File size: 3,336 Bytes
4559903 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 | #include "dcdhelper.h"
#include <fstream>
#include <iostream>
#include <string>
#include <unistd.h>
#include <algorithm>
#include <dirent.h>
#include <errno.h>
#include <sstream>
#include <iomanip>
#include <sys/stat.h>
double unifRand() {
return rand() / double(RAND_MAX);
}
std::vector<double> readDCDExafsScoreFile(std::string filename) {
std::vector<double> indexes;
std::ifstream index_file(filename.c_str());
if (index_file.is_open() && index_file.good()) {
std::string score_str;
while(index_file.good()) {
index_file >> score_str;
double score = atof(score_str.c_str());
indexes.push_back(score);
}
}
return indexes;
}
std::vector<int> dcdGetIndexLessThan(std::string filename, double limit) {
std::vector<int> indexes;
std::ifstream index_file(filename.c_str());
if (index_file.is_open() && index_file.good()) {
std::string score_str;
int i = 0;
while(index_file.good()) {
index_file >> score_str;
double score = atof(score_str.c_str());
if (score < limit) {
indexes.push_back(i);
}
++i;
}
}
return indexes;
}
int main(int argc, char **argv) {
int c;
std::string count_s, dcd_file_s, output_directory_s, exafs_score_file_s;
while ( (c = getopt(argc, argv, "c:f:o:s:")) != -1 ) {
switch(c) {
case 'c':
count_s.assign(optarg);
break;
case 'f':
dcd_file_s.assign(optarg);
break;
case 'o':
output_directory_s.assign(optarg);
break;
case 's':
exafs_score_file_s.assign(optarg);
break;
default:
exit(EXIT_FAILURE);
}
}
if (count_s.size() == 0) {
std::cout << "Frame count required. Use -c <count>." << std::endl;
exit(EXIT_FAILURE);
}
if (dcd_file_s.size() == 0) {
std::cout << "DCD Output file required. Use -f <file>." << std::endl;
exit(EXIT_FAILURE);
}
if (output_directory_s.size() == 0) {
std::cout << "Output directory required. Use -o <file>." << std::endl;
exit(EXIT_FAILURE);
}
if (exafs_score_file_s.size() == 0) {
std::cout << "EXAFS Score file required. Use -s <file>." << std::endl;
exit(EXIT_FAILURE);
}
// Read in EXAFS score file.
std::vector<double> dcdExafsScores = readDCDExafsScoreFile(exafs_score_file_s);
std::sort(dcdExafsScores.begin(), dcdExafsScores.end());
int frameCount = atoi(count_s.c_str());
if (frameCount > (int)dcdExafsScores.size()) {
std::cout << "Frame count is greater than the number of available frames." << std::endl;
exit(EXIT_FAILURE);
}
double maxExafsScore = dcdExafsScores.at(frameCount);
std::vector<int> frameIndexes = dcdGetIndexLessThan(exafs_score_file_s, maxExafsScore);
mkdir(output_directory_s.c_str(), 0755);
std::ostringstream oss;
DCDHelper dcd_helper = DCDHelper(dcd_file_s);
for (int i = 0; i < (int)frameIndexes.size(); ++i) {
std::vector<PDBAtom> frame = dcd_helper.getXYZAtFrame(frameIndexes.at(i));
oss << output_directory_s << "/" << (i+1) << ".xyz";
std::ofstream xyz_file(oss.str().c_str());
// Number of atoms
xyz_file << frame.size() << std::endl;
// Comment line
xyz_file << std::endl;
for (std::vector<PDBAtom>::iterator atom = frame.begin(); atom != frame.end(); ++atom) {
xyz_file << std::setprecision(15) << "H " << atom->x << " " << atom->y << " " << atom->z << std::endl;
}
xyz_file.close();
oss.clear();
oss.str("");
}
return 0;
}
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