ifndef YY_
+# if defined YYENABLE_NLS && YYENABLE_NLS
+#  if ENABLE_NLS
+#   include <libintl.h> /* INFRINGES ON USER NAME SPACE */
+#   define YY_(Msgid) dgettext ("bison-runtime", Msgid)
+#  endif
+# endif
+# ifndef YY_
+#  define YY_(Msgid) Msgid
+# endif
+#endif
+
+#ifndef YY_ATTRIBUTE
+# if (defined __GNUC__                                               \
+      && (2 < __GNUC__ || (__GNUC__ == 2 && 96 <= __GNUC_MINOR__)))  \
+     || defined __SUNPRO_C && 0x5110 <= __SUNPRO_C
+#  define YY_ATTRIBUTE(Spec) __attribute__(Spec)
+# else
+#  define YY_ATTRIBUTE(Spec) /* empty */
+# endif
+#endif
+
+#ifndef YY_ATTRIBUTE_PURE
+# define YY_ATTRIBUTE_PURE   YY_ATTRIBUTE ((__pure__))
+#endif
+
+#ifndef YY_ATTRIBUTE_UNUSED
+# define YY_ATTRIBUTE_UNUSED YY_ATTRIBUTE ((__unused__))
+#endif
+
+#if !defined _Noreturn \
+     && (!defined __STDC_VERSION__ || __STDC_VERSION__ < 201112)
+# if defined _MSC_VER && 1200 <= _MSC_VER
+#  define _Noreturn __declspec (noreturn)
+# else
+#  define _Noreturn YY_ATTRIBUTE ((__noreturn__))
+# endif
+#endif
+
+/* Suppress unused-variable warnings by "using" E.  */
+#if ! defined lint || defined __GNUC__
+# define YYUSE(E) ((void) (E))
+#else
+# define YYUSE(E) /* empty */
+#endif
+
+#if defined __GNUC__ && 407 <= __GNUC__ * 100 + __GNUC_MINOR__
+/* Suppress an incorrect diagnostic about yylval being uninitialized.  */
+# define YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN \
+    _Pragma ("GCC diagnostic push") \
+    _Pragma ("GCC diagnostic ignored \"-Wuninitialized\"")\
+    _Pragma ("GCC diagnostic ignored \"-Wmaybe-uninitialized\"")
+# define YY_IGNORE_MAYBE_UNINITIALIZED_END \
+    _Pragma ("GCC diagnostic pop")
+#else
+# define YY_INITIAL_VALUE(Value) Value
+#endif
+#ifndef YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
+# define YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
+# define YY_IGNORE_MAYBE_UNINITIALIZED_END
+#endif
+#ifndef YY_INITIAL_VALUE
+# define YY_INITIAL_VALUE(Value) /* Nothing. */
+#endif
+
+
+#if ! defined yyoverflow || YYERROR_VERBOSE
+
+/* The parser invokes alloca or malloc; define the necessary symbols.  */
+
+# ifdef YYSTACK_USE_ALLOCA
+#  if YYSTACK_USE_ALLOCA
+#   ifdef __GNUC__
+#    define YYSTACK_ALLOC __builtin_alloca
+#   elif defined __BUILTIN_VA_ARG_INCR
+#    include <alloca.h> /* INFRINGES ON USER NAME SPACE */
+#   elif defined _AIX
+#    define YYSTACK_ALLOC __alloca
+#   elif defined _MSC_VER
+#    include <malloc.h> /* INFRINGES ON USER NAME SPACE */
+#    define alloca _alloca
+#   else
+#    define YYSTACK_ALLOC alloca
+#    if ! defined _ALLOCA_H && ! defined EXIT_SUCCESS
+#     include <stdlib.h> /* INFRINGES ON USER NAME SPACE */
+      /* Use EXIT_SUCCESS as a witness for stdlib.h.  */
+#     ifndef EXIT_SUCCESS
+#      define EXIT_SUCCESS 0
+#     endif
+#    endif
+#   endif
+#  endif
+# endif
+
+# ifdef YYSTACK_ALLOC
+   /* Pacify GCC's 'empty if-body' warning.  */
+#  define YYSTACK_FREE(Ptr) do { /* empty */; } while (0)
+#  ifndef YYSTACK_ALLOC_MAXIMUM
+    /* The OS might guarantee only one guard page at the bottom of the stack,
+       and a page size can be as small as 4096 bytes.  So we cannot safely
+       invoke alloca (N) if N exceeds 4096.  Use a slightly smaller number
+       to allow for a few compiler-allocated temporary stack slots.  */
+#   define YYSTACK_ALLOC_MAXIMUM 4032 /* reasonable circa 2006 */
+#  endif
+# else
+#  define YYSTACK_ALLOC YYMALLOC
+#  define YYSTACK_FREE YYFREE
+#  ifndef YYSTACK_ALLOC_MAXIMUM
+#   define YYSTACK_ALLOC_MAXIMUM YYSIZE_MAXIMUM
+#  endif
+#  if (defined __cplusplus && ! defined EXIT_SUCCESS \
+       && ! ((defined YYMALLOC || defined malloc) \
+             && (defined YYFREE || defined free)))
+#   include <stdlib.h> /* INFRINGES ON USER NAME SPACE */
+#   ifndef EXIT_SUCCESS
+#    define EXIT_SUCCESS 0
+#   endif
+#  endif
+#  ifndef YYMALLOC
+#   define YYMALLOC malloc
+#   if ! defined malloc && ! defined EXIT_SUCCESS
+void *malloc (YYSIZE_T); /* INFRINGES ON USER NAME SPACE */
+#   endif
+#  endif
+#  ifndef YYFREE
+#   define YYFREE free
+#   if ! defined free && ! defined EXIT_SUCCESS
+void free (void *); /* INFRINGES ON USER NAME SPACE */
+#   endif
+#  endif
+# endif
+#endif /* ! defined yyoverflow || YYERROR_VERBOSE */
+
+
+#if (! defined yyoverflow \
+     && (! defined __cplusplus \
+         || (defined YYSTYPE_IS_TRIVIAL && YYSTYPE_IS_TRIVIAL)))
+
+/* A type that is properly aligned for any stack member.  */
+union yyalloc
+{
+  yytype_int16 yyss_alloc;
+  YYSTYPE yyvs_alloc;
+};
+
+/* The size of the maximum gap between one aligned stack and the next.  */
+# define YYSTACK_GAP_MAXIMUM (sizeof (union yyalloc) - 1)
+
+/* The size of an array large to enough to hold all stacks, each with
+   N elements.  */
+# define YYSTACK_BYTES(N) \
+     ((N) * (sizeof (yytype_int16) + sizeof (YYSTYPE)) \
+      + YYSTACK_GAP_MAXIMUM)
+
+# define YYCOPY_NEEDED 1
+
+/* Relocate STACK from its old location to the new one.  The
+   local variables YYSIZE and YYSTACKSIZE give the old and new number of
+   elements in the stack, and YYPTR gives the new location of the
+   stack.  Advance YYPTR to a properly aligned location for the next
+   stack.  */
+# define YYSTACK_RELOCATE(Stack_alloc, Stack)                           \
+    do                                                                  \
+      {                                                                 \
+        YYSIZE_T yynewbytes;                                            \
+        YYCOPY (&yyptr->Stack_alloc, Stack, yysize);                    \
+        Stack = &yyptr->Stack_alloc;                                    \
+        yynewbytes = yystacksize * sizeof (*Stack) + YYSTACK_GAP_MAXIMUM; \
+        yyptr += yynewbytes / sizeof (*yyptr);                          \
+      }                                                                 \
+    while (0)
+
+#endif
+
+#if defined YYCOPY_NEEDED && YYCOPY_NEEDED
+/* Copy COUNT objects from SRC to DST.  The source and destination do
+   not overlap.  */
+# ifndef YYCOPY
+#  if defined __GNUC__ && 1 < __GNUC__
+#   define YYCOPY(Dst, Src, Count) \
+      __builtin_memcpy (Dst, Src, (Count) * sizeof (*(Src)))
+#  else
+#   define YYCOPY(Dst, Src, Count)              \
+      do                                        \
+        {                                       \
+          YYSIZE_T yyi;                         \
+          for (yyi = 0; yyi < (Count); yyi++)   \
+            (Dst)[yyi] = (Src)[yyi];            \
+        }                                       \
+      while (0)
+#  endif
+# endif
+#endif /* !YYCOPY_NEEDED */
+
+/* YYFINAL -- State number of the termination state.  */
+#define YYFINAL  4
+/* YYLAST -- Last index in YYTABLE.  */
+#define YYLAST   45
+
+/* YYNTOKENS -- Number of terminals.  */
+#define YYNTOKENS  21
+/* YYNNTS -- Number of nonterminals.  */
+#define YYNNTS  7
+/* YYNRULES -- Number of rules.  */
+#define YYNRULES  24
+/* YYNSTATES -- Number of states.  */
+#define YYNSTATES  44
+
+/* YYTRANSLATE[YYX] -- Symbol number corresponding to YYX as returned
+   by yylex, with out-of-bounds checking.  */
+#define YYUNDEFTOK  2
+#define YYMAXUTOK   270
+
+#define YYTRANSLATE(YYX)                                                \
+  ((unsigned int) (YYX) <= YYMAXUTOK ? yytranslate[YYX] : YYUNDEFTOK)
+
+/* YYTRANSLATE[TOKEN-NUM] -- Symbol number corresponding to TOKEN-NUM
+   as returned by yylex, without out-of-bounds checking.  */
+static const yytype_uint8 yytranslate[] =
+{
+       0,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+      19,    20,     2,    16,    18,    17,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     2,     2,     2,     2,
+       2,     2,     2,     2,     2,     2,     1,     2,     3,     4,
+       5,     6,     7,     8,     9,    10,    11,    12,    13,    14,
+      15
+};
+
+#if YYDEBUG
+  /* YYRLINE[YYN] -- Source line where rule number YYN was defined.  */
+static const yytype_uint8 yyrline[] =
+{
+       0,    68,    68,    72,    73,    74,    75,    76,    77,    78,
+      79,    80,    84,    85,    89,    90,    91,    92,    93,    97,
+      98,    99,   103,   104,   105
+};
+#endif
+
+#if YYDEBUG || YYERROR_VERBOSE || 0
+/* YYTNAME[SYMBOL-NUM] -- String name of the symbol SYMBOL-NUM.
+   First, the terminals, then, starting at YYNTOKENS, nonterminals.  */
+static const char *const yytname[] =
+{
+  "$end", "error", "$undefined", "T_NUMBER", "T_ID", "T_SELID", "T_AND",
+  "T_OR", "T_NOT", "T_RESN", "T_RESI", "T_SYMBOL", "T_NAME", "T_CHAIN",
+  "T_MINUS", "ATOM", "'+'", "'-'", "','", "'('", "')'", "$accept", "stmt",
+  "expr", "list", "r_range", "c_range", "id", YY_NULLPTR
+};
+#endif
+
+# ifdef YYPRINT
+/* YYTOKNUM[NUM] -- (External) token number corresponding to the
+   (internal) symbol number NUM (which must be that of a token).  */
+static const yytype_uint16 yytoknum[] =
+{
+       0,   256,   257,   258,   259,   260,   261,   262,   263,   264,
+     265,   266,   267,   268,   269,   270,    43,    45,    44,    40,
+      41
+};
+# endif
+
+#define YYPACT_NINF -20
+
+#define yypact_value_is_default(Yystate) \
+  (!!((Yystate) == (-20)))
+
+#define YYTABLE_NINF -1
+
+#define yytable_value_is_error(Yytable_value) \
+  0
+
+  /* YYPACT[STATE-NUM] -- Index in YYTABLE of the portion describing
+     STATE-NUM.  */
+static const yytype_int8 yypact[] =
+{
+      -3,   -12,    14,    26,   -20,    26,     7,     1,     7,     7,
+       7,    26,    10,   -20,   -20,   -20,    19,   -20,    15,     7,
+      16,    12,   -20,   -20,    24,    25,    13,    26,    26,   -20,
+       7,   -20,     1,     7,     7,     7,   -20,   -20,    35,   -20,
+     -20,   -20,   -20,   -20
+};
+
+  /* YYDEFACT[STATE-NUM] -- Default reduction number in state STATE-NUM.
+     Performed when YYTABLE does not specify something else to do.  Zero
+     means the default is an error.  */
+static const yytype_uint8 yydefact[] =
+{
+       0,     0,     0,     0,     1,     0,     0,     0,     0,     0,
+       0,     0,     2,     6,    22,    23,     0,     7,    12,     0,
+       8,    14,     9,    10,    11,    19,     0,     0,     0,    24,
+       0,    17,     0,    18,     0,     0,     3,     4,     5,    13,
+      15,    16,    20,    21
+};
+
+  /* YYPGOTO[NTERM-NUM].  */
+static const yytype_int8 yypgoto[] =
+{
+     -20,   -20,    -4,     0,   -19,     9,    -7
+};
+
+  /* YYDEFGOTO[NTERM-NUM].  */
+static const yytype_int8 yydefgoto[] =
+{
+      -1,     2,    12,    17,    20,    24,    18
+};
+
+  /* YYTABLE[YYPACT[STATE-NUM]] -- What to do in state STATE-NUM.  If
+     positive, shift that token.  If negative, reduce the rule whose
+     number is the opposite.  If YYTABLE_NINF, syntax error.  */
+static const yytype_uint8 yytable[] =
+{
+      21,    13,     1,    25,    14,    15,     3,    26,    22,    23,
+      14,    15,    31,    40,     4,    16,    27,    28,    19,    27,
+      28,    16,    29,    37,    38,    21,    41,    25,    43,    33,
+      39,    30,    32,    36,     5,     6,     7,     8,     9,    10,
+      34,    27,    35,    42,     0,    11
+};
+
+static const yytype_int8 yycheck[] =
+{
+       7,     5,     5,    10,     3,     4,    18,    11,     8,     9,
+       3,     4,    19,    32,     0,    14,     6,     7,    17,     6,
+       7,    14,     3,    27,    28,    32,    33,    34,    35,    17,
+      30,    16,    16,    20,     8,     9,    10,    11,    12,    13,
+      16,     6,    17,    34,    -1,    19
+};
+
+  /* YYSTOS[STATE-NUM] -- The (internal number of the) accessing
+     symbol of state STATE-NUM.  */
+static const yytype_uint8 yystos[] =
+{
+       0,     5,    22,    18,     0,     8,     9,    10,    11,    12,
+      13,    19,    23,    23,     3,     4,    14,    24,    27,    17,
+      25,    27,    24,    24,    26,    27,    23,     6,     7,     3,
+      16,    27,    16,    17,    16,    17,    20,    23,    23,    24,
+      25,    27,    26,    27
+};
+
+  /* YYR1[YYN] -- Symbol number of symbol that rule YYN derives.  */
+static const yytype_uint8 yyr1[] =
+{
+       0,    21,    22,    23,    23,    23,    23,    23,    23,    23,
+      23,    23,    24,    24,    25,    25,    25,    25,    25,    26,
+      26,    26,    27,    27,    27
+};
+
+  /* YYR2[YYN] -- Number of symbols on the right hand side of rule YYN.  */
+static const yytype_uint8 yyr2[] =
+{
+       0,     2,     3,     3,     3,     3,     2,     2,     2,     2,
+       2,     2,     1,     3,     1,     3,     3,     2,     2,     1,
+       3,     3,     1,     1,     2
+};
+
+
+#define yyerrok         (yyerrstatus = 0)
+#define yyclearin       (yychar = YYEMPTY)
+#define YYEMPTY         (-2)
+#define YYEOF           0
+
+#define YYACCEPT        goto yyacceptlab
+#define YYABORT         goto yyabortlab
+#define YYERROR         goto yyerrorlab
+
+
+#define YYRECOVERING()  (!!yyerrstatus)
+
+#define YYBACKUP(Token, Value)                                  \
+do                                                              \
+  if (yychar == YYEMPTY)                                        \
+    {                                                           \
+      yychar = (Token);                                         \
+      yylval = (Value);                                         \
+      YYPOPSTACK (yylen);                                       \
+      yystate = *yyssp;                                         \
+      goto yybackup;                                            \
+    }                                                           \
+  else                                                          \
+    {                                                           \
+      yyerror (expression, scanner, YY_("syntax error: cannot back up")); \
+      YYERROR;                                                  \
+    }                                                           \
+while (0)
+
+/* Error token number */
+#define YYTERROR        1
+#define YYERRCODE       256
+
+
+
+/* Enable debugging if requested.  */
+#if YYDEBUG
+
+# ifndef YYFPRINTF
+#  include <stdio.h> /* INFRINGES ON USER NAME SPACE */
+#  define YYFPRINTF fprintf
+# endif
+
+# define YYDPRINTF(Args)                        \
+do {                                            \
+  if (yydebug)                                  \
+    YYFPRINTF Args;                             \
+} while (0)
+
+/* This macro is provided for backward compatibility. */
+#ifndef YY_LOCATION_PRINT
+# define YY_LOCATION_PRINT(File, Loc) ((void) 0)
+#endif
+
+
+# define YY_SYMBOL_PRINT(Title, Type, Value, Location)                    \
+do {                                                                      \
+  if (yydebug)                                                            \
+    {                                                                     \
+      YYFPRINTF (stderr, "%s ", Title);                                   \
+      yy_symbol_print (stderr,                                            \
+                  Type, Value, expression, scanner); \
+      YYFPRINTF (stderr, "\n");                                           \
+    }                                                                     \
+} while (0)
+
+
+/*----------------------------------------.
+| Print this symbol's value on YYOUTPUT.  |
+`----------------------------------------*/
+
+static void
+yy_symbol_value_print (FILE *yyoutput, int yytype, YYSTYPE const * const yyvaluep, expression **expression, freesasa_yyscan_t scanner)
+{
+  FILE *yyo = yyoutput;
+  YYUSE (yyo);
+  YYUSE (expression);
+  YYUSE (scanner);
+  if (!yyvaluep)
+    return;
+# ifdef YYPRINT
+  if (yytype < YYNTOKENS)
+    YYPRINT (yyoutput, yytoknum[yytype], *yyvaluep);
+# endif
+  YYUSE (yytype);
+}
+
+
+/*--------------------------------.
+| Print this symbol on YYOUTPUT.  |
+`--------------------------------*/
+
+static void
+yy_symbol_print (FILE *yyoutput, int yytype, YYSTYPE const * const yyvaluep, expression **expression, freesasa_yyscan_t scanner)
+{
+  YYFPRINTF (yyoutput, "%s %s (",
+             yytype < YYNTOKENS ? "token" : "nterm", yytname[yytype]);
+
+  yy_symbol_value_print (yyoutput, yytype, yyvaluep, expression, scanner);
+  YYFPRINTF (yyoutput, ")");
+}
+
+/*------------------------------------------------------------------.
+| yy_stack_print -- Print the state stack from its BOTTOM up to its |
+| TOP (included).                                                   |
+`------------------------------------------------------------------*/
+
+static void
+yy_stack_print (yytype_int16 *yybottom, yytype_int16 *yytop)
+{
+  YYFPRINTF (stderr, "Stack now");
+  for (; yybottom <= yytop; yybottom++)
+    {
+      int yybot = *yybottom;
+      YYFPRINTF (stderr, " %d", yybot);
+    }
+  YYFPRINTF (stderr, "\n");
+}
+
+# define YY_STACK_PRINT(Bottom, Top)                            \
+do {                                                            \
+  if (yydebug)                                                  \
+    yy_stack_print ((Bottom), (Top));                           \
+} while (0)
+
+
+/*------------------------------------------------.
+| Report that the YYRULE is going to be reduced.  |
+`------------------------------------------------*/
+
+static void
+yy_reduce_print (yytype_int16 *yyssp, YYSTYPE *yyvsp, int yyrule, expression **expression, freesasa_yyscan_t scanner)
+{
+  unsigned long int yylno = yyrline[yyrule];
+  int yynrhs = yyr2[yyrule];
+  int yyi;
+  YYFPRINTF (stderr, "Reducing stack by rule %d (line %lu):\n",
+             yyrule - 1, yylno);
+  /* The symbols being reduced.  */
+  for (yyi = 0; yyi < yynrhs; yyi++)
+    {
+      YYFPRINTF (stderr, "   $%d = ", yyi + 1);
+      yy_symbol_print (stderr,
+                       yystos[yyssp[yyi + 1 - yynrhs]],
+                       &(yyvsp[(yyi + 1) - (yynrhs)])
+                                              , expression, scanner);
+      YYFPRINTF (stderr, "\n");
+    }
+}
+
+# define YY_REDUCE_PRINT(Rule)          \
+do {                                    \
+  if (yydebug)                          \
+    yy_reduce_print (yyssp, yyvsp, Rule, expression, scanner); \
+} while (0)
+
+/* Nonzero means print parse trace.  It is left uninitialized so that
+   multiple parsers can coexist.  */
+int yydebug;
+#else /* !YYDEBUG */
+# define YYDPRINTF(Args)
+# define YY_SYMBOL_PRINT(Title, Type, Value, Location)
+# define YY_STACK_PRINT(Bottom, Top)
+# define YY_REDUCE_PRINT(Rule)
+#endif /* !YYDEBUG */
+
+
+/* YYINITDEPTH -- initial size of the parser's stacks.  */
+#ifndef YYINITDEPTH
+# define YYINITDEPTH 200
+#endif
+
+/* YYMAXDEPTH -- maximum size the stacks can grow to (effective only
+   if the built-in stack extension method is used).
+
+   Do not make this value too large; the results are undefined if
+   YYSTACK_ALLOC_MAXIMUM < YYSTACK_BYTES (YYMAXDEPTH)
+   evaluated with infinite-precision integer arithmetic.  */
+
+#ifndef YYMAXDEPTH
+# define YYMAXDEPTH 10000
+#endif
+
+
+#if YYERROR_VERBOSE
+
+# ifndef yystrlen
+#  if defined __GLIBC__ && defined _STRING_H
+#   define yystrlen strlen
+#  else
+/* Return the length of YYSTR.  */
+static YYSIZE_T
+yystrlen (const char *yystr)
+{
+  YYSIZE_T yylen;
+  for (yylen = 0; yystr[yylen]; yylen++)
+    continue;
+  return yylen;
+}
+#  endif
+# endif
+
+# ifndef yystpcpy
+#  if defined __GLIBC__ && defined _STRING_H && defined _GNU_SOURCE
+#   define yystpcpy stpcpy
+#  else
+/* Copy YYSRC to YYDEST, returning the address of the terminating '\0' in
+   YYDEST.  */
+static char *
+yystpcpy (char *yydest, const char *yysrc)
+{
+  char *yyd = yydest;
+  const char *yys = yysrc;
+
+  while ((*yyd++ = *yys++) != '\0')
+    continue;
+
+  return yyd - 1;
+}
+#  endif
+# endif
+
+# ifndef yytnamerr
+/* Copy to YYRES the contents of YYSTR after stripping away unnecessary
+   quotes and backslashes, so that it's suitable for yyerror.  The
+   heuristic is that double-quoting is unnecessary unless the string
+   contains an apostrophe, a comma, or backslash (other than
+   backslash-backslash).  YYSTR is taken from yytname.  If YYRES is
+   null, do not copy; instead, return the length of what the result
+   would have been.  */
+static YYSIZE_T
+yytnamerr (char *yyres, const char *yystr)
+{
+  if (*yystr == '"')
+    {
+      YYSIZE_T yyn = 0;
+      char const *yyp = yystr;
+
+      for (;;)
+        switch (*++yyp)
+          {
+          case '\'':
+          case ',':
+            goto do_not_strip_quotes;
+
+          case '\\':
+            if (*++yyp != '\\')
+              goto do_not_strip_quotes;
+            /* Fall through.  */
+          default:
+            if (yyres)
+              yyres[yyn] = *yyp;
+            yyn++;
+            break;
+
+          case '"':
+            if (yyres)
+              yyres[yyn] = '\0';
+            return yyn;
+          }
+    do_not_strip_quotes: ;
+    }
+
+  if (! yyres)
+    return yystrlen (yystr);
+
+  return yystpcpy (yyres, yystr) - yyres;
+}
+# endif
+
+/* Copy into *YYMSG, which is of size *YYMSG_ALLOC, an error message
+   about the unexpected token YYTOKEN for the state stack whose top is
+   YYSSP.
+
+   Return 0 if *YYMSG was successfully written.  Return 1 if *YYMSG is
+   not large enough to hold the message.  In that case, also set
+   *YYMSG_ALLOC to the required number of bytes.  Return 2 if the
+   required number of bytes is too large to store.  */
+static int
+yysyntax_error (YYSIZE_T *yymsg_alloc, char **yymsg,
+                yytype_int16 *yyssp, int yytoken)
+{
+  YYSIZE_T yysize0 = yytnamerr (YY_NULLPTR, yytname[yytoken]);
+  YYSIZE_T yysize = yysize0;
+  enum { YYERROR_VERBOSE_ARGS_MAXIMUM = 5 };
+  /* Internationalized format string. */
+  const char *yyformat = YY_NULLPTR;
+  /* Arguments of yyformat. */
+  char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
+  /* Number of reported tokens (one for the "unexpected", one per
+     "expected"). */
+  int yycount = 0;
+
+  /* There are many possibilities here to consider:
+     - If this state is a consistent state with a default action, then
+       the only way this function was invoked is if the default action
+       is an error action.  In that case, don't check for expected
+       tokens because there are none.
+     - The only way there can be no lookahead present (in yychar) is if
+       this state is a consistent state with a default action.  Thus,
+       detecting the absence of a lookahead is sufficient to determine
+       that there is no unexpected or expected token to report.  In that
+       case, just report a simple "syntax error".
+     - Don't assume there isn't a lookahead just because this state is a
+       consistent state with a default action.  There might have been a
+       previous inconsistent state, consistent state with a non-default
+       action, or user semantic action that manipulated yychar.
+     - Of course, the expected token list depends on states to have
+       correct lookahead information, and it depends on the parser not
+       to perform extra reductions after fetching a lookahead from the
+       scanner and before detecting a syntax error.  Thus, state merging
+       (from LALR or IELR) and default reductions corrupt the expected
+       token list.  However, the list is correct for canonical LR with
+       one exception: it will still contain any token that will not be
+       accepted due to an error action in a later state.
+  */
+  if (yytoken != YYEMPTY)
+    {
+      int yyn = yypact[*yyssp];
+      yyarg[yycount++] = yytname[yytoken];
+      if (!yypact_value_is_default (yyn))
+        {
+          /* Start YYX at -YYN if negative to avoid negative indexes in
+             YYCHECK.  In other words, skip the first -YYN actions for
+             this state because they are default actions.  */
+          int yyxbegin = yyn < 0 ? -yyn : 0;
+          /* Stay within bounds of both yycheck and yytname.  */
+          int yychecklim = YYLAST - yyn + 1;
+          int yyxend = yychecklim < YYNTOKENS ? yychecklim : YYNTOKENS;
+          int yyx;
+
+          for (yyx = yyxbegin; yyx < yyxend; ++yyx)
+            if (yycheck[yyx + yyn] == yyx && yyx != YYTERROR
+                && !yytable_value_is_error (yytable[yyx + yyn]))
+              {
+                if (yycount == YYERROR_VERBOSE_ARGS_MAXIMUM)
+                  {
+                    yycount = 1;
+                    yysize = yysize0;
+                    break;
+                  }
+                yyarg[yycount++] = yytname[yyx];
+                {
+                  YYSIZE_T yysize1 = yysize + yytnamerr (YY_NULLPTR, yytname[yyx]);
+                  if (! (yysize <= yysize1
+                         && yysize1 <= YYSTACK_ALLOC_MAXIMUM))
+                    return 2;
+                  yysize = yysize1;
+                }
+              }
+        }
+    }
+
+  switch (yycount)
+    {
+# define YYCASE_(N, S)                      \
+      case N:                               \
+        yyformat = S;                       \
+      break
+      YYCASE_(0, YY_("syntax error"));
+      YYCASE_(1, YY_("syntax error, unexpected %s"));
+      YYCASE_(2, YY_("syntax error, unexpected %s, expecting %s"));
+      YYCASE_(3, YY_("syntax error, unexpected %s, expecting %s or %s"));
+      YYCASE_(4, YY_("syntax error, unexpected %s, expecting %s or %s or %s"));
+      YYCASE_(5, YY_("syntax error, unexpected %s, expecting %s or %s or %s or %s"));
+# undef YYCASE_
+    }
+
+  {
+    YYSIZE_T yysize1 = yysize + yystrlen (yyformat);
+    if (! (yysize <= yysize1 && yysize1 <= YYSTACK_ALLOC_MAXIMUM))
+      return 2;
+    yysize = yysize1;
+  }
+
+  if (*yymsg_alloc < yysize)
+    {
+      *yymsg_alloc = 2 * yysize;
+      if (! (yysize <= *yymsg_alloc
+             && *yymsg_alloc <= YYSTACK_ALLOC_MAXIMUM))
+        *yymsg_alloc = YYSTACK_ALLOC_MAXIMUM;
+      return 1;
+    }
+
+  /* Avoid sprintf, as that infringes on the user's name space.
+     Don't have undefined behavior even if the translation
+     produced a string with the wrong number of "%s"s.  */
+  {
+    char *yyp = *yymsg;
+    int yyi = 0;
+    while ((*yyp = *yyformat) != '\0')
+      if (*yyp == '%' && yyformat[1] == 's' && yyi < yycount)
+        {
+          yyp += yytnamerr (yyp, yyarg[yyi++]);
+          yyformat += 2;
+        }
+      else
+        {
+          yyp++;
+          yyformat++;
+        }
+  }
+  return 0;
+}
+#endif /* YYERROR_VERBOSE */
+
+/*-----------------------------------------------.
+| Release the memory associated to this symbol.  |
+`-----------------------------------------------*/
+
+static void
+yydestruct (const char *yymsg, int yytype, YYSTYPE *yyvaluep, expression **expression, freesasa_yyscan_t scanner)
+{
+  YYUSE (yyvaluep);
+  YYUSE (expression);
+  YYUSE (scanner);
+  if (!yymsg)
+    yymsg = "Deleting";
+  YY_SYMBOL_PRINT (yymsg, yytype, yyvaluep, yylocationp);
+
+  YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
+  YYUSE (yytype);
+  YY_IGNORE_MAYBE_UNINITIALIZED_END
+}
+
+
+
+
+/*----------.
+| yyparse.  |
+`----------*/
+
+int
+yyparse (expression **expression, freesasa_yyscan_t scanner)
+{
+/* The lookahead symbol.  */
+int yychar;
+
+
+/* The semantic value of the lookahead symbol.  */
+/* Default value used for initialization, for pacifying older GCCs
+   or non-GCC compilers.  */
+YY_INITIAL_VALUE (static YYSTYPE yyval_default;)
+YYSTYPE yylval YY_INITIAL_VALUE (= yyval_default);
+
+    /* Number of syntax errors so far.  */
+    int yynerrs;
+
+    int yystate;
+    /* Number of tokens to shift before error messages enabled.  */
+    int yyerrstatus;
+
+    /* The stacks and their tools:
+       'yyss': related to states.
+       'yyvs': related to semantic values.
+
+       Refer to the stacks through separate pointers, to allow yyoverflow
+       to reallocate them elsewhere.  */
+
+    /* The state stack.  */
+    yytype_int16 yyssa[YYINITDEPTH];
+    yytype_int16 *yyss;
+    yytype_int16 *yyssp;
+
+    /* The semantic value stack.  */
+    YYSTYPE yyvsa[YYINITDEPTH];
+    YYSTYPE *yyvs;
+    YYSTYPE *yyvsp;
+
+    YYSIZE_T yystacksize;
+
+  int yyn;
+  int yyresult;
+  /* Lookahead token as an internal (translated) token number.  */
+  int yytoken = 0;
+  /* The variables used to return semantic value and location from the
+     action routines.  */
+  YYSTYPE yyval;
+
+#if YYERROR_VERBOSE
+  /* Buffer for error messages, and its allocated size.  */
+  char yymsgbuf[128];
+  char *yymsg = yymsgbuf;
+  YYSIZE_T yymsg_alloc = sizeof yymsgbuf;
+#endif
+
+#define YYPOPSTACK(N)   (yyvsp -= (N), yyssp -= (N))
+
+  /* The number of symbols on the RHS of the reduced rule.
+     Keep to zero when no symbol should be popped.  */
+  int yylen = 0;
+
+  yyssp = yyss = yyssa;
+  yyvsp = yyvs = yyvsa;
+  yystacksize = YYINITDEPTH;
+
+  YYDPRINTF ((stderr, "Starting parse\n"));
+
+  yystate = 0;
+  yyerrstatus = 0;
+  yynerrs = 0;
+  yychar = YYEMPTY; /* Cause a token to be read.  */
+  goto yysetstate;
+
+/*------------------------------------------------------------.
+| yynewstate -- Push a new state, which is found in yystate.  |
+`------------------------------------------------------------*/
+ yynewstate:
+  /* In all cases, when you get here, the value and location stacks
+     have just been pushed.  So pushing a state here evens the stacks.  */
+  yyssp++;
+
+ yysetstate:
+  *yyssp = yystate;
+
+  if (yyss + yystacksize - 1 <= yyssp)
+    {
+      /* Get the current used size of the three stacks, in elements.  */
+      YYSIZE_T yysize = yyssp - yyss + 1;
+
+#ifdef yyoverflow
+      {
+        /* Give user a chance to reallocate the stack.  Use copies of
+           these so that the &'s don't force the real ones into
+           memory.  */
+        YYSTYPE *yyvs1 = yyvs;
+        yytype_int16 *yyss1 = yyss;
+
+        /* Each stack pointer address is followed by the size of the
+           data in use in that stack, in bytes.  This used to be a
+           conditional around just the two extra args, but that might
+           be undefined if yyoverflow is a macro.  */
+        yyoverflow (YY_("memory exhausted"),
+                    &yyss1, yysize * sizeof (*yyssp),
+                    &yyvs1, yysize * sizeof (*yyvsp),
+                    &yystacksize);
+
+        yyss = yyss1;
+        yyvs = yyvs1;
+      }
+#else /* no yyoverflow */
+# ifndef YYSTACK_RELOCATE
+      goto yyexhaustedlab;
+# else
+      /* Extend the stack our own way.  */
+      if (YYMAXDEPTH <= yystacksize)
+        goto yyexhaustedlab;
+      yystacksize *= 2;
+      if (YYMAXDEPTH < yystacksize)
+        yystacksize = YYMAXDEPTH;
+
+      {
+        yytype_int16 *yyss1 = yyss;
+        union yyalloc *yyptr =
+          (union yyalloc *) YYSTACK_ALLOC (YYSTACK_BYTES (yystacksize));
+        if (! yyptr)
+          goto yyexhaustedlab;
+        YYSTACK_RELOCATE (yyss_alloc, yyss);
+        YYSTACK_RELOCATE (yyvs_alloc, yyvs);
+#  undef YYSTACK_RELOCATE
+        if (yyss1 != yyssa)
+          YYSTACK_FREE (yyss1);
+      }
+# endif
+#endif /* no yyoverflow */
+
+      yyssp = yyss + yysize - 1;
+      yyvsp = yyvs + yysize - 1;
+
+      YYDPRINTF ((stderr, "Stack size increased to %lu\n",
+                  (unsigned long int) yystacksize));
+
+      if (yyss + yystacksize - 1 <= yyssp)
+        YYABORT;
+    }
+
+  YYDPRINTF ((stderr, "Entering state %d\n", yystate));
+
+  if (yystate == YYFINAL)
+    YYACCEPT;
+
+  goto yybackup;
+
+/*-----------.
+| yybackup.  |
+`-----------*/
+yybackup:
+
+  /* Do appropriate processing given the current state.  Read a
+     lookahead token if we need one and don't already have one.  */
+
+  /* First try to decide what to do without reference to lookahead token.  */
+  yyn = yypact[yystate];
+  if (yypact_value_is_default (yyn))
+    goto yydefault;
+
+  /* Not known => get a lookahead token if don't already have one.  */
+
+  /* YYCHAR is either YYEMPTY or YYEOF or a valid lookahead symbol.  */
+  if (yychar == YYEMPTY)
+    {
+      YYDPRINTF ((stderr, "Reading a token: "));
+      yychar = yylex (&yylval, scanner);
+    }
+
+  if (yychar <= YYEOF)
+    {
+      yychar = yytoken = YYEOF;
+      YYDPRINTF ((stderr, "Now at end of input.\n"));
+    }
+  else
+    {
+      yytoken = YYTRANSLATE (yychar);
+      YY_SYMBOL_PRINT ("Next token is", yytoken, &yylval, &yylloc);
+    }
+
+  /* If the proper action on seeing token YYTOKEN is to reduce or to
+     detect an error, take that action.  */
+  yyn += yytoken;
+  if (yyn < 0 || YYLAST < yyn || yycheck[yyn] != yytoken)
+    goto yydefault;
+  yyn = yytable[yyn];
+  if (yyn <= 0)
+    {
+      if (yytable_value_is_error (yyn))
+        goto yyerrlab;
+      yyn = -yyn;
+      goto yyreduce;
+    }
+
+  /* Count tokens shifted since error; after three, turn off error
+     status.  */
+  if (yyerrstatus)
+    yyerrstatus--;
+
+  /* Shift the lookahead token.  */
+  YY_SYMBOL_PRINT ("Shifting", yytoken, &yylval, &yylloc);
+
+  /* Discard the shifted token.  */
+  yychar = YYEMPTY;
+
+  yystate = yyn;
+  YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
+  *++yyvsp = yylval;
+  YY_IGNORE_MAYBE_UNINITIALIZED_END
+
+  goto yynewstate;
+
+
+/*-----------------------------------------------------------.
+| yydefault -- do the default action for the current state.  |
+`-----------------------------------------------------------*/
+yydefault:
+  yyn = yydefact[yystate];
+  if (yyn == 0)
+    goto yyerrlab;
+  goto yyreduce;
+
+
+/*-----------------------------.
+| yyreduce -- Do a reduction.  |
+`-----------------------------*/
+yyreduce:
+  /* yyn is the number of a rule to reduce with.  */
+  yylen = yyr2[yyn];
+
+  /* If YYLEN is nonzero, implement the default value of the action:
+     '$$ = $1'.
+
+     Otherwise, the following line sets YYVAL to garbage.
+     This behavior is undocumented and Bison
+     users should not rely upon it.  Assigning to YYVAL
+     unconditionally makes the parser a bit smaller, and it avoids a
+     GCC warning that YYVAL may be used uninitialized.  */
+  yyval = yyvsp[1-yylen];
+
+
+  YY_REDUCE_PRINT (yyn);
+  switch (yyn)
+    {
+        case 2:
+#line 68 "parser.y" /* yacc.c:1646  */
+    { *expression = freesasa_selection_create((yyvsp[0].expression), (yyvsp[-2].value)); }
+#line 1277 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 3:
+#line 72 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = (yyvsp[-1].expression); }
+#line 1283 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 4:
+#line 73 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_operation(E_AND, (yyvsp[-2].expression), (yyvsp[0].expression)); }
+#line 1289 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 5:
+#line 74 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_operation(E_OR, (yyvsp[-2].expression), (yyvsp[0].expression)); }
+#line 1295 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 6:
+#line 75 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_operation(E_NOT, NULL, (yyvsp[0].expression)); }
+#line 1301 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 7:
+#line 76 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_selector(E_RESN, (yyvsp[0].expression)); }
+#line 1307 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 8:
+#line 77 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_selector(E_RESI, (yyvsp[0].expression)); }
+#line 1313 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 9:
+#line 78 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_selector(E_SYMBOL, (yyvsp[0].expression)); }
+#line 1319 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 10:
+#line 79 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_selector(E_NAME, (yyvsp[0].expression)); }
+#line 1325 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 11:
+#line 80 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_selector(E_CHAIN, (yyvsp[0].expression)); }
+#line 1331 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 12:
+#line 84 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = (yyvsp[0].expression); }
+#line 1337 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 13:
+#line 85 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_operation(E_PLUS, (yyvsp[-2].expression), (yyvsp[0].expression)); }
+#line 1343 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 14:
+#line 89 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = (yyvsp[0].expression); }
+#line 1349 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 15:
+#line 90 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_operation(E_PLUS, (yyvsp[-2].expression), (yyvsp[0].expression)); }
+#line 1355 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 16:
+#line 91 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_operation(E_RANGE, (yyvsp[-2].expression), (yyvsp[0].expression)); }
+#line 1361 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 17:
+#line 92 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_operation(E_RANGE_OPEN_L, NULL, (yyvsp[0].expression)); }
+#line 1367 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 18:
+#line 93 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_operation(E_RANGE_OPEN_R, (yyvsp[-1].expression), NULL); }
+#line 1373 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 19:
+#line 97 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = (yyvsp[0].expression); }
+#line 1379 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 20:
+#line 98 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_operation(E_PLUS, (yyvsp[-2].expression), (yyvsp[0].expression)); }
+#line 1385 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 21:
+#line 99 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_operation(E_RANGE, (yyvsp[-2].expression), (yyvsp[0].expression)); }
+#line 1391 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 22:
+#line 103 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_atom(E_NUMBER, (yyvsp[0].value)); }
+#line 1397 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 23:
+#line 104 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_atom(E_ID, (yyvsp[0].value)); }
+#line 1403 "parser.c" /* yacc.c:1646  */
+    break;
+
+  case 24:
+#line 105 "parser.y" /* yacc.c:1646  */
+    { (yyval.expression) = freesasa_selection_atom(E_NEGNUM, (yyvsp[0].value)); }
+#line 1409 "parser.c" /* yacc.c:1646  */
+    break;
+
+
+#line 1413 "parser.c" /* yacc.c:1646  */
+      default: break;
+    }
+  /* User semantic actions sometimes alter yychar, and that requires
+     that yytoken be updated with the new translation.  We take the
+     approach of translating immediately before every use of yytoken.
+     One alternative is translating here after every semantic action,
+     but that translation would be missed if the semantic action invokes
+     YYABORT, YYACCEPT, or YYERROR immediately after altering yychar or
+     if it invokes YYBACKUP.  In the case of YYABORT or YYACCEPT, an
+     incorrect destructor might then be invoked immediately.  In the
+     case of YYERROR or YYBACKUP, subsequent parser actions might lead
+     to an incorrect destructor call or verbose syntax error message
+     before the lookahead is translated.  */
+  YY_SYMBOL_PRINT ("-> $$ =", yyr1[yyn], &yyval, &yyloc);
+
+  YYPOPSTACK (yylen);
+  yylen = 0;
+  YY_STACK_PRINT (yyss, yyssp);
+
+  *++yyvsp = yyval;
+
+  /* Now 'shift' the result of the reduction.  Determine what state
+     that goes to, based on the state we popped back to and the rule
+     number reduced by.  */
+
+  yyn = yyr1[yyn];
+
+  yystate = yypgoto[yyn - YYNTOKENS] + *yyssp;
+  if (0 <= yystate && yystate <= YYLAST && yycheck[yystate] == *yyssp)
+    yystate = yytable[yystate];
+  else
+    yystate = yydefgoto[yyn - YYNTOKENS];
+
+  goto yynewstate;
+
+
+/*--------------------------------------.
+| yyerrlab -- here on detecting error.  |
+`--------------------------------------*/
+yyerrlab:
+  /* Make sure we have latest lookahead translation.  See comments at
+     user semantic actions for why this is necessary.  */
+  yytoken = yychar == YYEMPTY ? YYEMPTY : YYTRANSLATE (yychar);
+
+  /* If not already recovering from an error, report this error.  */
+  if (!yyerrstatus)
+    {
+      ++yynerrs;
+#if ! YYERROR_VERBOSE
+      yyerror (expression, scanner, YY_("syntax error"));
+#else
+# define YYSYNTAX_ERROR yysyntax_error (&yymsg_alloc, &yymsg, \
+                                        yyssp, yytoken)
+      {
+        char const *yymsgp = YY_("syntax error");
+        int yysyntax_error_status;
+        yysyntax_error_status = YYSYNTAX_ERROR;
+        if (yysyntax_error_status == 0)
+          yymsgp = yymsg;
+        else if (yysyntax_error_status == 1)
+          {
+            if (yymsg != yymsgbuf)
+              YYSTACK_FREE (yymsg);
+            yymsg = (char *) YYSTACK_ALLOC (yymsg_alloc);
+            if (!yymsg)
+              {
+                yymsg = yymsgbuf;
+                yymsg_alloc = sizeof yymsgbuf;
+                yysyntax_error_status = 2;
+              }
+            else
+              {
+                yysyntax_error_status = YYSYNTAX_ERROR;
+                yymsgp = yymsg;
+              }
+          }
+        yyerror (expression, scanner, yymsgp);
+        if (yysyntax_error_status == 2)
+          goto yyexhaustedlab;
+      }
+# undef YYSYNTAX_ERROR
+#endif
+    }
+
+
+
+  if (yyerrstatus == 3)
+    {
+      /* If just tried and failed to reuse lookahead token after an
+         error, discard it.  */
+
+      if (yychar <= YYEOF)
+        {
+          /* Return failure if at end of input.  */
+          if (yychar == YYEOF)
+            YYABORT;
+        }
+      else
+        {
+          yydestruct ("Error: discarding",
+                      yytoken, &yylval, expression, scanner);
+          yychar = YYEMPTY;
+        }
+    }
+
+  /* Else will try to reuse lookahead token after shifting the error
+     token.  */
+  goto yyerrlab1;
+
+
+/*---------------------------------------------------.
+| yyerrorlab -- error raised explicitly by YYERROR.  |
+`---------------------------------------------------*/
+yyerrorlab:
+
+  /* Pacify compilers like GCC when the user code never invokes
+     YYERROR and the label yyerrorlab therefore never appears in user
+     code.  */
+  if (/*CONSTCOND*/ 0)
+     goto yyerrorlab;
+
+  /* Do not reclaim the symbols of the rule whose action triggered
+     this YYERROR.  */
+  YYPOPSTACK (yylen);
+  yylen = 0;
+  YY_STACK_PRINT (yyss, yyssp);
+  yystate = *yyssp;
+  goto yyerrlab1;
+
+
+/*-------------------------------------------------------------.
+| yyerrlab1 -- common code for both syntax error and YYERROR.  |
+`-------------------------------------------------------------*/
+yyerrlab1:
+  yyerrstatus = 3;      /* Each real token shifted decrements this.  */
+
+  for (;;)
+    {
+      yyn = yypact[yystate];
+      if (!yypact_value_is_default (yyn))
+        {
+          yyn += YYTERROR;
+          if (0 <= yyn && yyn <= YYLAST && yycheck[yyn] == YYTERROR)
+            {
+              yyn = yytable[yyn];
+              if (0 < yyn)
+                break;
+            }
+        }
+
+      /* Pop the current state because it cannot handle the error token.  */
+      if (yyssp == yyss)
+        YYABORT;
+
+
+      yydestruct ("Error: popping",
+                  yystos[yystate], yyvsp, expression, scanner);
+      YYPOPSTACK (1);
+      yystate = *yyssp;
+      YY_STACK_PRINT (yyss, yyssp);
+    }
+
+  YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
+  *++yyvsp = yylval;
+  YY_IGNORE_MAYBE_UNINITIALIZED_END
+
+
+  /* Shift the error token.  */
+  YY_SYMBOL_PRINT ("Shifting", yystos[yyn], yyvsp, yylsp);
+
+  yystate = yyn;
+  goto yynewstate;
+
+
+/*-------------------------------------.
+| yyacceptlab -- YYACCEPT comes here.  |
+`-------------------------------------*/
+yyacceptlab:
+  yyresult = 0;
+  goto yyreturn;
+
+/*-----------------------------------.
+| yyabortlab -- YYABORT comes here.  |
+`-----------------------------------*/
+yyabortlab:
+  yyresult = 1;
+  goto yyreturn;
+
+#if !defined yyoverflow || YYERROR_VERBOSE
+/*-------------------------------------------------.
+| yyexhaustedlab -- memory exhaustion comes here.  |
+`-------------------------------------------------*/
+yyexhaustedlab:
+  yyerror (expression, scanner, YY_("memory exhausted"));
+  yyresult = 2;
+  /* Fall through.  */
+#endif
+
+yyreturn:
+  if (yychar != YYEMPTY)
+    {
+      /* Make sure we have latest lookahead translation.  See comments at
+         user semantic actions for why this is necessary.  */
+      yytoken = YYTRANSLATE (yychar);
+      yydestruct ("Cleanup: discarding lookahead",
+                  yytoken, &yylval, expression, scanner);
+    }
+  /* Do not reclaim the symbols of the rule whose action triggered
+     this YYABORT or YYACCEPT.  */
+  YYPOPSTACK (yylen);
+  YY_STACK_PRINT (yyss, yyssp);
+  while (yyssp != yyss)
+    {
+      yydestruct ("Cleanup: popping",
+                  yystos[*yyssp], yyvsp, expression, scanner);
+      YYPOPSTACK (1);
+    }
+#ifndef yyoverflow
+  if (yyss != yyssa)
+    YYSTACK_FREE (yyss);
+#endif
+#if YYERROR_VERBOSE
+  if (yymsg != yymsgbuf)
+    YYSTACK_FREE (yymsg);
+#endif
+  return yyresult;
+}

.venv_haddock/include/site/python3.12/freesasa/parser.h

@@ -0,0 +1,97 @@
+/* A Bison parser, made by GNU Bison 3.0.4.  */
+
+/* Bison interface for Yacc-like parsers in C
+
+   Copyright (C) 1984, 1989-1990, 2000-2015 Free Software Foundation, Inc.
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.  */
+
+/* As a special exception, you may create a larger work that contains
+   part or all of the Bison parser skeleton and distribute that work
+   under terms of your choice, so long as that work isn't itself a
+   parser generator using the skeleton or a modified version thereof
+   as a parser skeleton.  Alternatively, if you modify or redistribute
+   the parser skeleton itself, you may (at your option) remove this
+   special exception, which will cause the skeleton and the resulting
+   Bison output files to be licensed under the GNU General Public
+   License without this special exception.
+
+   This special exception was added by the Free Software Foundation in
+   version 2.2 of Bison.  */
+
+#ifndef YY_FREESASA_YY_PARSER_H_INCLUDED
+# define YY_FREESASA_YY_PARSER_H_INCLUDED
+/* Debug traces.  */
+#ifndef YYDEBUG
+# define YYDEBUG 0
+#endif
+#if YYDEBUG
+extern int freesasa_yydebug;
+#endif
+/* "%code requires" blocks.  */
+#line 13 "parser.y" /* yacc.c:1909  */
+
+
+#ifndef FREESASA_TYPEDEF_YY_SCANNER_T
+#define FREESASA_TYPEDEF_YY_SCANNER_T
+    typedef void* freesasa_yyscan_t;
+#endif
+
+
+#line 53 "parser.h" /* yacc.c:1909  */
+
+/* Token type.  */
+#ifndef YYTOKENTYPE
+# define YYTOKENTYPE
+  enum yytokentype
+  {
+    T_NUMBER = 258,
+    T_ID = 259,
+    T_SELID = 260,
+    T_AND = 261,
+    T_OR = 262,
+    T_NOT = 263,
+    T_RESN = 264,
+    T_RESI = 265,
+    T_SYMBOL = 266,
+    T_NAME = 267,
+    T_CHAIN = 268,
+    T_MINUS = 269,
+    ATOM = 270
+  };
+#endif
+
+/* Value type.  */
+#if ! defined YYSTYPE && ! defined YYSTYPE_IS_DECLARED
+
+union YYSTYPE
+{
+#line 30 "parser.y" /* yacc.c:1909  */
+
+    const char *value;
+    expression *expression;
+
+#line 86 "parser.h" /* yacc.c:1909  */
+};
+
+typedef union YYSTYPE YYSTYPE;
+# define YYSTYPE_IS_TRIVIAL 1
+# define YYSTYPE_IS_DECLARED 1
+#endif
+
+
+
+int freesasa_yyparse (expression **expression, freesasa_yyscan_t scanner);
+
+#endif /* !YY_FREESASA_YY_PARSER_H_INCLUDED  */

.venv_haddock/include/site/python3.12/freesasa/pdb.c

@@ -0,0 +1,432 @@
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <assert.h>
+#include <errno.h>
+#include <stdlib.h>
+
+#include "freesasa_internal.h"
+#include "pdb.h"
+
+/* len >= 6 */
+static inline int
+pdb_line_check(const char *line, size_t len)
+{
+    assert(line);
+    if (len < 6) return FREESASA_FAIL;
+    if (strlen(line) < len) return FREESASA_FAIL;
+    if (strncmp("ATOM", line, 4) != 0 &&
+        strncmp("HETATM", line, 6) != 0) {
+        return FREESASA_FAIL;
+    }
+    return FREESASA_SUCCESS;
+}
+
+/**
+    Extracts a double from the line of maximum width characters, to
+    allow checking for empty fields (instead of just reading the first
+    float that comes along.
+ */
+static inline int
+pdb_get_double(const char *line, size_t width, double *val)
+{
+    /* allow truncated lines */
+    char buf[PDB_LINE_STRL];
+    float tmp;
+
+    if (strlen(line) < width) width = strlen(line);
+
+    memcpy(buf, line, width);
+    buf[width] = '\0';
+
+    if (sscanf(buf, "%f", &tmp) == 1) {
+        *val = tmp;
+        return FREESASA_SUCCESS;
+    }
+
+    return FREESASA_FAIL;
+}
+
+int freesasa_pdb_get_models(FILE *pdb,
+                            struct file_range **ranges)
+{
+    char line[PDB_MAX_LINE_STRL];
+    int n = 0, n_end = 0, error = 0;
+    long last_pos = ftell(pdb);
+    struct file_range *it = NULL, *itb;
+
+    assert(pdb != NULL);
+
+    while (fgets(line, PDB_MAX_LINE_STRL, pdb) != NULL) {
+        if (strncmp("MODEL", line, 5) == 0) {
+            ++n;
+            itb = it;
+            it = realloc(it, sizeof(struct file_range) * n);
+            if (!it) {
+                free(itb);
+                error = mem_fail();
+                break;
+            }
+            it[n - 1].begin = last_pos;
+        }
+        if (strncmp("ENDMDL", line, 6) == 0) {
+            ++n_end;
+            if (n != n_end) {
+                error = fail_msg("mismatch between MODEL and ENDMDL in input");
+                break;
+            }
+            it[n - 1].end = ftell(pdb);
+        }
+        last_pos = ftell(pdb);
+    }
+    if (n == 0) { /* when there are no models, the whole file is the model */
+        free(it);
+        it = NULL;
+    }
+    if (error == FREESASA_FAIL) {
+        free(it);
+        *ranges = NULL;
+        return FREESASA_FAIL;
+    }
+    *ranges = it;
+    return n;
+}
+
+int freesasa_pdb_get_chains(FILE *pdb,
+                            struct file_range model,
+                            struct file_range **ranges,
+                            int options)
+{
+    /* it is assumed that 'model' is valid for 'pdb' */
+
+    int n_chains = 0;
+    char line[PDB_MAX_LINE_STRL];
+    struct file_range *chains = NULL, *chb;
+    char last_chain = '\0';
+    long last_pos = model.begin;
+
+    assert(pdb);
+    assert(ranges);
+
+    *ranges = NULL;
+
+    /* for each model, find file ranges for each chain, store them
+       in the dynamically growing array chains */
+    fseek(pdb, model.begin, SEEK_SET);
+    while (fgets(line, PDB_MAX_LINE_STRL, pdb) != NULL &&
+           ftell(pdb) < model.end) {
+        if (strncmp("ATOM", line, 4) == 0 || ((options & FREESASA_INCLUDE_HETATM) &&
+                                              (strncmp("HETATM", line, 6) == 0))) {
+            char chain = freesasa_pdb_get_chain_label(line);
+            if (chain != last_chain) {
+                if (n_chains > 0) chains[n_chains - 1].end = last_pos;
+                ++n_chains;
+                chb = chains;
+                chains = realloc(chains, sizeof(struct file_range) * n_chains);
+                if (!chains) {
+                    free(chb);
+                    return mem_fail();
+                }
+                chains[n_chains - 1].begin = last_pos;
+                last_chain = chain;
+            }
+        }
+        last_pos = ftell(pdb);
+    }
+
+    if (n_chains > 0) {
+        chains[n_chains - 1].end = last_pos;
+        chains[0].begin = model.begin; /* preserve model info */
+        *ranges = chains;
+    } else {
+        *ranges = NULL;
+    }
+    return n_chains;
+}
+
+int freesasa_pdb_get_atom_name(char *name,
+                               const char *line)
+{
+    assert(name);
+    assert(line);
+    if (pdb_line_check(line, PDB_ATOM_NAME_STRL + 12) == FREESASA_FAIL) {
+        name[0] = '\0';
+        return FREESASA_FAIL;
+    }
+    strncpy(name, line + 12, PDB_ATOM_NAME_STRL);
+    name[PDB_ATOM_NAME_STRL] = '\0';
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_pdb_get_res_name(char *name,
+                              const char *line)
+{
+    assert(name);
+    assert(line);
+    if (pdb_line_check(line, PDB_ATOM_RES_NAME_STRL + 17) == FREESASA_FAIL) {
+        name[0] = '\0';
+        return FREESASA_FAIL;
+    }
+    strncpy(name, line + 17, PDB_ATOM_RES_NAME_STRL);
+    name[PDB_ATOM_RES_NAME_STRL] = '\0';
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_pdb_get_coord(double *xyz,
+                           const char *line)
+{
+    int n_coord = 24; /* 54-30+1 */
+    char coord_section[25];
+
+    assert(xyz);
+    assert(line);
+
+    if (pdb_line_check(line, 54) == FREESASA_FAIL) {
+        return FREESASA_FAIL;
+    }
+
+    strncpy(coord_section, line + 30, n_coord);
+    coord_section[n_coord] = '\0';
+
+    if (sscanf(coord_section, "%lf%lf%lf", &xyz[0], &xyz[1], &xyz[2]) != 3) {
+        return fail_msg("could not read coordinates from line '%s'", line);
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_pdb_get_res_number(char *number,
+                                const char *line)
+{
+    assert(number);
+    assert(line);
+    if (pdb_line_check(line, PDB_ATOM_RES_NUMBER_STRL + 22) == FREESASA_FAIL) {
+        number[0] = '\0';
+        return FREESASA_FAIL;
+    }
+    strncpy(number, line + 22, PDB_ATOM_RES_NUMBER_STRL);
+    number[PDB_ATOM_RES_NUMBER_STRL] = '\0';
+    return FREESASA_SUCCESS;
+}
+char freesasa_pdb_get_chain_label(const char *line)
+{
+    assert(line);
+    if (pdb_line_check(line, 21) == FREESASA_FAIL) return '\0';
+    return line[21];
+}
+
+char freesasa_pdb_get_alt_coord_label(const char *line)
+{
+    assert(line);
+    if (pdb_line_check(line, 16) == FREESASA_FAIL) return '\0';
+    return line[16];
+}
+
+int freesasa_pdb_get_symbol(char *symbol,
+                            const char *line)
+{
+    assert(line);
+    if (pdb_line_check(line, 76 + PDB_ATOM_SYMBOL_STRL) == FREESASA_FAIL) {
+        symbol[0] = '\0';
+        return FREESASA_FAIL;
+    }
+    strncpy(symbol, line + 76, 2);
+    symbol[2] = '\0';
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_pdb_get_occupancy(double *occ,
+                               const char *line)
+{
+    assert(line);
+    /* allow truncated lines */
+    if (pdb_line_check(line, 55) == FREESASA_SUCCESS)
+        return pdb_get_double(line + 54, 6, occ);
+    return FREESASA_FAIL;
+}
+
+int freesasa_pdb_get_bfactor(double *bfac,
+                             const char *line)
+{
+    assert(line);
+    /* allow truncated lines */
+    if (pdb_line_check(line, 61) == FREESASA_SUCCESS)
+        return pdb_get_double(line + 60, 6, bfac);
+    return FREESASA_FAIL;
+}
+
+int freesasa_pdb_ishydrogen(const char *line)
+{
+    assert(line);
+    char symbol[PDB_ATOM_SYMBOL_STRL + 1];
+    freesasa_pdb_get_symbol(symbol, line);
+
+    if (pdb_line_check(line, 13) == FREESASA_FAIL) return FREESASA_FAIL;
+
+    /* Check symbol first */
+    if (strncmp(symbol, " H", 2) == 0) return 1;
+    if (strncmp(symbol, " D", 2) == 0) return 1;
+    /* If the symbol is not blank and not H or D */
+    if (!(strncmp(symbol, "  ", 2) == 0)) return 0;
+
+    /* When symbol is missing */
+    /* Cover elements such as Cd, Nd, Th, etc. ("CD  ", "ND  ") */
+    if (!(line[12] == ' ' || (line[12] >= '1' && line[12] <= '9'))) return 0;
+    /* Hydrogen, atom name "H**" or " H**" */
+    if (line[12] == 'H' || line[13] == 'H') return 1;
+    /* Deuterium */
+    if (line[12] == 'D' || line[13] == 'D') return 1;
+    return 0;
+}
+
+static int
+write_pdb_impl(FILE *output,
+               freesasa_node *structure)
+{
+    char buf[PDB_LINE_STRL + 1], buf2[6];
+    int model;
+    double radius;
+    const char *line = NULL;
+    freesasa_node *chain = NULL, *residue = NULL, *atom = NULL;
+    const freesasa_nodearea *area = NULL;
+    const char *last_res_name = NULL, *last_res_number = NULL, *last_chain = NULL;
+
+    assert(freesasa_node_type(structure) == FREESASA_NODE_STRUCTURE);
+
+    model = freesasa_node_structure_model(structure);
+    if (model > 0)
+        fprintf(output, "MODEL     %4d\n", model);
+    else
+        fprintf(output, "MODEL        1\n");
+
+    chain = freesasa_node_children(structure);
+
+    /* Write ATOM entries */
+    while (chain) {
+        residue = freesasa_node_children(chain);
+        while (residue) {
+            atom = freesasa_node_children(residue);
+            while (atom) {
+                line = freesasa_node_atom_pdb_line(atom);
+                area = freesasa_node_area(atom);
+                radius = freesasa_node_atom_radius(atom);
+
+                if (line == NULL) {
+                    return fail_msg("PDB input not valid or not present");
+                }
+
+                strncpy(buf, line, PDB_LINE_STRL);
+                sprintf(&buf[54], "%6.2f%6.2f", radius, area->total);
+                fprintf(output, "%s\n", buf);
+
+                atom = freesasa_node_next(atom);
+            }
+            last_res_name = freesasa_node_name(residue);
+            last_res_number = freesasa_node_residue_number(residue);
+            residue = freesasa_node_next(residue);
+        }
+        last_chain = freesasa_node_name(chain);
+        chain = freesasa_node_next(chain);
+    }
+
+    /* Write TER and ENDMDL lines */
+    strncpy(buf2, &buf[6], 5);
+    buf2[5] = '\0';
+    fprintf(output, "TER   %5d     %4s %c%5s\nENDMDL\n",
+            atoi(buf2) + 1, last_res_name, last_chain[0], last_res_number);
+
+    fflush(output);
+    if (ferror(output)) {
+        return fail_msg(strerror(errno));
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_write_pdb(FILE *output,
+                       freesasa_node *root)
+{
+    freesasa_node *result = freesasa_node_children(root), *structure;
+
+    assert(output);
+    assert(root);
+    assert(freesasa_node_type(root) == FREESASA_NODE_ROOT);
+
+    fprintf(output, "REMARK 999 This PDB file was generated by %s.\n", freesasa_string);
+    fprintf(output, "REMARK 999 In the ATOM records temperature factors have been\n"
+                    "REMARK 999 replaced by the SASA of the atom, and the occupancy\n"
+                    "REMARK 999 by the radius used in the calculation.\n");
+
+    while (result) {
+        structure = freesasa_node_children(result);
+        while (structure) {
+            if (write_pdb_impl(output, structure) == FREESASA_FAIL) {
+                return fail_msg("");
+            }
+            structure = freesasa_node_next(structure);
+        }
+        result = freesasa_node_next(result);
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+#if USE_CHECK
+#include <check.h>
+#include <math.h>
+
+START_TEST(test_pdb)
+{
+    double v;
+    ck_assert(pdb_line_check("", 6) == FREESASA_FAIL);
+    ck_assert(pdb_line_check("ATOM", 4) == FREESASA_FAIL);
+    ck_assert(pdb_line_check("ATOM", 6) == FREESASA_FAIL);
+    ck_assert(pdb_line_check("HETAT", 6) == FREESASA_FAIL);
+    ck_assert(pdb_line_check("HETAT ", 6) == FREESASA_FAIL);
+    ck_assert(pdb_line_check("BLA BLA BLA", 10) == FREESASA_FAIL);
+    ck_assert(pdb_line_check("BLA BLA BLA", 11) == FREESASA_FAIL);
+    ck_assert(pdb_line_check("BLA BLA BLA", 12) == FREESASA_FAIL);
+
+    /* these will pass, although they would be useless */
+    ck_assert(pdb_line_check("ATOM  ", 6) == FREESASA_SUCCESS);
+    ck_assert(pdb_line_check("HETATM", 6) == FREESASA_SUCCESS);
+
+    /* a more likely type of error */
+    ck_assert(pdb_line_check("HETATM", 7) == FREESASA_FAIL);
+
+    /* The normal case */
+    ck_assert(pdb_line_check("ATOM      1  N   MET A   1      27.340  "
+                             "24.430   2.614  1.00  9.67           N  ",
+                             80) == FREESASA_SUCCESS);
+
+    v = 0;
+    ck_assert(pdb_get_double("1.23", 4, &v) == FREESASA_SUCCESS);
+    ck_assert(fabs(1.23 - v) < 1e-5);
+    v = 0;
+    ck_assert(pdb_get_double(" 1.23", 5, &v) == FREESASA_SUCCESS);
+    ck_assert(fabs(1.23 - v) < 1e-5);
+    v = 0;
+    ck_assert(pdb_get_double("1.23", 10, &v) == FREESASA_SUCCESS);
+    ck_assert(fabs(1.23 - v) < 1e-5);
+    v = 0;
+    ck_assert(pdb_get_double("1.23 4.56", 10, &v) == FREESASA_SUCCESS);
+    ck_assert(fabs(1.23 - v) < 1e-5);
+
+    ck_assert(pdb_get_double("  ", 10, &v) == FREESASA_FAIL);
+    ck_assert(pdb_get_double("    1.23", 4, &v) == FREESASA_FAIL);
+    ck_assert(pdb_get_double("abc", 10, &v) == FREESASA_FAIL);
+    ck_assert(pdb_get_double("a 1.23", 6, &v) == FREESASA_FAIL);
+}
+END_TEST
+
+TCase *
+test_pdb_static()
+{
+    TCase *tc = tcase_create("pdb.c static");
+    tcase_add_test(tc, test_pdb);
+
+    return tc;
+}
+
+#endif /* USE_CHECK */

.venv_haddock/include/site/python3.12/freesasa/pdb.h

@@ -0,0 +1,187 @@
+#ifndef FREESASA_PDB_H
+#define FREESASA_PDB_H
+
+#include "freesasa.h"
+#include "freesasa_internal.h"
+
+/**
+    @file
+    @author Simon Mitternacht
+
+    The following functions all extract info from the PDB lines `ATOM`
+    and `HETATM`. Valid lines have to begin with either `ATOM` or
+    `HETATM` and be sufficiently long to contain the value in
+    question.
+*/
+
+#define PDB_ATOM_NAME_STRL 4       /**< Length of strings with atom names, such as `" CA "`. */
+#define PDB_ATOM_RES_NAME_STRL 3   /**< Length of string with residue names, such as `"ALA"`. */
+#define PDB_ATOM_RES_NUMBER_STRL 5 /**< Length of string with residue number, such as `" 123"`. */
+#define PDB_ATOM_SYMBOL_STRL 2     /**< Length for string with element symbol, such "FE". */
+#define PDB_LINE_STRL 80           /**< Length of a line in PDB file. */
+#define PDB_MAX_LINE_STRL 120      /**< for reading, allows nonstandard input with extra fields. */
+
+/**
+    Finds the location of all MODEL entries in the file pdb, returns
+    the number of models found.
+
+    The array *ranges will be dynamically allocated to contain a
+    file ranges for each model.
+
+    @return Returns 0 if no MODEL lines were found (for example an
+      X-ray structure with only one model) and sets *ranges to
+      NULL. A return value of 0 doesn't have to mean the file is
+      empty. ::FREESASA_FAIL if malloc-failure.
+ */
+int freesasa_pdb_get_models(FILE *pdb,
+                            struct file_range **ranges);
+
+/**
+    Finds the location of all chains within the file range 'model'.
+
+    @param pdb The pdb-file
+    @param model The ::file_range to search for chains within.
+    @param ranges The address to a dynamically allocated array
+      containing the ::file_range of each chain will be stored here.
+    @param options Bitfield, can be used to set
+      ::FREESASA_INCLUDE_HETATM.
+    @return Number of chains found. Returns ::FREESASA_FAIL if memory
+      allocation fails.
+ */
+int freesasa_pdb_get_chains(FILE *pdb,
+                            struct file_range model,
+                            struct file_range **ranges,
+                            int options);
+/**
+    Get atom name from a PDB line.
+
+    Extracts the whole atom name field from an `ATOM` or `HETATM` PDB
+    line, including padding, i.e. a string of ::PDB_ATOM_NAME_STRL
+    characters. For example `" CA "` for a regular C-alpha.  If the
+    line is invalid, the name will be an empty string and the function
+    returns ::FREESASA_FAIL.
+
+    @param name The name is written to this string.
+    @param line Line from a PDB file.
+    @return ::FREESASA_SUCCESS if input is readable, else ::FREESASA_FAIL.
+ */
+int freesasa_pdb_get_atom_name(char *name,
+                               const char *line);
+
+/**
+    Get residue name from a PDB line.
+
+    Extracts the whole residue name from an `ATOM` or `HETATM` PDB
+    line, i.e. a string of ::PDB_ATOM_RES_NAME_STRL characters. For
+    example `"ALA"` for an Alanine. If theline is invalid, the name
+    will be an empty string and the function returns ::FREESASA_FAIL.
+
+    @param name The name is written to this string.
+    @param line Line from a PDB file.
+    @return ::FREESASA_SUCCESS if input is readable, else ::FREESASA_FAIL.
+ */
+int freesasa_pdb_get_res_name(char *name,
+                              const char *line);
+
+/**
+    Get atom coordinates from a PDB line.
+
+    Extracts x-, y- and z-coordinates from an `ATOM` or `HETATM` PDB
+    line. If the line is invalid, the function returns ::FREESASA_FAIL
+    and coord will remain unchanged.
+
+    @param coord The coordiantes are written to this array as x,y,z.
+    @param line Line from a PDB file.
+    @return ::FREESASA_SUCCESS if input is readable, else ::FREESASA_FAIL.
+ */
+int freesasa_pdb_get_coord(double *coord,
+                           const char *line);
+
+/**
+    Get residue number from a PDB line.
+
+    Extracts residue number (ResSeq) as a string from an `ATOM` or
+    `HETATM` PDB line as a string. String format is used because not
+    all residue-numbers are numbers. The string should have length
+    ::PDB_ATOM_RES_NUMBER_STRL. If the line is invalid, the number will be an
+    empty string and the function returns ::FREESASA_FAIL.
+
+    @param number The residue number will be saved to this string.
+    @param line Line from a PDB file.
+    @return ::FREESASA_SUCCESS if input is readable, else ::FREESASA_FAIL.
+ */
+int freesasa_pdb_get_res_number(char *number,
+                                const char *line);
+
+/**
+    Get chain label from PDB line.
+
+    Extracts the one character chain label (Chain identifier) from an
+    `ATOM` or `HETATM` PDB line (i.e. `'A'`, `'B'`, `'C'`, ...)
+
+    @param line Line from a PDB file.
+    @return The chain label. If the line is invalid, the function
+    returns '\0'.
+ */
+char freesasa_pdb_get_chain_label(const char *line);
+
+/**
+    Get alternate coordinate label from PDB line.
+
+    If there is more than one set of coordinates for an atom there
+    will be a label 'A', 'B', etc (Alternate location indicator). Else
+    the label is ' '.
+
+    @param line Line from a PDB file.
+    @return The label. If line is invalid, the function returns
+      '\0'.
+ */
+char freesasa_pdb_get_alt_coord_label(const char *line);
+
+/**
+    Get element symbol from PDB line.
+
+    Writes padded string to argument symbol, i.e. " C", "SE", etc.
+
+    @param symbol The symbol will be written to this string.
+    @param line Line from a PDB file.
+    @return ::FREESASA_SUCCESS line has 78 or more characters. ::FREESASA_FAIL if
+      line too short. Does not check if symbol is valid.
+ */
+int freesasa_pdb_get_symbol(char *symbol,
+                            const char *line);
+
+/**
+    Get occupancy from PDB line
+
+    @param occ The occupancy will be written to this location.
+    @param line Line from a PDB file
+
+    @return ::FREESASA_SUCCESS if line is long enough, starts with
+      ATOM or HETATM, and characters 55-60 contain a number.
+ */
+int freesasa_pdb_get_occupancy(double *occ,
+                               const char *line);
+/**
+    Get temperature factor (B-factor) from PDB line
+
+    @param bfac The B-factor will be written to this location.
+    @param line Line from a PDB file
+    @return ::FREESASA_SUCCESS if line is long enough, starts with
+      ATOM or HETATM, and characters 61-66 contain a number.
+ */
+int freesasa_pdb_get_bfactor(double *bfac,
+                             const char *line);
+
+/**
+    Is atom Hydrogen?
+
+    Checks if an atom from an `ATOM` or `HETATM` PDB line is Hydrogen.
+
+    @param line Line from a PDB file.
+    @return 1 if Hydrogen (or deuterium). 0 otherwise. If line is
+      invalid, the function returns ::FREESASA_FAIL.
+ */
+int freesasa_pdb_ishydrogen(const char *line);
+
+#endif /* FREESASA_PDB_H */

.venv_haddock/include/site/python3.12/freesasa/rsa.c

@@ -0,0 +1,174 @@
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <assert.h>
+#include <errno.h>
+#include <math.h>
+#include <stdlib.h>
+
+#include "classifier.h"
+#include "freesasa_internal.h"
+#include "pdb.h"
+
+void freesasa_residue_rel_nodearea(freesasa_nodearea *rel,
+                                   const freesasa_nodearea *abs,
+                                   const freesasa_nodearea *ref)
+{
+    rel->total = 100. * abs->total / ref->total;
+    rel->side_chain = 100. * abs->side_chain / ref->side_chain;
+    rel->main_chain = 100. * abs->main_chain / ref->main_chain;
+    rel->polar = 100. * abs->polar / ref->polar;
+    rel->apolar = 100. * abs->apolar / ref->apolar;
+    rel->name = abs->name;
+}
+
+static void
+rsa_print_header(FILE *output,
+                 const char *config_name,
+                 const char *protein_name,
+                 const char *chains,
+                 const freesasa_parameters *parameters,
+                 int options)
+{
+    freesasa_algorithm alg = parameters->alg;
+#ifdef PACKAGE_VERSION
+    fprintf(output, "REM  FreeSASA " PACKAGE_VERSION "\n");
+#else
+    fprintf(output, "REM  FreeSASA\n");
+#endif
+    fprintf(output, "REM  Absolute and relative SASAs for %s\n", protein_name);
+    if (!(options & FREESASA_OUTPUT_SKIP_REL))
+        fprintf(output, "REM  Atomic radii and reference values for relative SASA: %s\n", config_name);
+    else
+        fprintf(output, "REM  No reference values available to calculate relative SASA\n");
+    fprintf(output, "REM  Chains: %s\n", chains);
+    fprintf(output, "REM  Algorithm: %s\n", freesasa_alg_name(alg));
+    fprintf(output, "REM  Probe-radius: %.2f\n", parameters->probe_radius);
+    if (alg == FREESASA_LEE_RICHARDS) {
+        fprintf(output, "REM  Slices: %d\n", parameters->lee_richards_n_slices);
+    } else if (alg == FREESASA_SHRAKE_RUPLEY) {
+        fprintf(output, "REM  Test-points: %d\n", parameters->shrake_rupley_n_points);
+    }
+    fprintf(output, "REM RES _ NUM      All-atoms   Total-Side   Main-Chain    Non-polar    All polar\n");
+    fprintf(output, "REM                ABS   REL    ABS   REL    ABS   REL    ABS   REL    ABS   REL\n");
+}
+
+static inline void
+rsa_print_abs_rel(FILE *output,
+                  double abs,
+                  double rel)
+{
+    fprintf(output, "%7.2f", abs);
+    if (isfinite(rel))
+        fprintf(output, "%6.1f", rel);
+    else
+        fprintf(output, "   N/A");
+}
+
+static inline void
+rsa_print_abs_only(FILE *output,
+                   double abs)
+{
+    fprintf(output, "%7.2f", abs);
+    fprintf(output, "   N/A");
+}
+
+static int
+rsa_print_residue(FILE *output,
+                  int iaa,
+                  const freesasa_nodearea *abs,
+                  const freesasa_nodearea *rel,
+                  freesasa_node *residue)
+{
+    const char *resi_str;
+    char chain;
+
+    resi_str = freesasa_node_residue_number(residue);
+    chain = freesasa_node_name(freesasa_node_parent(residue))[0];
+
+    fprintf(output, "RES %s %c%s ", abs->name, chain, resi_str);
+    if (rel->name != NULL) {
+        rsa_print_abs_rel(output, abs->total, rel->total);
+        rsa_print_abs_rel(output, abs->side_chain, rel->side_chain);
+        rsa_print_abs_rel(output, abs->main_chain, rel->main_chain);
+        rsa_print_abs_rel(output, abs->apolar, rel->apolar);
+        rsa_print_abs_rel(output, abs->polar, rel->polar);
+    } else {
+        rsa_print_abs_only(output, abs->total);
+        rsa_print_abs_only(output, abs->side_chain);
+        rsa_print_abs_only(output, abs->main_chain);
+        rsa_print_abs_only(output, abs->apolar);
+        rsa_print_abs_only(output, abs->polar);
+    }
+    fprintf(output, "\n");
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_write_rsa(FILE *output,
+                       freesasa_node *tree,
+                       int options)
+{
+    freesasa_node *residue, *chain, *structure_node, *result_node;
+    const freesasa_nodearea *abs, *reference;
+    freesasa_nodearea rel;
+    int res_index, chain_index;
+    const freesasa_parameters *parameters;
+
+    assert(output);
+    assert(tree);
+
+    result_node = freesasa_node_children(tree);
+    parameters = freesasa_node_result_parameters(result_node);
+    structure_node = freesasa_node_children(result_node);
+    chain = freesasa_node_children(structure_node);
+
+    rsa_print_header(output, freesasa_node_classified_by(result_node),
+                     freesasa_node_name(result_node), freesasa_node_name(structure_node), parameters, options);
+
+    res_index = chain_index = 0;
+    while (chain) {
+        residue = freesasa_node_children(chain);
+        while (residue) {
+            abs = freesasa_node_area(residue);
+            reference = freesasa_node_residue_reference(residue);
+            if (reference && !(options & FREESASA_OUTPUT_SKIP_REL)) {
+                freesasa_residue_rel_nodearea(&rel, abs, reference);
+            } else {
+                rel = freesasa_nodearea_null;
+            }
+            rsa_print_residue(output, res_index, abs, &rel, residue);
+            ++res_index;
+            residue = freesasa_node_next(residue);
+        }
+        chain = freesasa_node_next(chain);
+    }
+
+    fprintf(output, "END  Absolute sums over single chains surface\n");
+
+    chain = freesasa_node_children(structure_node);
+    chain_index = 0;
+    while (chain) {
+        const char *name = freesasa_node_name(chain);
+        abs = freesasa_node_area(chain);
+
+        fprintf(output, "CHAIN%3d %c %10.1f   %10.1f   %10.1f   %10.1f   %10.1f\n",
+                chain_index + 1, name[0], abs->total, abs->side_chain,
+                abs->main_chain, abs->apolar, abs->polar);
+
+        ++chain_index;
+        chain = freesasa_node_next(chain);
+    }
+
+    abs = freesasa_node_area(structure_node);
+    fprintf(output, "END  Absolute sums over all chains\n");
+    fprintf(output, "TOTAL      %10.1f   %10.1f   %10.1f   %10.1f   %10.1f\n",
+            abs->total, abs->side_chain, abs->main_chain, abs->apolar, abs->polar);
+
+    fflush(output);
+    if (ferror(output)) {
+        return fail_msg(strerror(errno));
+    }
+
+    return FREESASA_SUCCESS;
+}

.venv_haddock/include/site/python3.12/freesasa/sasa_lr.c

@@ -0,0 +1,487 @@
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+#include <assert.h>
+#include <errno.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#ifdef _MSC_VER
+#define _USE_MATH_DEFINES
+#endif
+#include <math.h>
+
+#if USE_THREADS
+#include <pthread.h>
+#define MAX_LR_THREADS 16
+#else
+#define MAX_LR_THREADS 1
+#endif
+
+#include "freesasa_internal.h"
+#include "nb.h"
+
+const double TWOPI = 2 * M_PI;
+
+/* calculation parameters and data (results stored in *sasa) */
+typedef struct {
+    int n_atoms;
+    double *radii; /* including probe */
+    const coord_t *xyz;
+    nb_list *adj;
+    int n_slices_per_atom;
+    double *sasa; /* results */
+    double *arc[MAX_LR_THREADS], *z_nb[MAX_LR_THREADS], *R_nb[MAX_LR_THREADS];
+    int n_threads;
+} lr_data;
+
+typedef struct {
+    int first_atom;
+    int last_atom;
+    int thread_id;
+    lr_data *lr;
+} lr_thread_interval;
+
+#if USE_THREADS
+static int lr_do_threads(int n_threads, lr_data *);
+static void *lr_thread(void *arg);
+#endif
+
+/** Returns the are of atom i */
+static double
+atom_area(lr_data *lr, int i, int thread_id);
+
+/** Sum of exposed arcs based on buried arc intervals arc, assumes no
+    intervals cross zero */
+static double
+exposed_arc_length(double *restrict arc, int n);
+
+/** Release contenst of lr_data pointer*/
+static void
+release_lr(lr_data *lr)
+{
+    int i;
+
+    free(lr->radii);
+    freesasa_nb_free(lr->adj);
+    lr->radii = NULL;
+    lr->adj = NULL;
+
+    for (i = 0; i < lr->n_threads; ++i) {
+        free(lr->arc[i]);
+        free(lr->z_nb[i]);
+        free(lr->R_nb[i]);
+    }
+}
+
+/* Allocate some helper arrays in area calculation that need to be pre-allocated */
+static int
+alloc_lr_calc_arrays(lr_data *lr, int n_threads)
+{
+    int max_nni = 0, i, nni;
+    const int n_atoms = lr->n_atoms;
+
+    for (i = 0; i < n_atoms; ++i) {
+        nni = lr->adj->nn[i];
+        max_nni = max_nni < nni ? nni : max_nni;
+    }
+
+    for (i = 0; i < n_threads; ++i) {
+        lr->arc[i] = malloc(sizeof(double) * 4 * max_nni);
+        lr->z_nb[i] = malloc(sizeof(double) * max_nni);
+        lr->R_nb[i] = malloc(sizeof(double) * max_nni);
+
+        if (!lr->arc[i] || !lr->z_nb[i] || !lr->R_nb[i]) {
+            return mem_fail();
+        }
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+/** Initialize object to be used for L&R calculation */
+static int
+init_lr(lr_data *lr,
+        double *sasa,
+        const coord_t *xyz,
+        const double *atom_radii,
+        double probe_radius,
+        int n_slices_per_atom,
+        int n_threads)
+{
+    const int n_atoms = freesasa_coord_n(xyz);
+    int i;
+
+    lr->n_atoms = n_atoms;
+    lr->xyz = xyz;
+    lr->adj = NULL;
+    lr->n_slices_per_atom = n_slices_per_atom;
+    lr->sasa = sasa;
+    lr->n_threads = n_threads;
+
+    for (i = 0; i < n_threads; ++i) {
+        lr->arc[i] = NULL;
+        lr->z_nb[i] = NULL;
+        lr->R_nb[i] = NULL;
+    }
+
+    lr->radii = malloc(sizeof(double) * n_atoms);
+    if (lr->radii == NULL) {
+        return mem_fail();
+    }
+
+    /* init some arrays */
+    for (i = 0; i < n_atoms; ++i) {
+        lr->radii[i] = atom_radii[i] + probe_radius;
+        sasa[i] = 0.;
+    }
+
+    /* determine which atoms are neighbours */
+    lr->adj = freesasa_nb_new(xyz, lr->radii);
+
+    if (lr->adj == NULL) {
+        release_lr(lr);
+        return fail_msg("");
+    }
+
+    if (alloc_lr_calc_arrays(lr, n_threads)) {
+        release_lr(lr);
+        return fail_msg("");
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_lee_richards(double *sasa,
+                          const coord_t *xyz,
+                          const double *atom_radii,
+                          const freesasa_parameters *param)
+{
+    int return_value, n_atoms, n_threads, resolution, i;
+    double probe_radius;
+    lr_data lr;
+
+    assert(sasa);
+    assert(xyz);
+    assert(atom_radii);
+
+    if (param == NULL) param = &freesasa_default_parameters;
+
+    return_value = FREESASA_SUCCESS;
+    n_atoms = freesasa_coord_n(xyz);
+    n_threads = param->n_threads;
+    resolution = param->lee_richards_n_slices;
+    probe_radius = param->probe_radius;
+
+    if (n_threads > MAX_LR_THREADS) {
+        return fail_msg("L&R does not support more than %d threads", MAX_LR_THREADS);
+    }
+
+    if (resolution <= 0) {
+        return fail_msg("%f slices per atom invalid resolution in L&R, must be > 0\n", resolution);
+    }
+
+    if (n_atoms == 0) {
+        return freesasa_warn("in %s(): empty coordinates", __func__);
+    }
+
+    if (n_threads > n_atoms) {
+        n_threads = n_atoms;
+        freesasa_warn("no sense in having more threads than atoms, only using %d threads",
+                      n_threads);
+    }
+
+    if (init_lr(&lr, sasa, xyz, atom_radii, probe_radius, resolution, n_threads))
+        return FREESASA_FAIL;
+
+    if (n_threads > 1) {
+#if USE_THREADS
+        return_value = lr_do_threads(n_threads, &lr);
+#else
+        return_value = freesasa_warn("in %s(): program compiled for single-threaded use, "
+                                     "but multiple threads were requested, will "
+                                     "proceed in single-threaded mode\n",
+                                     __func__);
+        n_threads = 1;
+#endif /* pthread */
+    }
+    if (n_threads == 1) {
+        for (i = 0; i < lr.n_atoms; ++i) {
+            lr.sasa[i] = atom_area(&lr, i, 0);
+        }
+    }
+    release_lr(&lr);
+    return return_value;
+}
+
+#if USE_THREADS
+static int
+lr_do_threads(int n_threads,
+              lr_data *lr)
+{
+    pthread_t thread[MAX_LR_THREADS];
+    lr_thread_interval t_data[MAX_LR_THREADS];
+    int n_perthread = lr->n_atoms / n_threads, res;
+    int threads_created = 0, return_value = FREESASA_SUCCESS;
+    int t;
+
+    for (t = 0; t < n_threads; ++t) {
+        t_data[t].first_atom = t * n_perthread;
+        if (t == n_threads - 1) {
+            t_data[t].last_atom = lr->n_atoms - 1;
+        } else {
+            t_data[t].last_atom = (t + 1) * n_perthread - 1;
+        }
+        t_data[t].lr = lr;
+        t_data[t].thread_id = t;
+        res = pthread_create(&thread[t], NULL, lr_thread,
+                             (void *)&t_data[t]);
+        if (res) {
+            return_value = fail_msg(freesasa_thread_error(res));
+            break;
+        }
+        ++threads_created;
+    }
+    for (int t = 0; t < threads_created; ++t) {
+        res = pthread_join(thread[t], NULL);
+        if (res) {
+            return_value = fail_msg(freesasa_thread_error(res));
+        }
+    }
+    return return_value;
+}
+
+static void *
+lr_thread(void *arg)
+{
+    int i;
+    lr_thread_interval *ti = ((lr_thread_interval *)arg);
+
+    for (i = ti->first_atom; i <= ti->last_atom; ++i) {
+        /* the different threads write to different parts of the
+           array, so locking shouldn't be necessary */
+        ti->lr->sasa[i] = atom_area(ti->lr, i, ti->thread_id);
+    }
+    pthread_exit(NULL);
+}
+#endif /* USE_THREADS */
+
+static double
+atom_area(lr_data *lr,
+          int i,
+          int thread_id)
+{
+    /* This function is large because a large number of pre-calculated
+       arrays need to be accessed efficiently. Partially dereferenced
+       here to make access more efficient.
+
+       Variables are named according to the documentation (see page
+       "Geometry of Lee & Richards' algorithm") */
+
+    const int nni = lr->adj->nn[i];
+    const double *restrict const v = freesasa_coord_all(lr->xyz);
+    const double *restrict const R = lr->radii;
+    const int *restrict const nbi = lr->adj->nb[i];
+    const double *restrict const xydi = lr->adj->xyd[i];
+    const double *restrict const xdi = lr->adj->xd[i];
+    const double *restrict const ydi = lr->adj->yd[i];
+    const double zi = v[3 * i + 2], Ri = R[i];
+    const int ns = lr->n_slices_per_atom;
+
+    int j, islice, n_arcs, is_buried, narc2;
+    double *arc = lr->arc[thread_id],
+           *z_nb = lr->z_nb[thread_id],
+           *R_nb = lr->R_nb[thread_id];
+    double z, delta, sasa = 0, alpha, beta, inf, sup;
+    double zj, di, dj, dij, Rj, Ri_prime2, Ri_prime, Rj_prime2, Rj_prime;
+
+    for (j = 0; j < nni; ++j) {
+        z_nb[j] = v[3 * nbi[j] + 2];
+        R_nb[j] = R[nbi[j]];
+    }
+
+    delta = 2 * Ri / ns;
+    z = zi - Ri - 0.5 * delta;
+    for (islice = 0; islice < ns; ++islice) {
+        z += delta;
+        di = fabs(zi - z);
+        Ri_prime2 = Ri * Ri - di * di;
+        if (Ri_prime2 < 0) continue; /* handle round-off errors */
+        Ri_prime = sqrt(Ri_prime2);
+        if (Ri_prime <= 0) continue; /* more round-off errors */
+        n_arcs = 0;
+        is_buried = 0;
+        for (j = 0; j < nni; ++j) {
+            zj = z_nb[j];
+            dj = fabs(zj - z);
+            Rj = R_nb[j];
+
+            if (dj < Rj) {
+                Rj_prime2 = Rj * Rj - dj * dj;
+                Rj_prime = sqrt(Rj_prime2);
+                dij = xydi[j];
+                if (dij >= Ri_prime + Rj_prime) { /* atoms aren't in contact */
+                    continue;
+                }
+                if (dij + Ri_prime < Rj_prime) { /* circle i is completely inside j */
+                    is_buried = 1;
+                    break;
+                }
+                if (dij + Rj_prime < Ri_prime) { /* circle j is completely inside i */
+                    continue;
+                }
+                /* arc of circle i intersected by circle j */
+                alpha = acos((Ri_prime2 + dij * dij - Rj_prime2) / (2.0 * Ri_prime * dij));
+                /* position of mid-point of intersection along circle i */
+                beta = atan2(ydi[j], xdi[j]) + M_PI;
+                inf = beta - alpha;
+                sup = beta + alpha;
+                if (inf < 0) inf += TWOPI;
+                if (sup > 2 * M_PI) sup -= TWOPI;
+                narc2 = 2 * n_arcs;
+                /* store the arc, if arc passes 2*PI split into two */
+                if (sup < inf) {
+                    /* store arcs as contiguous pairs of angles */
+                    arc[narc2] = 0;
+                    arc[narc2 + 1] = sup;
+                    /* second arc */
+                    arc[narc2 + 2] = inf;
+                    arc[narc2 + 3] = TWOPI;
+                    n_arcs += 2;
+                } else {
+                    arc[narc2] = inf;
+                    arc[narc2 + 1] = sup;
+                    ++n_arcs;
+                }
+            }
+        }
+        if (is_buried == 0) {
+            sasa += delta * Ri * exposed_arc_length(arc, n_arcs);
+        }
+    }
+    return sasa;
+}
+
+/* insertion sort (faster than qsort for these short lists) */
+inline static void
+sort_arcs(double *restrict arc,
+          int n)
+{
+    double tmp[2];
+    double *end = arc + 2 * n, *arcj, *arci;
+    for (arci = arc + 2; arci < end; arci += 2) {
+        *tmp = *arci;
+        *(tmp + 1) = *(arci + 1);
+        arcj = arci;
+        while (arcj > arc && *(arcj - 2) > tmp[0]) {
+            *arcj = *(arcj - 2);
+            *(arcj + 1) = *(arcj - 1);
+            arcj -= 2;
+        }
+        *arcj = *tmp;
+        *(arcj + 1) = *(tmp + 1);
+    }
+}
+
+/* sort arcs by start-point, loop through them to sum parts of circle
+   not covered by any of the arcs */
+inline static double
+exposed_arc_length(double *restrict arc,
+                   int n)
+{
+    int i2;
+    double sum, sup, tmp;
+
+    if (n == 0) return TWOPI;
+
+    sort_arcs(arc, n);
+    sum = arc[0];
+    sup = arc[1];
+    /* in the following it is assumed that the arc[i2] <= arc[i2+1] */
+    for (i2 = 2; i2 < 2 * n; i2 += 2) {
+        if (sup < arc[i2]) sum += arc[i2] - sup;
+        tmp = arc[i2 + 1];
+        if (tmp > sup) sup = tmp;
+    }
+    return sum + TWOPI - sup;
+}
+
+#if USE_CHECK
+#include <check.h>
+
+static int
+is_identical(const double *l1, const double *l2, int n)
+{
+    int i;
+
+    for (i = 0; i < n; ++i) {
+        if (l1[i] != l2[i]) return 0;
+    }
+
+    return 1;
+}
+
+static int
+is_sorted(const double *list, int n)
+{
+    int i;
+
+    for (i = 0; i < n - 1; ++i)
+        if (list[2 * i] > list[2 * i + 1]) return 0;
+
+    return 1;
+}
+
+START_TEST(test_sort_arcs)
+{
+    double a_ref[] = {0, 1, 2, 3}, b_ref[] = {-2, 0, -1, 0, -1, 1};
+    double a1[4] = {0, 1, 2, 3}, a2[4] = {2, 3, 0, 1};
+    double b1[6] = {-2, 0, -1, 0, -1, 1}, b2[6] = {-1, 1, -2, 0, -1, 1};
+    sort_arcs(a1, 2);
+    sort_arcs(a2, 2);
+    sort_arcs(b1, 3);
+    sort_arcs(b2, 3);
+    ck_assert(is_sorted(a1, 2));
+    ck_assert(is_sorted(a2, 2));
+    ck_assert(is_sorted(b1, 3));
+    ck_assert(is_sorted(b2, 3));
+    ck_assert(is_identical(a_ref, a1, 4));
+    ck_assert(is_identical(a_ref, a2, 4));
+    ck_assert(is_identical(b_ref, b1, 6));
+}
+END_TEST
+
+START_TEST(test_exposed_arc_length)
+{
+    double a1[4] = {0, 0.1 * TWOPI, 0.9 * TWOPI, TWOPI}, a2[4] = {0.9 * TWOPI, TWOPI, 0, 0.1 * TWOPI};
+    double a3[4] = {0, TWOPI, 1, 2}, a4[4] = {1, 2, 0, TWOPI};
+    double a5[4] = {0.1 * TWOPI, 0.2 * TWOPI, 0.5 * TWOPI, 0.6 * TWOPI};
+    double a6[4] = {0.1 * TWOPI, 0.2 * TWOPI, 0.5 * TWOPI, 0.6 * TWOPI};
+    double a7[4] = {0.1 * TWOPI, 0.3 * TWOPI, 0.15 * TWOPI, 0.2 * TWOPI};
+    double a8[4] = {0.15 * TWOPI, 0.2 * TWOPI, 0.1 * TWOPI, 0.3 * TWOPI};
+    double a9[10] = {0.05, 0.1, 0.5, 0.6, 0, 0.15, 0.7, 0.8, 0.75, TWOPI};
+    ck_assert(fabs(exposed_arc_length(a1, 2) - 0.8 * TWOPI) < 1e-10);
+    ck_assert(fabs(exposed_arc_length(a2, 2) - 0.8 * TWOPI) < 1e-10);
+    ck_assert(fabs(exposed_arc_length(a3, 2)) < 1e-10);
+    ck_assert(fabs(exposed_arc_length(a4, 2)) < 1e-10);
+    ck_assert(fabs(exposed_arc_length(a5, 2) - 0.8 * TWOPI) < 1e-10);
+    ck_assert(fabs(exposed_arc_length(a6, 2) - 0.8 * TWOPI) < 1e-10);
+    ck_assert(fabs(exposed_arc_length(a7, 2) - 0.8 * TWOPI) < 1e-10);
+    ck_assert(fabs(exposed_arc_length(a8, 2) - 0.8 * TWOPI) < 1e-10);
+    ck_assert(fabs(exposed_arc_length(a9, 5) - 0.45) < 1e-10);
+    /* can't think of anything more qualitatively different here */
+}
+END_TEST
+
+TCase *
+test_LR_static()
+{
+    TCase *tc = tcase_create("sasa_lr.c static");
+    tcase_add_test(tc, test_sort_arcs);
+    tcase_add_test(tc, test_exposed_arc_length);
+
+    return tc;
+}
+
+#endif /* USE_CHECK */

.venv_haddock/include/site/python3.12/freesasa/sasa_sr.c

@@ -0,0 +1,338 @@
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+#include <assert.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#ifdef _MSC_VER
+#define _USE_MATH_DEFINES
+#endif
+#include <math.h>
+
+#if USE_THREADS
+#include <pthread.h>
+#define MAX_SR_THREADS 16
+#else
+#define MAX_SR_THREADS 1
+#endif
+
+#include "freesasa_internal.h"
+#include "nb.h"
+
+#ifdef __GNUC__
+#define __attrib_pure__ __attribute__((pure))
+#else
+#define __attrib_pure__
+#endif
+
+/* calculation parameters (results stored in *sasa) */
+typedef struct {
+    int i1, i2; /* for multithreading, range of atoms */
+    int thread_index;
+    int n_atoms;
+    int n_points;
+    int n_threads;
+    double probe_radius;
+    const coord_t *xyz;
+    coord_t *srp;                      /* test-points */
+    coord_t *tp_local[MAX_SR_THREADS]; /* coord object for storing intermediates */
+    int *spcount[MAX_SR_THREADS];
+    double *r;
+    double *r2;
+    nb_list *nb;
+    double *sasa;
+} sr_data;
+
+#if USE_THREADS
+static int sr_do_threads(int n_threads, sr_data *sr);
+static void *sr_thread(void *arg);
+#endif
+
+static double
+sr_atom_area(int i, const sr_data *sr, int thread_index) __attrib_pure__;
+
+static coord_t *
+test_points(int N)
+{
+    /* Golden section spiral on a sphere
+       from http://web.archive.org/web/20120421191837/http://www.cgafaq.info/wiki/Evenly_distributed_points_on_sphere */
+    double dlong = M_PI * (3 - sqrt(5)), dz = 2.0 / N, longitude = 0, z = 1 - dz / 2, r;
+    coord_t *coord = freesasa_coord_new();
+    double *tp = malloc(3 * N * sizeof(double)), *p;
+    if (tp == NULL || coord == NULL) {
+        mem_fail();
+        goto cleanup;
+    }
+
+    for (p = tp; p - tp < 3 * N; p += 3) {
+        r = sqrt(1 - z * z);
+        p[0] = cos(longitude) * r;
+        p[1] = sin(longitude) * r;
+        p[2] = z;
+        z -= dz;
+        longitude += dlong;
+    }
+
+    if (freesasa_coord_append(coord, tp, N) == FREESASA_FAIL) {
+        fail_msg("");
+        goto cleanup;
+    }
+    free(tp);
+
+    return coord;
+
+cleanup:
+    free(tp);
+    freesasa_coord_free(coord);
+    return NULL;
+}
+
+/* free contents */
+void release_sr(sr_data *sr)
+{
+    int i;
+
+    freesasa_coord_free(sr->srp);
+    freesasa_nb_free(sr->nb);
+    free(sr->r);
+    free(sr->r2);
+
+    for (i = 0; i < sr->n_threads; ++i) {
+        freesasa_coord_free(sr->tp_local[i]);
+        free(sr->spcount[i]);
+    }
+}
+
+int init_sr(sr_data *sr,
+            double *sasa,
+            const coord_t *xyz,
+            const double *r,
+            double probe_radius,
+            int n_points,
+            int n_threads)
+{
+    int n_atoms = freesasa_coord_n(xyz), i;
+    coord_t *srp = test_points(n_points);
+    double ri;
+
+    if (srp == NULL) return fail_msg("failed to initialize test points");
+
+    /* store parameters and reference arrays */
+    sr->n_atoms = n_atoms;
+    sr->n_points = n_points;
+    sr->n_threads = n_threads;
+    sr->probe_radius = probe_radius;
+    sr->xyz = xyz;
+    sr->srp = srp;
+    sr->sasa = sasa;
+    sr->nb = NULL;
+
+    /* should be done before any mallocs (to avoid problems in potential cleanup) */
+    for (i = 0; i < n_threads; ++i) {
+        sr->tp_local[i] = NULL;
+        sr->spcount[i] = NULL;
+    }
+
+    sr->r = malloc(sizeof(double) * n_atoms);
+    sr->r2 = malloc(sizeof(double) * n_atoms);
+
+    if (sr->r == NULL || sr->r2 == NULL) goto cleanup;
+
+    for (i = 0; i < n_atoms; ++i) {
+        ri = r[i] + probe_radius;
+        sr->r[i] = ri;
+        sr->r2[i] = ri * ri;
+    }
+
+    for (i = 0; i < n_threads; ++i) {
+        sr->tp_local[i] = freesasa_coord_clone(sr->srp);
+        sr->spcount[i] = malloc(sizeof(int) * n_points);
+        if (sr->tp_local[i] == NULL || sr->spcount[i] == NULL) {
+            goto cleanup;
+        }
+    }
+
+    /* calculate distances */
+    sr->nb = freesasa_nb_new(xyz, sr->r);
+    if (sr->nb == NULL) goto cleanup;
+
+    return FREESASA_SUCCESS;
+
+cleanup:
+    release_sr(sr);
+    return mem_fail();
+}
+
+int freesasa_shrake_rupley(double *sasa,
+                           const coord_t *xyz,
+                           const double *r,
+                           const freesasa_parameters *param)
+{
+    int i, n_atoms, n_threads = param->n_threads, resolution, return_value;
+    double probe_radius = param->probe_radius;
+    sr_data sr;
+
+    assert(sasa);
+    assert(xyz);
+    assert(r);
+
+    if (param == NULL) param = &freesasa_default_parameters;
+
+    n_atoms = freesasa_coord_n(xyz);
+    n_threads = param->n_threads;
+    resolution = param->shrake_rupley_n_points;
+    return_value = FREESASA_SUCCESS;
+
+    if (n_threads > MAX_SR_THREADS) {
+        return fail_msg("S&R does not support more than %d threads", MAX_SR_THREADS);
+    }
+    if (resolution <= 0) {
+        return fail_msg("%f test points invalid resolution in S&R, must be > 0\n", resolution);
+    }
+    if (n_atoms == 0) return freesasa_warn("in %s(): empty coordinates", __func__);
+    if (n_threads > n_atoms) {
+        n_threads = n_atoms;
+        freesasa_warn("no sense in having more threads than atoms, only using %d threads",
+                      n_threads);
+    }
+
+    if (init_sr(&sr, sasa, xyz, r, probe_radius, resolution, n_threads))
+        return FREESASA_FAIL;
+
+    /* calculate SASA */
+    if (n_threads > 1) {
+#if USE_THREADS
+        return_value = sr_do_threads(n_threads, &sr);
+#else
+        return_value = freesasa_warn("in %s(): program compiled for single-threaded use, "
+                                     "but multiple threads were requested, will "
+                                     "proceed in single-threaded mode\n",
+                                     __func__);
+        n_threads = 1;
+#endif
+    }
+    if (n_threads == 1) {
+        /* don't want the overhead of generating threads if only one is used */
+        for (i = 0; i < n_atoms; ++i) {
+            sasa[i] = sr_atom_area(i, &sr, 0);
+        }
+    }
+    release_sr(&sr);
+    return return_value;
+}
+
+#if USE_THREADS
+static int
+sr_do_threads(int n_threads,
+              sr_data *sr)
+{
+    pthread_t thread[MAX_SR_THREADS];
+    sr_data srt[MAX_SR_THREADS];
+    int thread_block_size = sr->n_atoms / n_threads;
+    int res, return_value = FREESASA_SUCCESS;
+    int threads_created = 0, t;
+
+    /*  divide atoms evenly over threads */
+    for (t = 0; t < n_threads; ++t) {
+        srt[t] = *sr;
+        srt[t].i1 = t * thread_block_size;
+        if (t == n_threads - 1)
+            srt[t].i2 = sr->n_atoms;
+        else
+            srt[t].i2 = (t + 1) * thread_block_size;
+        srt[t].thread_index = t;
+        res = pthread_create(&thread[t], NULL, sr_thread, (void *)&srt[t]);
+        if (res) {
+            return_value = fail_msg(freesasa_thread_error(res));
+            break;
+        }
+        ++threads_created;
+    }
+    for (t = 0; t < threads_created; ++t) {
+        res = pthread_join(thread[t], NULL);
+        if (res) {
+            return_value = fail_msg(freesasa_thread_error(res));
+        }
+    }
+    return return_value;
+}
+
+static void *
+sr_thread(void *arg)
+{
+    int i;
+    sr_data *sr = ((sr_data *)arg);
+
+    for (i = sr->i1; i < sr->i2; ++i) {
+        /* mutex should not be necessary, writes to non-overlapping regions */
+        sr->sasa[i] = sr_atom_area(i, sr, sr->thread_index);
+    }
+    pthread_exit(NULL);
+}
+#endif
+
+static double
+sr_atom_area(int i,
+             const sr_data *sr,
+             int thread_index)
+{
+    const int n_points = sr->n_points;
+    /* this array keeps track of which testpoints belonging to
+       a certain atom do not overlap with any other atoms */
+    int *spcount = sr->spcount[thread_index];
+    const int nni = sr->nb->nn[i];
+    const int *restrict nbi = sr->nb->nb[i];
+    const double ri = sr->r[i];
+    const double *restrict r2 = sr->r2;
+    const double *restrict v = freesasa_coord_all(sr->xyz);
+    const double *restrict vi = v + 3 * i;
+    const double *restrict tp;
+    int n_surface = 0, current_nb, a, j, k;
+    double dx, dy, dz;
+    /* testpoints for this atom */
+    coord_t *restrict tp_coord_ri = sr->tp_local[thread_index];
+
+    freesasa_coord_copy(tp_coord_ri, sr->srp);
+    freesasa_coord_scale(tp_coord_ri, ri);
+    freesasa_coord_translate(tp_coord_ri, vi);
+    tp = freesasa_coord_all(tp_coord_ri);
+
+    /* initialize with all surface points hidden */
+    memset(spcount, 0, n_points * sizeof(int));
+
+    /* Using the trick from NSOL to check points one by one for all
+       atoms, start comparing with the first neighbor. If there is no
+       overlap for a given test-point, try with other neighbors
+       instead. Would probably work even better if test points were
+       organized in patches and not spirals. */
+    current_nb = 0;
+    for (j = 0; j < n_points; ++j) {
+        /* a is the index of the atom under consideration */
+        a = nbi[current_nb];
+        dx = tp[j * 3] - v[a * 3];
+        dy = tp[j * 3 + 1] - v[a * 3 + 1];
+        dz = tp[j * 3 + 2] - v[a * 3 + 2];
+        if (dx * dx + dy * dy + dz * dz > r2[a]) {
+            k = 0;
+            for (; k < nni; ++k) {
+                a = nbi[k];
+                dx = tp[j * 3] - v[a * 3];
+                dy = tp[j * 3 + 1] - v[a * 3 + 1];
+                dz = tp[j * 3 + 2] - v[a * 3 + 2];
+                if (dx * dx + dy * dy + dz * dz <= r2[a]) {
+                    current_nb = k;
+                    break;
+                }
+            }
+            /* we have gone through the whole list without overlap */
+            if (k == nni) spcount[j] = 1;
+        }
+    }
+    for (k = 0; k < n_points; ++k) {
+        if (spcount[k]) ++n_surface;
+    }
+
+    return (4.0 * M_PI * ri * ri * n_surface) / n_points;
+}

.venv_haddock/include/site/python3.12/freesasa/selection.c

@@ -0,0 +1,1003 @@
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <assert.h>
+#include <ctype.h>
+#include <stdlib.h>
+
+#include "freesasa_internal.h"
+#include "pdb.h"
+#include "selection.h"
+
+#include "parser.h"
+
+#include "lexer.h"
+
+struct freesasa_selection {
+    char *name;
+    char *command;
+    double area;
+    int n_atoms;
+};
+
+struct selection {
+    const char *name;
+    int *atom;
+    int size;
+};
+
+static const char *
+e_str(expression_type e)
+{
+    switch (e) {
+    case E_SELECTION:
+        return "<selection>";
+    case E_SYMBOL:
+        return "symbol";
+    case E_NAME:
+        return "name";
+    case E_RESN:
+        return "resn";
+    case E_RESI:
+        return "resi";
+    case E_CHAIN:
+        return "chain";
+    case E_ID:
+        return "<id>";
+    case E_NUMBER:
+        return "<number>";
+    case E_NEGNUM:
+        return "<neg_number>";
+    case E_AND:
+        return "and";
+    case E_OR:
+        return "or";
+    case E_NOT:
+        return "not";
+    case E_PLUS:
+        return "< + >";
+    case E_RANGE:
+        return "< - >";
+    case E_RANGE_OPEN_R:
+        return "< - R >";
+    case E_RANGE_OPEN_L:
+        return "< - L >";
+    }
+    return NULL;
+}
+
+extern int freesasa_yyparse(expression **expression, yyscan_t scanner);
+
+static expression *
+expression_new()
+{
+    struct expression *e = malloc(sizeof(expression));
+
+    if (e == NULL)
+        mem_fail();
+    else {
+        e->type = E_SELECTION;
+        e->left = NULL;
+        e->right = NULL;
+        e->value = NULL;
+    }
+    return e;
+}
+
+static void
+expression_free(expression *expression)
+{
+    if (expression) {
+        expression_free(expression->left);
+        expression_free(expression->right);
+        free(expression->value);
+        free(expression);
+    }
+}
+
+expression *
+freesasa_selection_atom(expression_type type,
+                        const char *val)
+{
+    expression *e = expression_new();
+    int i, n;
+    char *buf;
+
+    assert(val);
+
+    if (e != NULL) {
+        if (type == E_NEGNUM) {
+            n = strlen(val) + 2;
+            buf = malloc(n);
+            if (buf == NULL) {
+                mem_fail();
+                expression_free(e);
+                return NULL;
+            }
+            sprintf(buf, "-%s", val);
+            e->type = E_NUMBER;
+            e->value = strdup(buf);
+            free(buf);
+        } else {
+            e->type = type;
+            e->value = strdup(val);
+        }
+
+        if (e->value == NULL) {
+            mem_fail();
+            expression_free(e);
+            return NULL;
+        }
+
+        for (i = 0; i < strlen(e->value); ++i)
+            e->value[i] = toupper(e->value[i]);
+    }
+    return e;
+}
+
+expression *
+freesasa_selection_create(expression *selection,
+                          const char *id)
+{
+    expression *e = expression_new();
+
+    assert(id);
+
+    if (e == NULL)
+        expression_free(selection);
+    else {
+        e->type = E_SELECTION;
+        e->left = selection;
+        e->value = strdup(id);
+
+        if (e->value == NULL) {
+            mem_fail();
+            expression_free(e);
+            e = NULL;
+        }
+    }
+
+    return e;
+}
+
+expression *
+freesasa_selection_selector(expression_type type,
+                            expression *list)
+{
+    expression *e = expression_new();
+
+    if (e == NULL) {
+        expression_free(list);
+    } else {
+        e->type = type;
+        e->left = list;
+    }
+
+    return e;
+}
+
+expression *
+freesasa_selection_operation(expression_type type,
+                             expression *left,
+                             expression *right)
+{
+    expression *e = expression_new();
+
+    if (e == NULL) {
+        expression_free(left);
+        expression_free(right);
+    } else {
+        e->type = type;
+        e->left = left;
+        e->right = right;
+    }
+
+    return e;
+}
+
+/* for debugging */
+static void
+print_expr(FILE *output, const expression *e, int level)
+{
+    int i;
+    fprintf(output, "\n");
+    for (i = 0; i < level; ++i)
+        fprintf(output, "  ");
+
+    if (e == NULL) {
+        fprintf(output, "()");
+    } else {
+        fprintf(output, "(%s ", e_str(e->type));
+        if (e->value) fprintf(output, ": %s ", e->value);
+        print_expr(output, e->left, level + 1);
+        print_expr(output, e->right, level + 1);
+        fprintf(output, ")");
+    }
+    fflush(output);
+}
+
+static expression *
+get_expression(const char *selector)
+{
+    freesasa_yyscan_t scanner;
+    YY_BUFFER_STATE state;
+    int err;
+    expression *expression = NULL;
+
+    if (freesasa_yylex_init(&scanner)) {
+        fail_msg("lexer failed");
+    } else {
+        state = freesasa_yy_scan_string(selector, scanner);
+        err = freesasa_yyparse(&expression, scanner);
+        if (err) {
+            if (err == 1) fail_msg("parser failed");
+            if (err == 2) mem_fail();
+            expression_free(expression);
+            expression = NULL;
+        }
+        freesasa_yy_delete_buffer(state, scanner);
+        freesasa_yylex_destroy(scanner);
+    }
+
+    return expression;
+}
+
+static struct selection *
+selection_new(int n)
+{
+    struct selection *selection = malloc(sizeof(struct selection));
+    int i;
+
+    if (selection == NULL) {
+        mem_fail();
+    } else {
+        selection->size = n;
+        selection->atom = malloc(sizeof(int) * n);
+
+        if (selection->atom == NULL) {
+            free(selection);
+            mem_fail();
+            selection = NULL;
+        } else {
+            for (i = 0; i < n; ++i)
+                selection->atom[i] = 0;
+        }
+    }
+
+    return selection;
+}
+
+static void
+selection_free(struct selection *selection)
+{
+    if (selection) {
+        free(selection->atom);
+        free(selection);
+    }
+}
+
+/* Looks for exact match between the atom-name and expr->value */
+static int
+match_name(const freesasa_structure *structure,
+           const char *id,
+           int i)
+{
+    char atom[PDB_ATOM_NAME_STRL + 1];
+    sscanf(freesasa_structure_atom_name(structure, i), "%s", atom);
+    if (strcmp(atom, id) == 0)
+        return 1;
+    return 0;
+}
+
+/** Looks for match of strlen(expr->value) first characters of atom-name and expr->value */
+static int
+match_symbol(const freesasa_structure *structure,
+             const char *id,
+             int i)
+{
+    char symbol[PDB_ATOM_SYMBOL_STRL + 1];
+    sscanf(freesasa_structure_atom_symbol(structure, i), "%s", symbol);
+    if (strcmp(id, symbol) == 0) {
+        return 1;
+    }
+    return 0;
+}
+
+static int
+match_resn(const freesasa_structure *structure,
+           const char *id,
+           int i)
+{
+    char resn[PDB_ATOM_RES_NAME_STRL + 1];
+    sscanf(freesasa_structure_atom_res_name(structure, i), "%s", resn);
+    if (strcmp(resn, id) == 0)
+        return 1;
+    return 0;
+}
+
+static int
+match_resi(const freesasa_structure *structure,
+           const char *id,
+           int i)
+{
+    char resi[PDB_ATOM_RES_NUMBER_STRL + 1];
+    sscanf(freesasa_structure_atom_res_number(structure, i), "%s", resi);
+    if (strcmp(resi, id) == 0)
+        return 1;
+    return 0;
+}
+
+static int
+match_chain(const freesasa_structure *structure,
+            const char *id,
+            int i)
+{
+    return id[0] == freesasa_structure_atom_chain(structure, i);
+}
+
+static void
+select_id(expression_type parent_type,
+          struct selection *selection,
+          const freesasa_structure *structure,
+          const char *id)
+{
+    int count = 0, match, i;
+
+    assert(id);
+
+    for (i = 0; i < selection->size; ++i) {
+        match = 0;
+        switch (parent_type) {
+        case E_NAME:
+            match = match_name(structure, id, i);
+            break;
+        case E_SYMBOL:
+            match = match_symbol(structure, id, i);
+            break;
+        case E_RESN:
+            match = match_resn(structure, id, i);
+            break;
+        case E_RESI:
+            match = match_resi(structure, id, i);
+            break;
+        case E_CHAIN:
+            match = match_chain(structure, id, i);
+            break;
+        default:
+            assert(0);
+            break;
+        }
+        if (match) selection->atom[i] = 1;
+        count += match;
+    }
+    if (count == 0) freesasa_warn("Found no matches to %s '%s', typo?",
+                                  e_str(parent_type), id);
+}
+
+static int
+is_valid_id(int parent_type,
+            const expression *expr)
+{
+    int type, n, warn, i;
+    const char *val;
+
+    assert(expr->type == E_NUMBER || expr->type == E_ID);
+
+    type = expr->type;
+    val = expr->value;
+
+    switch (parent_type) {
+    case E_NAME:
+        if (strlen(val) > PDB_ATOM_NAME_STRL)
+            return freesasa_warn("select: %s: atom name '%s' invalid (string too long), "
+                                 "will be ignored",
+                                 e_str(parent_type), val);
+        break;
+    case E_SYMBOL:
+        if (type != E_ID)
+            return freesasa_warn("select: %s: '%s' invalid (should be 1 or 2 letters, 'C', 'N', 'SE', etc), "
+                                 "will be ignored",
+                                 e_str(parent_type), val);
+        if (strlen(val) > 2)
+            return freesasa_warn("select: %s: '%s' invalid (element names have 1 or 2 characters), "
+                                 "will be ignored",
+                                 e_str(parent_type), val);
+        break;
+    case E_RESN:
+        if (strlen(val) > PDB_ATOM_RES_NAME_STRL)
+            return freesasa_warn("select: %s: '%s' invalid (string too long), "
+                                 "will be ignored",
+                                 e_str(parent_type), val);
+        break;
+    case E_RESI:
+        if (type == E_ID) {
+            /* these should have format 1, 2, 345, etc or 12A, 12B, etc. */
+            n = strlen(val);
+            if (n > PDB_ATOM_RES_NUMBER_STRL) {
+                return freesasa_warn("select: %s: '%s' invalid (string too long), "
+                                     "will be ignored",
+                                     e_str(parent_type), val);
+            } else {
+                warn = 0;
+                if (n == 1) ++warn;
+                if (!warn && (toupper(val[n - 1]) < 'A' || toupper(val[n - 1]) > 'Z')) {
+                    ++warn;
+                }
+                for (i = 0; !warn && i < n - 1; ++i) {
+                    if (val[i] < '0' || val[i] > '9') {
+                        ++warn;
+                    }
+                }
+                if (warn) {
+                    return freesasa_warn("select: %s: '%s' invalid, should either be "
+                                         "number (1, 2, 3) or number with insertion code (1A, 1B, ...), "
+                                         "will be ignored",
+                                         e_str(parent_type), val);
+                }
+            }
+        } else if (type != E_NUMBER) {
+            return freesasa_warn("select: %s: '%s' invalid, will be ignored",
+                                 e_str(parent_type), val);
+        }
+        break;
+    case E_CHAIN:
+        if (strlen(val) > 1)
+            return freesasa_warn("select: %s: '%s' invalid (string too long), "
+                                 "will be ignored",
+                                 e_str(parent_type), val);
+        break;
+    default:
+        assert(0);
+        break;
+    }
+    return FREESASA_SUCCESS;
+}
+
+static int
+select_range(expression_type range_type,
+             expression_type parent_type,
+             struct selection *selection,
+             const freesasa_structure *structure,
+             const expression *left,
+             const expression *right)
+{
+    int lower, upper, i, j;
+
+    assert(range_type == E_RANGE || range_type == E_RANGE_OPEN_L || range_type == E_RANGE_OPEN_R);
+    assert(parent_type == E_RESI || parent_type == E_CHAIN);
+
+    if (parent_type == E_RESI) { /* residues have integer numbering */
+        if ((left && left->type != E_NUMBER) ||
+            (right && right->type != E_NUMBER)) {
+            return freesasa_warn("select: %s: range '%s-%s' invalid, needs to be two numbers, "
+                                 "will be ignored",
+                                 e_str(parent_type), left->value, right->value);
+        }
+    } else { /* chains can be numbered by both letters (common) and numbers (uncommon) */
+        if (left->type != right->type ||
+            (left->type == E_ID && (strlen(left->value) > 1 || strlen(right->value) > 1)))
+            return freesasa_warn("select: %s: range '%s-%s' invalid, should be two letters (A-C) or numbers (1-5), "
+                                 "will be ignored",
+                                 e_str(parent_type), left->value, right->value);
+    }
+    if (range_type == E_RANGE_OPEN_L) {
+        lower = atoi(freesasa_structure_atom_res_number(structure, 0));
+        upper = atoi(right->value);
+    } else if (range_type == E_RANGE_OPEN_R) {
+        lower = atoi(left->value);
+        upper = atoi(freesasa_structure_atom_res_number(structure, freesasa_structure_n(structure) - 1));
+    } else if (left->type == E_NUMBER) {
+        lower = atoi(left->value);
+        upper = atoi(right->value);
+    } else {
+        lower = (int)left->value[0];
+        upper = (int)right->value[0];
+    }
+    for (i = 0; i < selection->size; ++i) {
+        if (parent_type == E_RESI)
+            j = atoi(freesasa_structure_atom_res_number(structure, i));
+        else
+            j = (int)freesasa_structure_atom_chain(structure, i);
+        if (j >= lower && j <= upper)
+            selection->atom[i] = 1;
+    }
+    return FREESASA_SUCCESS;
+}
+
+static int
+select_list(expression_type parent_type,
+            struct selection *selection,
+            const freesasa_structure *structure,
+            const expression *expr)
+{
+    int resr, resl;
+    expression *left, *right;
+
+    if (expr == NULL)
+        return fail_msg("NULL expression");
+
+    left = expr->left;
+    right = expr->right;
+
+    switch (expr->type) {
+    case E_PLUS:
+        if (left == NULL || right == NULL)
+            return fail_msg("NULL expression");
+        resl = select_list(parent_type, selection, structure, left);
+        resr = select_list(parent_type, selection, structure, right);
+        if (resl == FREESASA_WARN || resr == FREESASA_WARN)
+            return FREESASA_WARN;
+        break;
+    case E_RANGE:
+        if (left == NULL || right == NULL)
+            return fail_msg("NULL expression");
+        return select_range(E_RANGE, parent_type, selection, structure, left, right);
+    case E_RANGE_OPEN_L:
+        if (left != NULL || right == NULL)
+            return fail_msg("NULL expression");
+        return select_range(E_RANGE_OPEN_L, parent_type, selection, structure, left, right);
+    case E_RANGE_OPEN_R:
+        if (left == NULL || right != NULL)
+            return fail_msg("NULL expression");
+        return select_range(E_RANGE_OPEN_R, parent_type, selection, structure, left, right);
+    case E_ID:
+    case E_NUMBER:
+        if (is_valid_id(parent_type, expr) == FREESASA_SUCCESS)
+            select_id(parent_type, selection, structure, expr->value);
+        else
+            return freesasa_warn("select: %s: '%s' invalid %s",
+                                 e_str(parent_type), expr->value, e_str(expr->type));
+        break;
+    default:
+        return freesasa_fail("select: parse error (expression: '%s %s')",
+                             e_str(parent_type), e_str(expr->type));
+    }
+    return FREESASA_SUCCESS;
+}
+
+static int
+selection_join(struct selection *target,
+               const struct selection *s1,
+               const struct selection *s2,
+               int type)
+{
+    int n, i;
+
+    if (s1 == NULL || s2 == NULL || target == NULL)
+        return fail_msg("trying to join NULL selections");
+
+    assert(s1->size == s2->size);
+    assert(s1->size == target->size);
+
+    n = target->size;
+
+    switch (type) {
+    case E_AND:
+        for (i = 0; i < n; ++i)
+            target->atom[i] = s1->atom[i] && s2->atom[i];
+        break;
+    case E_OR:
+        for (i = 0; i < n; ++i)
+            target->atom[i] = s1->atom[i] || s2->atom[i];
+        break;
+    default:
+        assert(0);
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+static int
+selection_not(struct selection *s)
+{
+    int i;
+
+    if (s == NULL) return fail_msg("NULL selection");
+
+    for (i = 0; i < s->size; ++i) {
+        s->atom[i] = !s->atom[i];
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+/* Called recursively, the selection is built as we cover the expression tree */
+static int
+select_atoms(struct selection *selection,
+             const expression *expr,
+             const freesasa_structure *structure)
+{
+    int warn = 0, err = 0, n, ret;
+    struct selection *sl, *sr;
+
+    assert(selection);
+    assert(structure);
+
+    n = selection->size;
+
+    /* this should only happen if memory allocation failed during parsing */
+    if (expr == NULL) return fail_msg("NULL expression");
+
+    switch (expr->type) {
+    case E_SELECTION:
+        assert(expr->value != NULL);
+        selection->name = expr->value;
+        return select_atoms(selection, expr->left, structure);
+        break;
+    case E_SYMBOL:
+    case E_NAME:
+    case E_RESN:
+    case E_RESI:
+    case E_CHAIN:
+        return select_list(expr->type, selection, structure, expr->left);
+        break;
+    case E_AND:
+    case E_OR: {
+        sl = selection_new(n);
+        sr = selection_new(n);
+
+        if (sl != NULL && sr != NULL) {
+            if ((ret = select_atoms(sl, expr->left, structure))) {
+                if (ret == FREESASA_WARN) ++warn;
+                if (ret == FREESASA_FAIL) ++err;
+            }
+            if ((ret = select_atoms(sr, expr->right, structure))) {
+                if (ret == FREESASA_WARN) ++warn;
+                if (ret == FREESASA_FAIL) ++err;
+            }
+            selection_join(selection, sl, sr, expr->type);
+        } else {
+            ++err;
+        }
+
+        selection_free(sl);
+        selection_free(sr);
+
+        if (err) return fail_msg("error joining selections");
+        break;
+    }
+    case E_NOT: {
+        ret = select_atoms(selection, expr->right, structure);
+        if (ret == FREESASA_WARN) ++warn;
+        if (ret == FREESASA_FAIL) return FREESASA_FAIL;
+        if (selection_not(selection)) return FREESASA_FAIL;
+        break;
+    }
+    case E_ID:
+    case E_NUMBER:
+    case E_PLUS:
+    case E_RANGE:
+        /* these four are handled by the RESN,SYMBOL,ETC */
+    default:
+        return fail_msg("parser error");
+    }
+    if (warn) return FREESASA_WARN;
+    return FREESASA_SUCCESS;
+}
+
+static int
+select_area_impl(const char *command,
+                 char *name,
+                 double *area,
+                 const freesasa_structure *structure,
+                 const freesasa_result *result)
+{
+    struct selection *selection = NULL;
+    struct expression *expression = NULL;
+    const int maxlen = FREESASA_MAX_SELECTION_NAME;
+    double sasa = 0;
+    int err = 0, warn = 0, n_atoms = 0, j, len;
+
+    assert(name);
+    assert(area);
+    assert(command);
+    assert(structure);
+    assert(result);
+    assert(freesasa_structure_n(structure) == result->n_atoms);
+
+    *area = 0;
+    name[0] = '\0';
+
+    expression = get_expression(command);
+    selection = selection_new(result->n_atoms);
+
+    if (selection == NULL) {
+        return fail_msg("");
+    }
+
+    if (expression != NULL && selection != NULL) {
+        switch (select_atoms(selection, expression, structure)) {
+        case FREESASA_FAIL:
+            err = 1;
+            break;
+        case FREESASA_WARN:
+            warn = 1; /* proceed with calculation, print warning later */
+        case FREESASA_SUCCESS: {
+            for (j = 0; j < selection->size; ++j) {
+                ++n_atoms;
+                sasa += selection->atom[j] * result->sasa[j];
+            }
+
+            *area = sasa;
+            len = strlen(selection->name);
+            strncpy(name, selection->name, maxlen);
+
+            if (len > maxlen) {
+                name[maxlen] = '\0';
+            } else {
+                name[len] = '\0';
+            }
+
+            break;
+        }
+        default:
+            assert(0);
+        }
+    } else {
+        err = 1;
+    }
+    selection_free(selection);
+    expression_free(expression);
+
+    if (err)
+        return fail_msg("problems parsing expression '%s'", command);
+    if (warn)
+        return freesasa_warn("in %s(): There were warnings", __func__);
+    return n_atoms;
+}
+
+freesasa_selection *
+freesasa_selection_alloc(const char *name, const char *command)
+{
+    freesasa_selection *selection = malloc(sizeof(freesasa_selection));
+
+    if (selection == NULL) {
+        mem_fail();
+        return NULL;
+    }
+
+    selection->name = NULL;
+    selection->command = NULL;
+    selection->area = 0;
+    selection->n_atoms = 0;
+
+    selection->name = strdup(name);
+    if (selection->name == NULL) {
+        mem_fail();
+        goto cleanup;
+    }
+
+    selection->command = strdup(command);
+    if (selection->command == NULL) {
+        mem_fail();
+        goto cleanup;
+    }
+
+    return selection;
+
+cleanup:
+    freesasa_selection_free(selection);
+    return NULL;
+}
+
+void freesasa_selection_free(freesasa_selection *selection)
+{
+    if (selection != NULL) {
+        free(selection->name);
+        free(selection->command);
+        free(selection);
+    }
+}
+
+freesasa_selection *
+freesasa_selection_clone(const freesasa_selection *src)
+{
+    freesasa_selection *cpy = freesasa_selection_alloc(src->name, src->command);
+
+    if (cpy == NULL) {
+        fail_msg("");
+        goto cleanup;
+    }
+
+    cpy->area = src->area;
+    cpy->n_atoms = src->n_atoms;
+
+    return cpy;
+
+cleanup:
+    freesasa_selection_free(cpy);
+    return NULL;
+}
+
+const char *
+freesasa_selection_name(const freesasa_selection *selection)
+{
+    assert(selection);
+    return selection->name;
+}
+
+const char *
+freesasa_selection_command(const freesasa_selection *selection)
+{
+    assert(selection);
+    return selection->command;
+}
+
+double
+freesasa_selection_area(const freesasa_selection *selection)
+{
+    assert(selection);
+    return selection->area;
+}
+
+freesasa_selection *
+freesasa_selection_new(const char *command,
+                       const freesasa_structure *structure,
+                       const freesasa_result *result)
+{
+    char name[FREESASA_MAX_SELECTION_NAME];
+    double area;
+    freesasa_selection *selection;
+    int n_atoms;
+
+    n_atoms = select_area_impl(command, name, &area, structure, result);
+
+    if (n_atoms == FREESASA_FAIL) {
+        fail_msg("");
+        return NULL;
+    }
+
+    selection = freesasa_selection_alloc(name, command);
+    if (selection == NULL) {
+        mem_fail();
+        return NULL;
+    }
+
+    selection->area = area;
+    selection->n_atoms = n_atoms;
+
+    return selection;
+}
+
+int freesasa_select_area(const char *command,
+                         char *name,
+                         double *area,
+                         const freesasa_structure *structure,
+                         const freesasa_result *result)
+{
+    int ret = select_area_impl(command, name, area, structure, result);
+    if (ret >= 0) return FREESASA_SUCCESS;
+    return ret;
+}
+
+int freesasa_selection_parse_error(expression *e,
+                                   yyscan_t scanner,
+                                   const char *msg)
+{
+    if (freesasa_get_verbosity() == FREESASA_V_DEBUG) print_expr(stderr, e, 0);
+    if (freesasa_get_verbosity() == FREESASA_V_NORMAL) fprintf(stderr, "\n");
+    return freesasa_fail(msg);
+}
+
+#if USE_CHECK
+#include <check.h>
+
+START_TEST(test_selection)
+{
+    struct selection *s1, *s2, *s3, *s4;
+    static const expression empty_expression = {
+        .right = NULL, .left = NULL, .value = NULL, .type = E_SELECTION};
+    freesasa_structure *structure = freesasa_structure_new();
+    expression r, l, e, e_symbol;
+
+    freesasa_structure_add_atom(structure, " CA ", "ALA", "   1", 'A', 0, 0, 0);
+    freesasa_structure_add_atom(structure, " O  ", "ALA", "   1", 'A', 10, 10, 10);
+
+    s1 = selection_new(freesasa_structure_n(structure));
+    s2 = selection_new(freesasa_structure_n(structure));
+    s3 = selection_new(freesasa_structure_n(structure));
+    s4 = selection_new(freesasa_structure_n(structure));
+
+    r = l = e = e_symbol = empty_expression;
+    e.type = E_PLUS;
+    e.right = &r;
+    e.left = &l;
+    r.value = "C";
+    r.type = E_ID;
+    l.value = "O";
+    l.type = E_ID;
+    e_symbol.type = E_SYMBOL;
+    e_symbol.left = &e;
+
+    /* select_symbol */
+    select_list(E_SYMBOL, s1, structure, &r);
+    ck_assert_int_eq(s1->atom[0], 1);
+    ck_assert_int_eq(s1->atom[1], 0);
+    select_list(E_SYMBOL, s2, structure, &l);
+    ck_assert_int_eq(s2->atom[0], 0);
+    ck_assert_int_eq(s2->atom[1], 1);
+    select_list(E_SYMBOL, s3, structure, &e);
+    ck_assert_int_eq(s3->atom[0], 1);
+    ck_assert_int_eq(s3->atom[1], 1);
+    select_atoms(s4, &e_symbol, structure);
+    ck_assert_int_eq(s4->atom[0], 1);
+    ck_assert_int_eq(s4->atom[1], 1);
+
+    /* selection_join */
+    selection_join(s3, s1, s2, E_AND);
+    ck_assert_int_eq(s3->atom[0], 0);
+    ck_assert_int_eq(s3->atom[1], 0);
+    selection_join(s3, s1, s2, E_OR);
+    ck_assert_int_eq(s3->atom[0], 1);
+    ck_assert_int_eq(s3->atom[1], 1);
+    freesasa_set_verbosity(FREESASA_V_SILENT);
+    ck_assert_int_eq(selection_join(NULL, s1, s2, E_OR), FREESASA_FAIL);
+    ck_assert_int_eq(selection_join(s3, NULL, s1, E_OR), FREESASA_FAIL);
+    ck_assert_int_eq(selection_join(NULL, NULL, NULL, E_OR), FREESASA_FAIL);
+
+    /* selection_not */
+    ck_assert_int_eq(selection_not(s3), FREESASA_SUCCESS);
+    ck_assert_int_eq(s3->atom[0], 0);
+    ck_assert_int_eq(s3->atom[1], 0);
+    ck_assert_int_eq(selection_not(NULL), FREESASA_FAIL);
+    freesasa_set_verbosity(FREESASA_V_NORMAL);
+}
+END_TEST
+
+START_TEST(test_expression)
+{
+    int i;
+    expression *e = get_expression("c1, symbol O+C");
+
+    ck_assert_ptr_ne(e, NULL);
+    ck_assert_int_eq(e->type, E_SELECTION);
+    ck_assert_ptr_ne(e->left, NULL);
+    ck_assert_ptr_eq(e->right, NULL);
+    ck_assert_str_eq(e->value, "c1");
+    ck_assert_int_eq(e->left->type, E_SYMBOL);
+    ck_assert_ptr_ne(e->left->left, NULL);
+    ck_assert_ptr_eq(e->left->right, NULL);
+    ck_assert_int_eq(e->left->left->type, E_PLUS);
+    ck_assert_int_eq(e->left->left->left->type, E_ID);
+    ck_assert_int_eq(e->left->left->right->type, E_ID);
+    ck_assert_str_eq(e->left->left->right->value, "C");
+    ck_assert_str_eq(e->left->left->left->value, "O");
+    for (i = E_SELECTION; i <= E_RANGE_OPEN_R; ++i) {
+        ck_assert_ptr_ne(e_str(i), NULL);
+    }
+    ck_assert_ptr_eq(e_str(E_RANGE_OPEN_R + 1), NULL);
+}
+END_TEST
+
+START_TEST(test_debug) /* this test just runs the debug output code to not get artificially low coverage */
+{
+    FILE *devnull = fopen("/dev/null", "w");
+    expression *e = get_expression("c1, symbol O+C");
+    print_expr(devnull, e, 0);
+}
+END_TEST
+
+struct selection selection_dummy = {.size = 1, .name = NULL, .atom = NULL};
+
+void *freesasa_selection_dummy_ptr = &selection_dummy;
+
+int freesasa_wrap_select_atoms(struct selection *selection,
+                               const expression *expr,
+                               const freesasa_structure *structure)
+{
+    return select_atoms(selection, expr, structure);
+}
+
+TCase *
+test_selection_static()
+{
+    TCase *tc = tcase_create("selection.c static");
+    tcase_add_test(tc, test_selection);
+    tcase_add_test(tc, test_expression);
+    tcase_add_test(tc, test_debug);
+
+    return tc;
+}
+
+#endif /* USE_CHECK */

.venv_haddock/include/site/python3.12/freesasa/selection.h

@@ -0,0 +1,49 @@
+#ifndef SELECTION_H
+#define SELECTION_H
+
+typedef enum { E_SELECTION,
+               E_SYMBOL,
+               E_NAME,
+               E_RESN,
+               E_RESI,
+               E_CHAIN,
+               E_ID,
+               E_NUMBER,
+               E_NEGNUM,
+               E_AND,
+               E_OR,
+               E_NOT,
+               E_PLUS,
+               E_RANGE,
+               E_RANGE_OPEN_L,
+               E_RANGE_OPEN_R } expression_type;
+
+typedef struct expression {
+    struct expression *left;
+    struct expression *right;
+    expression_type type;
+    char *value;
+} expression;
+
+/** Create an atomic value E_ID or E_NUMBER */
+expression *
+freesasa_selection_atom(expression_type type,
+                        const char *val);
+
+/** Create a top level selection (E_SELECTION) */
+expression *
+freesasa_selection_create(expression *selection,
+                          const char *id);
+
+/** Create a property selector (E_SYMBOL, E_NAME, E_RESN, E_RESI or E_CHAIN) */
+expression *
+freesasa_selection_selector(expression_type type,
+                            expression *list);
+
+/** Create an operation (E_AND, E_OR, E_NOT, E_PLUS or E_RANGE) */
+expression *
+freesasa_selection_operation(expression_type type,
+                             expression *left,
+                             expression *right);
+
+#endif /* SELECTION_H */

.venv_haddock/include/site/python3.12/freesasa/structure.c

@@ -0,0 +1,1243 @@
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <assert.h>
+#include <stdlib.h>
+
+#include "classifier.h"
+#include "coord.h"
+#include "freesasa_internal.h"
+#include "pdb.h"
+
+/**
+   This file contains the functions that turn lines in PDB files to
+   atom records. It's all pretty messy because one needs to keep track
+   of when a new chain/new residue is encountered, and skip atoms that
+   are duplicates (only first of alt coordinates are used). It is both
+   possible to add atoms one by one, or by reading a whole file at
+   once, and the user can supply some options about what to do when
+   encountering atoms that are not recognized, whether to include
+   hydrogrens, hetatm, etc. The current implementation results in a
+   rather convoluted logic, that is difficult to maintain, debug and
+   extend.
+
+   TODO: Refactor.
+*/
+#define ATOMS_CHUNK 512
+#define RESIDUES_CHUNK 64
+#define CHAINS_CHUNK 64
+
+struct atom {
+    char *res_name;
+    char *res_number;
+    char *atom_name;
+    char *symbol;
+    char *line;
+    int res_index;
+    char chain_label;
+    freesasa_atom_class the_class;
+};
+
+static const struct atom empty_atom = {
+    NULL,                 /* res_name */
+    NULL,                 /* res_number */
+    NULL,                 /* atom_name */
+    NULL,                 /* symbol */
+    NULL,                 /* line */
+    -1,                   /* res_index */
+    '\0',                 /* chain_label */
+    FREESASA_ATOM_UNKNOWN /* the_class */
+};
+
+struct atoms {
+    int n;
+    int n_alloc;
+    struct atom **atom;
+    double *radius;
+};
+
+struct residues {
+    int n;
+    int n_alloc;
+    int *first_atom;
+    freesasa_nodearea **reference_area;
+};
+
+struct chains {
+    int n;
+    int n_alloc;
+    char *labels;    /* all chain labels found (as string) */
+    int *first_atom; /* first atom of each chain */
+};
+
+struct freesasa_structure {
+    struct atoms atoms;
+    struct residues residues;
+    struct chains chains;
+    char *classifier_name;
+    coord_t *xyz;
+    int model; /* model number */
+    size_t cif_ref;
+    void (*release_cif_ref)(size_t);
+};
+
+static int
+guess_symbol(char *symbol,
+             const char *name);
+
+static void
+atom_free(struct atom *a)
+{
+    if (a != NULL) {
+        free(a->res_name);
+        free(a->res_number);
+        free(a->atom_name);
+        free(a->symbol);
+        free(a->line);
+        free(a);
+    }
+}
+
+struct atoms
+atoms_init(void)
+{
+    struct atoms atoms;
+    atoms.n = 0;
+    atoms.n_alloc = 0;
+    atoms.atom = NULL;
+    atoms.radius = NULL;
+    return atoms;
+}
+
+/* Allocates memory in chunks, ticks up atoms->n if allocation successful */
+static int
+atoms_alloc(struct atoms *atoms)
+{
+    int i, new_size;
+    void *aa, *ar;
+
+    assert(atoms);
+    assert(atoms->n <= atoms->n_alloc);
+
+    if (atoms->n == atoms->n_alloc) {
+        new_size = atoms->n_alloc + ATOMS_CHUNK;
+        aa = atoms->atom;
+        ar = atoms->radius;
+
+        atoms->atom = realloc(atoms->atom, sizeof(struct atom *) * new_size);
+        if (atoms->atom == NULL) {
+            atoms->atom = aa;
+            return mem_fail();
+        }
+
+        for (i = atoms->n_alloc; i < new_size; ++i) {
+            atoms->atom[i] = NULL;
+        }
+
+        atoms->radius = realloc(atoms->radius, sizeof(double) * new_size);
+        if (atoms->radius == NULL) {
+            atoms->radius = ar;
+            return mem_fail();
+        }
+
+        atoms->n_alloc = new_size;
+    }
+    ++atoms->n;
+    return FREESASA_SUCCESS;
+}
+
+static void
+atoms_dealloc(struct atoms *atoms)
+{
+    int i;
+    struct atom **atom;
+
+    if (atoms) {
+        atom = atoms->atom;
+        if (atom) {
+            for (i = 0; i < atoms->n; ++i)
+                if (atom[i]) atom_free(atom[i]);
+            free(atom);
+        }
+        free(atoms->radius);
+        *atoms = atoms_init();
+    }
+}
+
+static struct atom *
+atom_new(const char *residue_name,
+         const char *residue_number,
+         const char *atom_name,
+         const char *symbol,
+         char chain_label)
+{
+    struct atom *a = malloc(sizeof(struct atom));
+    if (a == NULL) goto memerr;
+
+    *a = empty_atom;
+
+    a->line = NULL;
+    a->chain_label = chain_label;
+    a->res_index = -1;
+
+    a->res_name = strdup(residue_name);
+    a->res_number = strdup(residue_number);
+    a->atom_name = strdup(atom_name);
+    a->symbol = strdup(symbol);
+    a->the_class = FREESASA_ATOM_UNKNOWN;
+
+    if (!a->res_name || !a->res_number || !a->atom_name ||
+        !a->symbol) {
+        goto memerr;
+    }
+
+    return a;
+
+memerr:
+    mem_fail();
+    atom_free(a);
+    return NULL;
+}
+
+static struct atom *
+atom_new_from_line(const char *line,
+                   char *alt_label)
+{
+    char aname[PDB_ATOM_NAME_STRL + 1], rname[PDB_ATOM_RES_NAME_STRL + 1],
+        rnumber[PDB_ATOM_RES_NUMBER_STRL + 1], symbol[PDB_ATOM_SYMBOL_STRL + 1];
+    int flag;
+    struct atom *a;
+
+    assert(line);
+
+    if (alt_label) *alt_label = freesasa_pdb_get_alt_coord_label(line);
+
+    freesasa_pdb_get_atom_name(aname, line);
+    freesasa_pdb_get_res_name(rname, line);
+    freesasa_pdb_get_res_number(rnumber, line);
+
+    flag = freesasa_pdb_get_symbol(symbol, line);
+    if (flag == FREESASA_FAIL || (symbol[0] == ' ' && symbol[1] == ' ')) {
+        guess_symbol(symbol, aname);
+    }
+
+    a = atom_new(rname, rnumber, aname, symbol, freesasa_pdb_get_chain_label(line));
+
+    if (a != NULL) {
+        a->line = strdup(line);
+        if (a->line == NULL) {
+            mem_fail();
+            atom_free(a);
+            a = NULL;
+        }
+    }
+
+    return a;
+}
+
+static struct residues
+residues_init(void)
+{
+    struct residues res;
+
+    res.n = 0;
+    res.n_alloc = 0;
+    res.first_atom = 0;
+    res.reference_area = 0;
+
+    return res;
+}
+
+static int
+residues_alloc(struct residues *residues)
+{
+    int new_size;
+    void *fa, *ra;
+
+    assert(residues);
+    assert(residues->n <= residues->n_alloc);
+
+    if (residues->n == residues->n_alloc) {
+        new_size = residues->n_alloc + RESIDUES_CHUNK;
+        fa = residues->first_atom;
+        ra = residues->reference_area;
+
+        residues->first_atom = realloc(residues->first_atom,
+                                       sizeof(int) * new_size);
+        if (residues->first_atom == NULL) {
+            residues->first_atom = fa;
+            return mem_fail();
+        }
+
+        residues->reference_area = realloc(residues->reference_area,
+                                           sizeof(freesasa_nodearea *) * new_size);
+        if (residues->reference_area == NULL) {
+            residues->reference_area = ra;
+            return mem_fail();
+        }
+
+        residues->n_alloc = new_size;
+    }
+    ++residues->n;
+    return FREESASA_SUCCESS;
+}
+
+static void
+residues_dealloc(struct residues *residues)
+{
+    int i;
+
+    if (residues) {
+        free(residues->first_atom);
+        if (residues->reference_area) {
+            for (i = 0; i < residues->n; ++i) {
+                free(residues->reference_area[i]);
+            }
+        }
+        free(residues->reference_area);
+        *residues = residues_init();
+    }
+}
+
+static struct chains
+chains_init(void)
+{
+    struct chains ch;
+
+    ch.n = 0;
+    ch.n_alloc = 0;
+    ch.first_atom = NULL;
+    ch.labels = NULL;
+
+    return ch;
+}
+
+static int
+chains_alloc(struct chains *chains)
+{
+    int new_size;
+    void *fa, *lbl;
+
+    assert(chains);
+    assert(chains->n <= chains->n_alloc);
+
+    if (chains->n == chains->n_alloc) {
+        new_size = chains->n_alloc + CHAINS_CHUNK;
+        fa = chains->first_atom;
+        lbl = chains->labels;
+
+        chains->first_atom = realloc(chains->first_atom,
+                                     sizeof(int) * new_size);
+        if (chains->first_atom == NULL) {
+            chains->first_atom = fa;
+            return mem_fail();
+        }
+
+        chains->labels = realloc(chains->labels, new_size + 1);
+        if (chains->labels == NULL) {
+            chains->labels = lbl;
+            return mem_fail();
+        }
+
+        chains->n_alloc = new_size;
+    }
+    ++chains->n;
+    return FREESASA_SUCCESS;
+}
+
+static void
+chains_dealloc(struct chains *chains)
+{
+    if (chains) {
+        free(chains->first_atom);
+        free(chains->labels);
+        *chains = chains_init();
+    }
+}
+
+freesasa_structure *
+freesasa_structure_new(void)
+{
+    freesasa_structure *s = malloc(sizeof(freesasa_structure));
+
+    if (s == NULL) goto memerr;
+
+    s->atoms = atoms_init();
+    s->residues = residues_init();
+    s->chains = chains_init();
+    s->xyz = freesasa_coord_new();
+    s->model = 1;
+    s->classifier_name = NULL;
+    s->cif_ref = 0;
+    s->release_cif_ref = 0;
+
+    if (s->xyz == NULL) goto memerr;
+
+    return s;
+memerr:
+    freesasa_structure_free(s);
+    mem_fail();
+    return NULL;
+}
+
+void freesasa_structure_free(freesasa_structure *s)
+{
+    if (s != NULL) {
+        atoms_dealloc(&s->atoms);
+        residues_dealloc(&s->residues);
+        chains_dealloc(&s->chains);
+
+        if (s->xyz != NULL) {
+            freesasa_coord_free(s->xyz);
+        }
+
+        free(s->classifier_name);
+
+        if (s->cif_ref > 0 && s->release_cif_ref != NULL) {
+            s->release_cif_ref(s->cif_ref);
+        }
+
+        free(s);
+    }
+}
+
+/**
+    This function is called when either the symbol field is missing
+    from an ATOM record, or when an atom is added directly using
+    freesasa_structure_add_atom() or
+    freesasa_structure_add_atom_wopt(). The symbol is in turn only
+    used if the atom cannot be recognized by the classifier.
+*/
+static int
+guess_symbol(char *symbol,
+             const char *name)
+{
+    /* if the first position is empty, or a number, assume that it is
+       a one letter element e.g. " C ", or "1H " */
+    if (name[0] == ' ' || (name[0] >= '1' && name[0] <= '9')) {
+        symbol[0] = ' ';
+        symbol[1] = name[1];
+        symbol[2] = '\0';
+    } else {
+        /* if the string has padding to the right, it's a
+           two-letter element, e.g. "FE  " */
+        if (name[3] == ' ') {
+            strncpy(symbol, name, 2);
+            symbol[2] = '\0';
+        } else {
+            /* If it's a four-letter string, it's hard to say,
+               assume only the first letter signifies the element */
+            symbol[0] = ' ';
+            symbol[1] = name[0];
+            symbol[2] = '\0';
+            return freesasa_warn("guessing that atom '%s' is symbol '%s'",
+                                 name, symbol);
+        }
+    }
+    return FREESASA_SUCCESS;
+}
+static int
+structure_add_chain(freesasa_structure *s,
+                    char chain_label,
+                    int i_latest_atom)
+{
+    int n;
+    if (s->chains.n == 0 || strchr(s->chains.labels, chain_label) == NULL) {
+
+        if (chains_alloc(&s->chains) == FREESASA_FAIL)
+            return fail_msg("");
+
+        n = s->chains.n;
+        s->chains.labels[n - 1] = chain_label;
+        s->chains.labels[n] = '\0';
+
+        assert(strlen(s->chains.labels) == s->chains.n);
+
+        s->chains.first_atom[n - 1] = i_latest_atom;
+    }
+    return FREESASA_SUCCESS;
+}
+
+static int
+structure_add_residue(freesasa_structure *s,
+                      const freesasa_classifier *classifier,
+                      const struct atom *a,
+                      int i_latest_atom)
+{
+    int n = s->residues.n + 1;
+    const freesasa_nodearea *reference = NULL;
+
+    /* register a new residue if it's the first atom, or if the
+       residue number or chain label of the current atom is different
+       from the previous one */
+    if (!(s->residues.n == 0 ||
+          (i_latest_atom > 0 &&
+           (strcmp(a->res_number, s->atoms.atom[i_latest_atom - 1]->res_number) ||
+            a->chain_label != s->atoms.atom[i_latest_atom - 1]->chain_label)))) {
+        return FREESASA_SUCCESS;
+    }
+
+    if (residues_alloc(&s->residues) == FREESASA_FAIL) {
+        return fail_msg("");
+    }
+    s->residues.first_atom[n - 1] = i_latest_atom;
+
+    s->residues.reference_area[n - 1] = NULL;
+    reference = freesasa_classifier_residue_reference(classifier, a->res_name);
+    if (reference != NULL) {
+        s->residues.reference_area[n - 1] = malloc(sizeof(freesasa_nodearea));
+        if (s->residues.reference_area[n - 1] == NULL)
+            return mem_fail();
+        *s->residues.reference_area[n - 1] = *reference;
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+/**
+    Get the radius of an atom, and fail, warn and/or guess depending
+    on the options.
+ */
+static int
+structure_check_atom_radius(double *radius,
+                            struct atom *a,
+                            const freesasa_classifier *classifier,
+                            int options)
+{
+    *radius = freesasa_classifier_radius(classifier, a->res_name, a->atom_name);
+    if (*radius < 0) {
+        if (options & FREESASA_HALT_AT_UNKNOWN) {
+            return fail_msg("atom '%s %s' unknown",
+                            a->res_name, a->atom_name);
+        } else if (options & FREESASA_SKIP_UNKNOWN) {
+            return freesasa_warn("skipping unknown atom '%s %s'",
+                                 a->res_name, a->atom_name, a->symbol, *radius);
+        } else {
+            *radius = freesasa_guess_radius(a->symbol);
+            if (*radius < 0) {
+                *radius = +0.;
+                freesasa_warn("atom '%s %s' unknown and "
+                              "can't guess radius of symbol '%s', "
+                              "assigning radius 0 A",
+                              a->res_name, a->atom_name, a->symbol);
+            } else {
+                freesasa_warn("atom '%s %s' unknown, guessing element is '%s', "
+                              "and radius %.3f A",
+                              a->res_name, a->atom_name, a->symbol, *radius);
+            }
+            /* do not return FREESASA_WARN here, because we will keep the atom */
+        }
+    }
+    return FREESASA_SUCCESS;
+}
+
+static int
+structure_register_classifier(freesasa_structure *structure,
+                              const freesasa_classifier *classifier)
+{
+    if (structure->classifier_name == NULL) {
+        structure->classifier_name = strdup(freesasa_classifier_name(classifier));
+        if (structure->classifier_name == NULL) {
+            return mem_fail();
+        }
+    } else if (strcmp(structure->classifier_name, freesasa_classifier_name(classifier)) != 0) {
+        structure->classifier_name = strdup(FREESASA_CONFLICTING_CLASSIFIERS);
+        if (structure->classifier_name == NULL) {
+            return mem_fail();
+        }
+        return FREESASA_WARN;
+    }
+
+    return FREESASA_SUCCESS;
+}
+
+/**
+   Adds an atom to the structure using the rules specified by
+   'options'. If it includes FREESASA_RADIUS_FROM_* a dummy radius is
+   assigned and the caller is expected to replace it with a correct
+   radius later.
+
+   The atom a should be a pointer to a heap address, this will not be cloned.
+ */
+static int
+structure_add_atom(freesasa_structure *structure,
+                   struct atom *atom,
+                   double *xyz,
+                   const freesasa_classifier *classifier,
+                   int options)
+{
+    int na, ret;
+    double r;
+
+    assert(structure);
+    assert(atom);
+    assert(xyz);
+
+    /* let the stricter option override if both are specified */
+    if (options & FREESASA_SKIP_UNKNOWN && options & FREESASA_HALT_AT_UNKNOWN)
+        options &= ~FREESASA_SKIP_UNKNOWN;
+
+    if (classifier == NULL) {
+        classifier = &freesasa_default_classifier;
+    }
+    structure_register_classifier(structure, classifier);
+
+    /* calculate radius and check if we should keep the atom (based on options) */
+    if (options & FREESASA_RADIUS_FROM_OCCUPANCY) {
+        r = 1; /* fix it later */
+    } else {
+        ret = structure_check_atom_radius(&r, atom, classifier, options);
+        if (ret == FREESASA_FAIL) return fail_msg("halting at unknown atom");
+        if (ret == FREESASA_WARN) return FREESASA_WARN;
+    }
+    assert(r >= 0);
+
+    /* If it's a keeper, allocate memory */
+    if (atoms_alloc(&structure->atoms) == FREESASA_FAIL)
+        return fail_msg("");
+    na = structure->atoms.n;
+
+    /* Store coordinates */
+    if (freesasa_coord_append(structure->xyz, xyz, 1) == FREESASA_FAIL)
+        return mem_fail();
+
+    /* Check if this is a new chain and if so add it */
+    if (structure_add_chain(structure, atom->chain_label, na - 1) == FREESASA_FAIL)
+        return mem_fail();
+
+    /* Check if this is a new residue, and if so add it */
+    if (structure_add_residue(structure, classifier, atom, na - 1) == FREESASA_FAIL)
+        return mem_fail();
+
+    atom->the_class = freesasa_classifier_class(classifier, atom->res_name, atom->atom_name);
+    atom->res_index = structure->residues.n - 1;
+    structure->atoms.radius[na - 1] = r;
+    structure->atoms.atom[na - 1] = atom;
+
+    return FREESASA_SUCCESS;
+}
+
+/**
+    Handles the reading of PDB-files, returns NULL if problems reading
+    or input or malloc failure. Error-messages should explain what
+    went wrong.
+ */
+static freesasa_structure *
+from_pdb_impl(FILE *pdb_file,
+              struct file_range it,
+              const freesasa_classifier *classifier,
+              int options)
+{
+    char line[PDB_MAX_LINE_STRL];
+    char alt, the_alt = ' ';
+    double v[3], r;
+    int ret;
+    struct atom *a = NULL;
+    freesasa_structure *s = freesasa_structure_new();
+
+    assert(pdb_file);
+
+    if (s == NULL) return NULL;
+
+    fseek(pdb_file, it.begin, SEEK_SET);
+
+    while (fgets(line, PDB_MAX_LINE_STRL, pdb_file) != NULL && ftell(pdb_file) <= it.end) {
+
+        if (strncmp("ATOM", line, 4) == 0 || ((options & FREESASA_INCLUDE_HETATM) &&
+                                              (strncmp("HETATM", line, 6) == 0))) {
+            if (freesasa_pdb_ishydrogen(line) &&
+                !(options & FREESASA_INCLUDE_HYDROGEN))
+                continue;
+
+            a = atom_new_from_line(line, &alt);
+            if (a == NULL)
+                goto cleanup;
+
+            if ((alt != ' ' && the_alt == ' ') || (alt == ' '))
+                the_alt = alt;
+            else if (alt != ' ' && alt != the_alt) {
+                atom_free(a);
+                a = NULL;
+                continue;
+            }
+
+            ret = freesasa_pdb_get_coord(v, line);
+            if (ret == FREESASA_FAIL)
+                goto cleanup;
+
+            ret = structure_add_atom(s, a, v, classifier, options);
+            if (ret == FREESASA_FAIL) {
+                goto cleanup;
+            } else if (ret == FREESASA_WARN) {
+                atom_free(a);
+                a = NULL;
+                continue;
+            }
+
+            if (options & FREESASA_RADIUS_FROM_OCCUPANCY) {
+                ret = freesasa_pdb_get_occupancy(&r, line);
+                if (ret == FREESASA_FAIL)
+                    goto cleanup;
+                s->atoms.radius[s->atoms.n - 1] = r;
+            }
+        }
+
+        if (!(options & FREESASA_JOIN_MODELS)) {
+            if (strncmp("MODEL", line, 5) == 0) sscanf(line + 10, "%d", &s->model);
+            if (strncmp("ENDMDL", line, 6) == 0) break;
+        }
+    }
+
+    if (s->atoms.n == 0) {
+        fail_msg("input had no valid ATOM or HETATM lines");
+        goto cleanup;
+    }
+
+    return s;
+
+cleanup:
+    fail_msg("");
+    atom_free(a);
+    freesasa_structure_free(s);
+    return NULL;
+}
+
+static int
+structure_add_atom_wopt_impl(freesasa_structure *structure,
+                             const char *atom_name,
+                             const char *residue_name,
+                             const char *residue_number,
+                             const char *symbol,
+                             char chain_label,
+                             double x, double y, double z,
+                             const freesasa_classifier *classifier,
+                             int options)
+{
+    struct atom *a;
+    char my_symbol[PDB_ATOM_SYMBOL_STRL + 1];
+    double v[3] = {x, y, z};
+    int ret, warn = 0;
+
+    assert(structure);
+    assert(atom_name);
+    assert(residue_name);
+    assert(residue_number);
+
+    /* this option can not be used here, and needs to be unset */
+    options &= ~FREESASA_RADIUS_FROM_OCCUPANCY;
+
+    if (symbol != NULL) {
+        strncpy(my_symbol, symbol, sizeof(my_symbol));
+    } else if (guess_symbol(my_symbol, atom_name) == FREESASA_WARN &&
+               options & FREESASA_SKIP_UNKNOWN) {
+        ++warn;
+    }
+
+    a = atom_new(residue_name, residue_number, atom_name, my_symbol, chain_label);
+    if (a == NULL) return mem_fail();
+
+    ret = structure_add_atom(structure, a, v, classifier, options);
+
+    if (ret == FREESASA_FAIL ||
+        (ret == FREESASA_WARN && options & FREESASA_SKIP_UNKNOWN))
+        atom_free(a);
+
+    if (!ret && warn) return FREESASA_WARN;
+
+    return ret;
+}
+
+int freesasa_structure_add_atom_wopt(freesasa_structure *structure,
+                                     const char *atom_name,
+                                     const char *residue_name,
+                                     const char *residue_number,
+                                     char chain_label,
+                                     double x, double y, double z,
+                                     const freesasa_classifier *classifier,
+                                     int options)
+{
+    return structure_add_atom_wopt_impl(structure, atom_name, residue_name, residue_number, NULL,
+                                        chain_label, x, y, z, classifier, options);
+}
+int freesasa_structure_add_atom(freesasa_structure *structure,
+                                const char *atom_name,
+                                const char *residue_name,
+                                const char *residue_number,
+                                char chain_label,
+                                double x, double y, double z)
+{
+    return structure_add_atom_wopt_impl(structure, atom_name, residue_name, residue_number, NULL,
+                                        chain_label, x, y, z, NULL, 0);
+}
+
+int freesasa_structure_add_cif_atom(freesasa_structure *structure,
+                                    freesasa_cif_atom *atom,
+                                    const freesasa_classifier *classifier,
+                                    int options)
+{
+    char res_number[PDB_ATOM_RES_NUMBER_STRL + 1];
+
+    if (atom->pdbx_PDB_ins_code[0] != '?') {
+        snprintf(res_number, sizeof res_number, "%s%c", atom->auth_seq_id, atom->pdbx_PDB_ins_code[0]);
+    } else {
+        snprintf(res_number, sizeof res_number, "%s", atom->auth_seq_id);
+    }
+
+    return structure_add_atom_wopt_impl(structure, atom->auth_atom_id, atom->auth_comp_id,
+                                        res_number, atom->type_symbol, atom->auth_asym_id,
+                                        atom->Cartn_x, atom->Cartn_y, atom->Cartn_z,
+                                        classifier, options);
+}
+
+freesasa_structure *
+freesasa_structure_from_pdb(FILE *pdb_file,
+                            const freesasa_classifier *classifier,
+                            int options)
+{
+    assert(pdb_file);
+    return from_pdb_impl(pdb_file, freesasa_whole_file(pdb_file),
+                         classifier, options);
+}
+
+freesasa_structure **
+freesasa_structure_array(FILE *pdb,
+                         int *n,
+                         const freesasa_classifier *classifier,
+                         int options)
+{
+    struct file_range *models = NULL, *chains = NULL;
+    struct file_range whole_file;
+    int n_models = 0, n_chains = 0, j0, n_new_chains, i, j;
+    freesasa_structure **ss = NULL, **ssb;
+
+    assert(pdb);
+    assert(n);
+
+    if (!(options & FREESASA_SEPARATE_MODELS ||
+          options & FREESASA_SEPARATE_CHAINS)) {
+        fail_msg("options need to specify at least one of FREESASA_SEPARATE_CHAINS "
+                 "and FREESASA_SEPARATE_MODELS");
+        return NULL;
+    }
+
+    whole_file = freesasa_whole_file(pdb);
+    n_models = freesasa_pdb_get_models(pdb, &models);
+
+    if (n_models == FREESASA_FAIL) {
+        fail_msg("problems reading PDB-file");
+        return NULL;
+    }
+    if (n_models == 0) {
+        models = &whole_file;
+        n_models = 1;
+    }
+
+    /* only keep first model if option not provided */
+    if (!(options & FREESASA_SEPARATE_MODELS)) n_models = 1;
+
+    /* for each model read chains if requested */
+    if (options & FREESASA_SEPARATE_CHAINS) {
+        for (i = 0; i < n_models; ++i) {
+            chains = NULL;
+            n_new_chains = freesasa_pdb_get_chains(pdb, models[i], &chains, options);
+
+            if (n_new_chains == FREESASA_FAIL) goto cleanup;
+            if (n_new_chains == 0) {
+                freesasa_warn("in %s(): no chains found (in model %d)", __func__, i + 1);
+                continue;
+            }
+
+            ssb = ss;
+            ss = realloc(ss, sizeof(freesasa_structure *) * (n_chains + n_new_chains));
+
+            if (!ss) {
+                ss = ssb;
+                mem_fail();
+                goto cleanup;
+            }
+
+            j0 = n_chains;
+            n_chains += n_new_chains;
+
+            for (j = 0; j < n_new_chains; ++j)
+                ss[j0 + j] = NULL;
+
+            for (j = 0; j < n_new_chains; ++j) {
+                ss[j0 + j] = from_pdb_impl(pdb, chains[j], classifier, options);
+                if (ss[j0 + j] == NULL) goto cleanup;
+                ss[j0 + j]->model = i + 1;
+            }
+
+            free(chains);
+        }
+        *n = n_chains;
+    } else {
+        ss = malloc(sizeof(freesasa_structure *) * n_models);
+        if (!ss) {
+            mem_fail();
+            goto cleanup;
+        }
+
+        for (i = 0; i < n_models; ++i)
+            ss[i] = NULL;
+        *n = n_models;
+
+        for (i = 0; i < n_models; ++i) {
+            ss[i] = from_pdb_impl(pdb, models[i], classifier, options);
+            if (ss[i] == NULL) goto cleanup;
+            ss[i]->model = i + 1;
+        }
+    }
+
+    if (*n == 0) goto cleanup;
+
+    if (models != &whole_file) free(models);
+
+    return ss;
+
+cleanup:
+    if (ss)
+        for (i = 0; i < *n; ++i)
+            freesasa_structure_free(ss[i]);
+    if (models != &whole_file) free(models);
+    free(chains);
+    *n = 0;
+    free(ss);
+    return NULL;
+}
+
+freesasa_structure *
+freesasa_structure_get_chains(const freesasa_structure *structure,
+                              const char *chains,
+                              const freesasa_classifier *classifier,
+                              int options)
+{
+    freesasa_structure *new_s;
+    struct atom *ai;
+    int i, res;
+    char c;
+    const double *v;
+
+    assert(structure);
+    if (strlen(chains) == 0) return NULL;
+
+    new_s = freesasa_structure_new();
+
+    if (!new_s) {
+        mem_fail();
+        return NULL;
+    }
+
+    new_s->model = structure->model;
+
+    for (i = 0; i < structure->atoms.n; ++i) {
+        ai = structure->atoms.atom[i];
+        c = ai->chain_label;
+        if (strchr(chains, c) != NULL) {
+            v = freesasa_coord_i(structure->xyz, i);
+            res = structure_add_atom_wopt_impl(new_s, ai->atom_name,
+                                               ai->res_name, ai->res_number, ai->symbol,
+                                               c, v[0], v[1], v[2], classifier, options);
+            if (res == FREESASA_FAIL) {
+                fail_msg("");
+                goto cleanup;
+            }
+        }
+    }
+
+    /* the following two tests could have been done by comparing the
+       chain-strings before the loop, but this logic is simpler. */
+    if (new_s->atoms.n == 0) {
+        goto cleanup;
+    }
+    if (strlen(new_s->chains.labels) != strlen(chains)) {
+        fail_msg("structure has chains '%s', but '%s' requested",
+                 structure->chains.labels, chains);
+        goto cleanup;
+    }
+
+    return new_s;
+
+cleanup:
+    freesasa_structure_free(new_s);
+    return NULL;
+}
+
+const char *
+freesasa_structure_chain_labels(const freesasa_structure *structure)
+{
+    assert(structure);
+    return structure->chains.labels;
+}
+
+const coord_t *
+freesasa_structure_xyz(const freesasa_structure *structure)
+{
+    assert(structure);
+    return structure->xyz;
+}
+
+int freesasa_structure_n(const freesasa_structure *structure)
+{
+    assert(structure);
+    return structure->atoms.n;
+}
+
+int freesasa_structure_n_residues(const freesasa_structure *structure)
+{
+    assert(structure);
+    return structure->residues.n;
+}
+
+const char *
+freesasa_structure_atom_name(const freesasa_structure *structure,
+                             int i)
+{
+    assert(structure);
+    assert(i < structure->atoms.n && i >= 0);
+    return structure->atoms.atom[i]->atom_name;
+}
+
+const char *
+freesasa_structure_atom_res_name(const freesasa_structure *structure,
+                                 int i)
+{
+    assert(structure);
+    assert(i < structure->atoms.n && i >= 0);
+    return structure->atoms.atom[i]->res_name;
+}
+
+const char *
+freesasa_structure_atom_res_number(const freesasa_structure *structure,
+                                   int i)
+{
+    assert(structure);
+    assert(i < structure->atoms.n && i >= 0);
+    return structure->atoms.atom[i]->res_number;
+}
+
+char freesasa_structure_atom_chain(const freesasa_structure *structure,
+                                   int i)
+{
+    assert(structure);
+    assert(i < structure->atoms.n && i >= 0);
+    return structure->atoms.atom[i]->chain_label;
+}
+const char *
+freesasa_structure_atom_symbol(const freesasa_structure *structure,
+                               int i)
+{
+    assert(structure);
+    assert(i < structure->atoms.n && i >= 0);
+    return structure->atoms.atom[i]->symbol;
+}
+
+double
+freesasa_structure_atom_radius(const freesasa_structure *structure,
+                               int i)
+{
+    assert(structure);
+    assert(i < structure->atoms.n && i >= 0);
+    return structure->atoms.radius[i];
+}
+
+void freesasa_structure_atom_set_radius(freesasa_structure *structure,
+                                        int i,
+                                        double radius)
+{
+    assert(structure);
+    assert(i < structure->atoms.n && i >= 0);
+    structure->atoms.radius[i] = radius;
+}
+
+freesasa_atom_class
+freesasa_structure_atom_class(const freesasa_structure *structure,
+                              int i)
+{
+    assert(structure);
+    assert(i < structure->atoms.n && i >= 0);
+    return structure->atoms.atom[i]->the_class;
+}
+
+const char *
+freesasa_structure_atom_pdb_line(const freesasa_structure *structure,
+                                 int i)
+{
+    assert(structure);
+    assert(i < structure->atoms.n && i >= 0);
+    return structure->atoms.atom[i]->line;
+}
+const freesasa_nodearea *
+freesasa_structure_residue_reference(const freesasa_structure *structure,
+                                     int r_i)
+{
+    assert(structure);
+    assert(r_i >= 0 && r_i < structure->residues.n);
+
+    return structure->residues.reference_area[r_i];
+}
+int freesasa_structure_residue_atoms(const freesasa_structure *structure,
+                                     int r_i,
+                                     int *first,
+                                     int *last)
+{
+    int naa;
+    assert(structure);
+    assert(first);
+    assert(last);
+
+    naa = structure->residues.n;
+
+    assert(r_i >= 0 && r_i < naa);
+
+    *first = structure->residues.first_atom[r_i];
+    if (r_i == naa - 1)
+        *last = structure->atoms.n - 1;
+    else
+        *last = structure->residues.first_atom[r_i + 1] - 1;
+    assert(*last >= *first);
+
+    return FREESASA_SUCCESS;
+}
+
+const char *
+freesasa_structure_residue_name(const freesasa_structure *structure,
+                                int r_i)
+{
+    assert(structure);
+    assert(r_i < structure->residues.n && r_i >= 0);
+    return structure->atoms.atom[structure->residues.first_atom[r_i]]->res_name;
+}
+
+const char *
+freesasa_structure_residue_number(const freesasa_structure *structure,
+                                  int r_i)
+{
+    assert(structure);
+    assert(r_i < structure->residues.n && r_i >= 0);
+    return structure->atoms.atom[structure->residues.first_atom[r_i]]->res_number;
+}
+
+char freesasa_structure_residue_chain(const freesasa_structure *structure,
+                                      int r_i)
+{
+    assert(structure);
+    assert(r_i < structure->residues.n && r_i >= 0);
+
+    return structure->atoms.atom[structure->residues.first_atom[r_i]]->chain_label;
+}
+
+int freesasa_structure_n_chains(const freesasa_structure *structure)
+{
+    return structure->chains.n;
+}
+
+int freesasa_structure_chain_index(const freesasa_structure *structure,
+                                   char chain)
+{
+    int i;
+
+    assert(structure);
+
+    for (i = 0; i < structure->chains.n; ++i) {
+        if (structure->chains.labels[i] == chain) return i;
+    }
+    return fail_msg("chain %c not found", chain);
+}
+
+int freesasa_structure_chain_atoms(const freesasa_structure *structure,
+                                   char chain,
+                                   int *first,
+                                   int *last)
+{
+    int c_i, n;
+
+    assert(structure);
+
+    c_i = freesasa_structure_chain_index(structure, chain);
+    n = freesasa_structure_n_chains(structure);
+
+    if (c_i < 0) return fail_msg("");
+
+    *first = structure->chains.first_atom[c_i];
+    if (c_i == n - 1)
+        *last = freesasa_structure_n(structure) - 1;
+    else
+        *last = structure->chains.first_atom[c_i + 1] - 1;
+    assert(*last >= *first);
+
+    return FREESASA_SUCCESS;
+}
+
+int freesasa_structure_chain_residues(const freesasa_structure *structure,
+                                      char chain,
+                                      int *first,
+                                      int *last)
+{
+    int first_atom, last_atom;
+
+    assert(structure);
+
+    if (freesasa_structure_chain_atoms(structure, chain, &first_atom, &last_atom))
+        return fail_msg("");
+
+    *first = structure->atoms.atom[first_atom]->res_index;
+    *last = structure->atoms.atom[last_atom]->res_index;
+
+    return FREESASA_SUCCESS;
+}
+
+const char *
+freesasa_structure_classifier_name(const freesasa_structure *structure)
+{
+    assert(structure);
+    return structure->classifier_name;
+}
+
+int freesasa_structure_model(const freesasa_structure *structure)
+{
+    return structure->model;
+}
+
+const double *
+freesasa_structure_coord_array(const freesasa_structure *structure)
+{
+    return freesasa_coord_all(structure->xyz);
+}
+
+const double *
+freesasa_structure_radius(const freesasa_structure *structure)
+{
+    assert(structure);
+    return structure->atoms.radius;
+}
+
+void freesasa_structure_set_radius(freesasa_structure *structure,
+                                   const double *radii)
+{
+    assert(structure);
+    assert(radii);
+    memcpy(structure->atoms.radius, radii, structure->atoms.n * sizeof(double));
+}
+
+void freesasa_structure_set_model(freesasa_structure *structure,
+                                  int model)
+{
+    structure->model = model;
+}
+
+void freesasa_structure_set_cif_ref(freesasa_structure *structure,
+                                    size_t ref,
+                                    void (*release_func)(size_t))
+{
+    assert(structure);
+    structure->cif_ref = ref;
+    structure->release_cif_ref = release_func;
+}
+
+size_t freesasa_structure_cif_ref(const freesasa_structure *structure)
+{
+    assert(structure);
+    return structure->cif_ref;
+}

.venv_haddock/include/site/python3.12/freesasa/util.c

@@ -0,0 +1,141 @@
+#if HAVE_CONFIG_H
+#include <config.h>
+#endif
+#include <assert.h>
+#include <errno.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <string.h>
+
+#include "freesasa_internal.h"
+
+#ifdef PACKAGE_NAME
+const char *freesasa_name = PACKAGE_NAME;
+#else
+const char *freesasa_name = "freesasa";
+#endif
+
+static FILE *errlog = NULL;
+
+struct file_range
+freesasa_whole_file(FILE *file)
+{
+    struct file_range range;
+
+    assert(file);
+    rewind(file);
+    range.begin = ftell(file);
+    fseek(file, 0, SEEK_END);
+    range.end = ftell(file);
+    rewind(file);
+    assert(range.begin <= range.end);
+
+    return range;
+}
+
+static void
+freesasa_err_impl(int err,
+                  const char *format,
+                  va_list arg)
+{
+    FILE *fp = stderr;
+
+    if (errlog != NULL) fp = errlog;
+
+    fprintf(fp, "%s: ", freesasa_name);
+    switch (err) {
+    case FREESASA_FAIL:
+        fputs("error: ", fp);
+        break;
+    case FREESASA_WARN:
+        fputs("warning: ", fp);
+        break;
+    default:
+        break;
+    }
+    vfprintf(fp, format, arg);
+    va_end(arg);
+    fputc('\n', fp);
+    fflush(fp);
+}
+
+int freesasa_fail(const char *format, ...)
+{
+    va_list arg;
+
+    if (freesasa_get_verbosity() == FREESASA_V_SILENT) return FREESASA_FAIL;
+
+    va_start(arg, format);
+    freesasa_err_impl(FREESASA_FAIL, format, arg);
+    va_end(arg);
+
+    return FREESASA_FAIL;
+}
+
+int freesasa_warn(const char *format, ...)
+{
+    va_list arg;
+    int v = freesasa_get_verbosity();
+
+    if (v == FREESASA_V_NOWARNINGS || v == FREESASA_V_SILENT) return FREESASA_WARN;
+
+    va_start(arg, format);
+    freesasa_err_impl(FREESASA_WARN, format, arg);
+    va_end(arg);
+
+    return FREESASA_WARN;
+}
+
+int freesasa_fail_wloc(const char *file,
+                       int line,
+                       const char *format,
+                       ...)
+{
+    FILE *fp = stderr;
+    va_list arg;
+
+    if (freesasa_get_verbosity() == FREESASA_V_SILENT) return FREESASA_FAIL;
+    if (errlog != NULL) fp = errlog;
+
+    fprintf(fp, "%s:%s:%d: error: ", freesasa_name, file, line);
+    va_start(arg, format);
+    vfprintf(fp, format, arg);
+    va_end(arg);
+    fputc('\n', fp);
+    fflush(fp);
+
+    return FREESASA_FAIL;
+}
+
+int freesasa_mem_fail(const char *file, int line)
+{
+    return freesasa_fail_wloc(file, line, "Out of memory");
+}
+
+const char *
+freesasa_thread_error(int error_code)
+{
+    switch (error_code) {
+    case EDEADLK:
+        return "deadlock (EDEADLK)";
+    case EINVAL:
+        return "(EINVAL)";
+    case ESRCH:
+        return "no matching thread (ESRCH)";
+    case EAGAIN:
+        return "no resources to create thread (EAGAIN)";
+    }
+    return "Unknown thread error";
+}
+
+void freesasa_set_err_out(FILE *fp)
+{
+    assert(fp);
+    errlog = fp;
+}
+
+FILE *
+freesasa_get_err_out()
+{
+    return errlog;
+}

.venv_haddock/lib/python3.12/site-packages/Bio/Affy/CelFile.py

@@ -0,0 +1,577 @@
+# Copyright 2004 by Harry Zuzan. All rights reserved.
+# Copyright 2016 by Adam Kurkiewicz. All rights reserved.
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+
+"""Reading information from Affymetrix CEL files version 3 and 4."""
+
+import struct
+
+try:
+    import numpy as np
+except ImportError:
+    from Bio import MissingPythonDependencyError
+
+    raise MissingPythonDependencyError(
+        "Install NumPy if you want to use Bio.Affy.CelFile"
+    ) from None
+
+
+class ParserError(ValueError):
+    """Affymetrix parser error."""
+
+    def __init__(self, *args):
+        """Initialise class."""
+        super().__init__(*args)
+
+
+class Record:
+    """Stores the information in a cel file.
+
+    Example usage:
+
+    >>> from Bio.Affy import CelFile
+    >>> with open("Affy/affy_v3_example.CEL") as handle:
+    ...     c = CelFile.read(handle)
+    ...
+    >>> print(c.ncols, c.nrows)
+    5 5
+    >>> print(c.intensities)
+    [[  234.   170. 22177.   164. 22104.]
+     [  188.   188. 21871.   168. 21883.]
+     [  188.   193. 21455.   198. 21300.]
+     [  188.   182. 21438.   188. 20945.]
+     [  193. 20370.   174. 20605.   168.]]
+    >>> print(c.stdevs)
+    [[  24.    34.5 2669.    19.7 3661.2]
+     [  29.8   29.8 2795.9   67.9 2792.4]
+     [  29.8   88.7 2976.5   62.  2914.5]
+     [  29.8   76.2 2759.5   49.2 2762. ]
+     [  38.8 2611.8   26.6 2810.7   24.1]]
+    >>> print(c.npix)
+    [[25 25 25 25 25]
+     [25 25 25 25 25]
+     [25 25 25 25 25]
+     [25 25 25 25 25]
+     [25 25 25 25 25]]
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.version = None
+        self.GridCornerUL = None
+        self.GridCornerUR = None
+        self.GridCornerLR = None
+        self.GridCornerLL = None
+        self.DatHeader = None
+        self.Algorithm = None
+        self.AlgorithmParameters = None
+        self.NumberCells = None
+        self.intensities = None
+        self.stdevs = None
+        self.npix = None
+        self.nrows = None
+        self.ncols = None
+        self.nmask = None
+        self.mask = None
+        self.noutliers = None
+        self.outliers = None
+        self.modified = None
+
+
+def read(handle, version=None):
+    """Read Affymetrix CEL file and return Record object.
+
+    CEL files format versions 3 and 4 are supported.
+    Please specify the CEL file format as 3 or 4 if known for the version
+    argument. If the version number is not specified, the parser will attempt
+    to detect the version from the file contents.
+
+    The Record object returned by this function stores the intensities from
+    the CEL file in record.intensities.
+    Currently, record.mask and record.outliers are not set in when parsing
+    version 4 CEL files.
+
+    Example Usage:
+
+    >>> from Bio.Affy import CelFile
+    >>> with open("Affy/affy_v3_example.CEL") as handle:
+    ...     record = CelFile.read(handle)
+    ...
+    >>> record.version == 3
+    True
+    >>> print("%i by %i array" % record.intensities.shape)
+    5 by 5 array
+
+    >>> with open("Affy/affy_v4_example.CEL", "rb") as handle:
+    ...     record = CelFile.read(handle, version=4)
+    ...
+    >>> record.version == 4
+    True
+    >>> print("%i by %i array" % record.intensities.shape)
+    5 by 5 array
+
+    """
+    try:
+        data = handle.read(0)
+    except AttributeError:
+        raise ValueError("handle should be a file handle") from None
+    data = handle.read(4)
+    if not data:
+        raise ValueError("Empty file.")
+    if data == b"[CEL":
+        raise ValueError("CEL file in version 3 format should be opened in text mode")
+    if data == "[CEL":
+        # Version 3 format. Continue to read the header here before passing
+        # control to _read_v3 to avoid having to seek to the beginning of
+        # the file.
+        data += next(handle)
+        if data.strip() != "[CEL]":
+            raise ValueError("Failed to parse Affy Version 3 CEL file.")
+        line = next(handle)
+        keyword, value = line.split("=", 1)
+        if keyword != "Version":
+            raise ValueError("Failed to parse Affy Version 3 CEL file.")
+        version = int(value)
+        if version != 3:
+            raise ValueError("Incorrect version number in Affy Version 3 CEL file.")
+        return _read_v3(handle)
+    try:
+        magicNumber = struct.unpack("<i", data)
+    except TypeError:
+        raise ValueError(
+            "CEL file in version 4 format should be opened in binary mode"
+        ) from None
+    except struct.error:
+        raise ValueError(
+            "Failed to read magic number from Affy Version 4 CEL file"
+        ) from None
+    if magicNumber != (64,):
+        raise ValueError("Incorrect magic number in Affy Version 4 CEL file")
+    return _read_v4(handle)
+
+
+def _read_v4(f):
+    # We follow the documentation here:
+    # http://www.affymetrix.com/estore/support/developer/powertools/changelog/gcos-agcc/cel.html.affx
+    record = Record()
+    preHeaders = ["version", "columns", "rows", "cellNo", "headerLen"]
+    preHeadersMap = {}
+    headersMap = {}
+
+    # Load pre-headers. The magic number was already parsed in the read
+    # function calling _read_v4.
+    preHeadersMap["magic"] = 64
+    try:
+        for name in preHeaders:
+            preHeadersMap[name] = struct.unpack("<i", f.read(4))[0]
+    except struct.error:
+        raise ParserError("Failed to parse CEL version 4 file") from None
+
+    char = f.read(preHeadersMap["headerLen"])
+    header = char.decode("ascii", "ignore")
+    for line in header.split("\n"):
+        if "=" in line:
+            headline = line.split("=")
+            headersMap[headline[0]] = "=".join(headline[1:])
+
+    record.version = preHeadersMap["version"]
+    if record.version != 4:
+        raise ParserError("Incorrect version number in CEL version 4 file")
+
+    record.GridCornerUL = headersMap["GridCornerUL"]
+    record.GridCornerUR = headersMap["GridCornerUR"]
+    record.GridCornerLR = headersMap["GridCornerLR"]
+    record.GridCornerLL = headersMap["GridCornerLL"]
+    record.DatHeader = headersMap["DatHeader"]
+    record.Algorithm = headersMap["Algorithm"]
+    record.AlgorithmParameters = headersMap["AlgorithmParameters"]
+    record.NumberCells = preHeadersMap["cellNo"]
+    # record.intensities are set below
+    # record.stdevs are set below
+    # record.npix are set below
+    record.nrows = int(headersMap["Rows"])
+    record.ncols = int(headersMap["Cols"])
+
+    # These cannot be reliably set in v4, because of discrepancies between real
+    # data and the documented format.
+    record.nmask = None
+    record.mask = None
+    record.noutliers = None
+    record.outliers = None
+    record.modified = None
+
+    # Real data never seems to have anything but zeros here, but we don't want
+    # to take chances. Raising an error is better than returning unreliable
+    # data.
+    def raiseBadHeader(field, expected):
+        actual = int(headersMap[field])
+        message = f"The header {field} is expected to be 0, not {actual}"
+        if actual != expected:
+            raise ParserError(message)
+
+    raiseBadHeader("Axis-invertX", 0)
+
+    raiseBadHeader("AxisInvertY", 0)
+
+    raiseBadHeader("OffsetX", 0)
+
+    raiseBadHeader("OffsetY", 0)
+
+    # This is unfortunately undocumented, but it turns out that real data has
+    # the record.AlgorithmParameters repeated in the data section, until an
+    # EOF, i.e. b"\x04".
+    char = b"\x00"
+    safetyValve = 10**4
+    for i in range(safetyValve):
+        char = f.read(1)
+        # For debugging
+        # print([i for i in char], end="")
+        if char == b"\x04":
+            break
+        if i == safetyValve:
+            raise ParserError(
+                "Parse Error. The parser expects a short, "
+                "undocumented binary blob terminating with "
+                "ASCII EOF, x04"
+            )
+
+    # After that there are precisely 15 bytes padded. Again, undocumented.
+    padding = f.read(15)
+
+    # That's how we pull out the values (triplets of the form float, float,
+    # signed short).
+    structa = struct.Struct("< f f h")
+
+    # There are 10 bytes in our struct.
+    structSize = 10
+
+    # We initialize the most important: intensities, stdevs and npixs.
+    record.intensities = np.empty(record.NumberCells, dtype=float)
+    record.stdevs = np.empty(record.NumberCells, dtype=float)
+    record.npix = np.empty(record.NumberCells, dtype=int)
+
+    b = f.read(structSize * record.NumberCells)
+    for i in range(record.NumberCells):
+        binaryFragment = b[i * structSize : (i + 1) * structSize]
+        intensity, stdevs, npix = structa.unpack(binaryFragment)
+        record.intensities[i] = intensity
+        record.stdevs[i] = stdevs
+        record.npix[i] = npix
+
+    # reshape without copying.
+    def reshape(array):
+        view = array.view()
+        view.shape = (record.nrows, record.ncols)
+        return view
+
+    record.intensities = reshape(record.intensities)
+    record.stdevs = reshape(record.stdevs)
+    record.npix = reshape(record.npix)
+
+    return record
+
+
+def _read_v3(handle):
+    # Needs error handling.
+    # Needs to know the chip design.
+    record = Record()
+    # The version number was already obtained when the read function calling
+    # _read_v3 parsed the CEL section.
+    record.version = 3
+    section = ""
+    for line in handle:
+        line = line.rstrip("\r\n")
+        if not line:
+            continue
+        # Set current section
+        if line.startswith("[HEADER]"):
+            section = "HEADER"
+        elif line.startswith("[INTENSITY]"):
+            section = "INTENSITY"
+            record.intensities = np.zeros((record.nrows, record.ncols))
+            record.stdevs = np.zeros((record.nrows, record.ncols))
+            record.npix = np.zeros((record.nrows, record.ncols), int)
+        elif line.startswith("[MASKS]"):
+            section = "MASKS"
+            record.mask = np.zeros((record.nrows, record.ncols), bool)
+        elif line.startswith("[OUTLIERS]"):
+            section = "OUTLIERS"
+            record.outliers = np.zeros((record.nrows, record.ncols), bool)
+        elif line.startswith("[MODIFIED]"):
+            section = "MODIFIED"
+            record.modified = np.zeros((record.nrows, record.ncols))
+        elif line.startswith("["):
+            raise ParserError("Unknown section found in version 3 CEL file")
+        else:  # read the data in a section
+            if section == "HEADER":
+                # Set record.ncols and record.nrows, remaining data goes into
+                # record.header dict
+                key, value = line.split("=", 1)
+                if key == "Cols":
+                    record.ncols = int(value)
+                elif key == "Rows":
+                    record.nrows = int(value)
+                elif key == "GridCornerUL":
+                    x, y = value.split()
+                    record.GridCornerUL = (int(x), int(y))
+                elif key == "GridCornerUR":
+                    x, y = value.split()
+                    record.GridCornerUR = (int(x), int(y))
+                elif key == "GridCornerLR":
+                    x, y = value.split()
+                    record.GridCornerLR = (int(x), int(y))
+                elif key == "GridCornerLL":
+                    x, y = value.split()
+                    record.GridCornerLL = (int(x), int(y))
+                elif key == "DatHeader":
+                    # not sure if all parameters here are interpreted correctly
+                    record.DatHeader = {}
+                    i = value.find(":")
+                    if i >= 0:
+                        min_max_pixel_intensity, filename = value[:i].split()
+                        record.DatHeader["filename"] = filename
+                        assert min_max_pixel_intensity[0] == "["
+                        assert min_max_pixel_intensity[-1] == "]"
+                        (
+                            min_pixel_intensity,
+                            max_pixel_intensity,
+                        ) = min_max_pixel_intensity[1:-1].split("..")
+                        record.DatHeader["min-pixel_intensity"] = int(
+                            min_pixel_intensity
+                        )
+                        record.DatHeader["max-pixel_intensity"] = int(
+                            max_pixel_intensity
+                        )
+                        value = value[i + 1 :]
+                        index = 0
+                        field = value[index : index + 9]
+                        if field[:4] != "CLS=" or field[8] != " ":
+                            raise ValueError(
+                                "Field does not start with 'CLS=' or have a blank space at position 8"
+                            )
+                        record.DatHeader["CLS"] = int(field[4:8])
+                        index += 9
+                        field = value[index : index + 9]
+                        if field[:4] != "RWS=" or field[8] != " ":
+                            raise ValueError(
+                                "Field does not start with 'RWS=' or have a blank space at position 8"
+                            )
+                        record.DatHeader["RWS"] = int(field[4:8])
+                        index += 9
+                        field = value[index : index + 7]
+                        if field[:4] != "XIN=" or field[6] != " ":
+                            raise ValueError(
+                                "Field does not start with 'XIN=' or have a blank space at position 6"
+                            )
+                        record.DatHeader["XIN"] = int(field[4:6])
+                        index += 7
+                        field = value[index : index + 7]
+                        if field[:4] != "YIN=" or field[6] != " ":
+                            raise ValueError(
+                                "Field does not start with 'YIN=' or have a blank space at poition 6"
+                            )
+                        record.DatHeader["YIN"] = int(field[4:6])
+                        index += 7
+                        field = value[index : index + 6]
+                        if field[:3] != "VE=" or field[5] != " ":
+                            raise ValueError(
+                                "Field does not start with 'VE=' or have a blank space at position 5"
+                            )
+                        record.DatHeader["VE"] = int(field[3:5])
+                        index += 6
+                        field = value[index : index + 7]
+                        if field[6] != " ":
+                            raise ValueError(
+                                "Field value for position 6 isn't a blank space"
+                            )
+                        temperature = field[:6].strip()
+                        if temperature:
+                            record.DatHeader["temperature"] = int(temperature)
+                        else:
+                            record.DatHeader["temperature"] = None
+                        index += 7
+                        field = value[index : index + 4]
+                        if not field.endswith(" "):
+                            raise ValueError("Field doesn't end with a blank space")
+                        record.DatHeader["laser-power"] = float(field)
+                        index += 4
+                        field = value[index : index + 18]
+                        if field[8] != " ":
+                            raise ValueError(
+                                "Field value for position 8 isn't a blank space"
+                            )
+                        record.DatHeader["scan-date"] = field[:8]
+                        if field[17] != " ":
+                            raise ValueError(
+                                "Field value for position 17 isn't a blank space"
+                            )
+                        record.DatHeader["scan-date"] = field[:8]
+                        record.DatHeader["scan-time"] = field[9:17]
+                        index += 18
+                        value = value[index:]
+                    subfields = value.split("\x14")
+                    if len(subfields) != 12:
+                        ValueError("Subfields length isn't 12")
+                    subfield = subfields[0]
+                    try:
+                        scanner_id, scanner_type = subfield.split()
+                    except ValueError:
+                        scanner_id = subfield.strip()
+                    else:
+                        record.DatHeader["scanner-type"] = scanner_type
+                    record.DatHeader["scanner-id"] = scanner_id
+                    record.DatHeader["array-type"] = subfields[2].strip()
+                    field = subfields[7].strip()
+                    if field:
+                        record.DatHeader["filter-wavelength"] = int(field)
+                    field = subfields[8].strip()
+                    if field:
+                        record.DatHeader["arc-radius"] = float(field)
+                    field = subfields[9].strip()
+                    if field:
+                        record.DatHeader["laser-spotsize"] = float(field)
+                    field = subfields[10].strip()
+                    if field:
+                        record.DatHeader["pixel-size"] = float(field)
+                    field = subfields[11].strip()
+                    if field:
+                        record.DatHeader["image-orientation"] = int(field)
+                elif key == "Algorithm":
+                    record.Algorithm = value
+                elif key == "AlgorithmParameters":
+                    parameters = value.split(";")
+                    values = {}
+                    for parameter in parameters:
+                        key, value = parameter.split(":", 1)
+                        if key in (
+                            "Percentile",
+                            "CellMargin",
+                            "FullFeatureWidth",
+                            "FullFeatureHeight",
+                            "PoolWidthExtenstion",
+                            "PoolHeightExtension",
+                            "NumPixelsToUse",
+                            "ExtendPoolWidth",
+                            "ExtendPoolHeight",
+                            "OutlierRatioLowPercentile",
+                            "OutlierRatioHighPercentile",
+                            "HalfCellRowsDivisor",
+                            "HalfCellRowsRemainder",
+                            "HighCutoff",
+                            "LowCutoff",
+                            "featureRows",
+                            "featureColumns",
+                        ):
+                            values[key] = int(value)
+                        elif key in (
+                            "OutlierHigh",
+                            "OutlierLow",
+                            "StdMult",
+                            "PercentileSpread",
+                            "PairCutoff",
+                            "featureWidth",
+                            "featureHeight",
+                        ):
+                            values[key] = float(value)
+                        elif key in (
+                            "FixedCellSize",
+                            "IgnoreOutliersInShiftRows",
+                            "FeatureExtraction",
+                            "UseSubgrids",
+                            "RandomizePixels",
+                            "ImageCalibration",
+                            "IgnoreShiftRowOutliers",
+                        ):
+                            if value == "TRUE":
+                                value = True
+                            elif value == "FALSE":
+                                value = False
+                            else:
+                                raise ValueError("Unexpected boolean value")
+                            values[key] = value
+                        elif key in (
+                            "AlgVersion",
+                            "ErrorBasis",
+                            "CellIntensityCalculationType",
+                        ):
+                            values[key] = value
+                        else:
+                            raise ValueError("Unexpected tag in AlgorithmParameters")
+                    record.AlgorithmParameters = values
+            elif section == "INTENSITY":
+                if line.startswith("NumberCells="):
+                    key, value = line.split("=", 1)
+                    record.NumberCells = int(value)
+                elif line.startswith("CellHeader="):
+                    key, value = line.split("=", 1)
+                    if value.split() != ["X", "Y", "MEAN", "STDV", "NPIXELS"]:
+                        raise ParserError(
+                            "Unexpected CellHeader in INTENSITY "
+                            "section CEL version 3 file"
+                        )
+                else:
+                    words = line.split()
+                    y = int(words[0])
+                    x = int(words[1])
+                    record.intensities[x, y] = float(words[2])
+                    record.stdevs[x, y] = float(words[3])
+                    record.npix[x, y] = int(words[4])
+            elif section == "MASKS":
+                if line.startswith("NumberCells="):
+                    key, value = line.split("=", 1)
+                    record.nmask = int(value)
+                elif line.startswith("CellHeader="):
+                    key, value = line.split("=", 1)
+                    if value.split() != ["X", "Y"]:
+                        raise ParserError(
+                            "Unexpected CellHeader in MASKS "
+                            "section in CEL version 3 file"
+                        )
+                else:
+                    words = line.split()
+                    y = int(words[0])
+                    x = int(words[1])
+                    record.mask[x, y] = True
+            elif section == "OUTLIERS":
+                if line.startswith("NumberCells="):
+                    key, value = line.split("=", 1)
+                    record.noutliers = int(value)
+                elif line.startswith("CellHeader="):
+                    key, value = line.split("=", 1)
+                    if value.split() != ["X", "Y"]:
+                        raise ParserError(
+                            "Unexpected CellHeader in OUTLIERS "
+                            "section in CEL version 3 file"
+                        )
+                else:
+                    words = line.split()
+                    y = int(words[0])
+                    x = int(words[1])
+                    record.outliers[x, y] = True
+            elif section == "MODIFIED":
+                if line.startswith("NumberCells="):
+                    key, value = line.split("=", 1)
+                    record.nmodified = int(value)
+                elif line.startswith("CellHeader="):
+                    key, value = line.split("=", 1)
+                    if value.split() != ["X", "Y", "ORIGMEAN"]:
+                        raise ParserError(
+                            "Unexpected CellHeader in MODIFIED "
+                            "section in CEL version 3 file"
+                        )
+                else:
+                    words = line.split()
+                    y = int(words[0])
+                    x = int(words[1])
+                    record.modified[x, y] = float(words[2])
+    return record
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

.venv_haddock/lib/python3.12/site-packages/Bio/Affy/__init__.py

@@ -0,0 +1,6 @@
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+
+"""Deal with Affymetrix related data such as cel files."""

.venv_haddock/lib/python3.12/site-packages/Bio/Align/AlignInfo.py

@@ -0,0 +1,54 @@
+# Copyright 2000 Brad Chapman.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Extract information from alignment objects.
+
+In order to try and avoid huge alignment objects with tons of functions,
+functions which return summary type information about alignments should
+be put into classes in this module.
+"""
+
+import warnings
+
+from Bio import BiopythonDeprecationWarning
+
+
+class SummaryInfo:
+    """Calculate summary info about the alignment.  (DEPRECATED)
+
+    This class should be used to calculate information summarizing the
+    results of an alignment. This may either be straight consensus info
+    or more complicated things.
+    """
+
+    def __init__(self, alignment):
+        """Initialize with the alignment to calculate information on.
+
+        ic_vector attribute. A list of ic content for each column number.
+        """
+        warnings.warn(
+            """\
+The class SummaryInfo has been deprecated. Instead of
+
+>>> align_info = AlignInfo.SummaryInfo(msa)
+>>> sequence = align_info.get_column(1)
+
+please use
+
+>>> alignment = msa.alignment  # to get a new-style Alignment object
+>>> sequence = alignment[:, 1]
+
+Here, `msa` is a MultipleSeqAlignment object and `alignment` is an
+`Alignment` object.""",
+            BiopythonDeprecationWarning,
+        )
+        self.alignment = alignment
+        self.ic_vector = []
+
+    def get_column(self, col):
+        """Return column of alignment."""
+        # TODO - Deprecate this and implement slicing?
+        return self.alignment[:, col]