"""CA RMSD between CASP12's target file and the PDB chain TAPE used, after optimal superposition."""
import sys, glob, os, json
sys.path.insert(0, "scripts")
import gemmi
import ss_assign as A
from Bio import Align
from Bio.Align import substitution_matrices
D = "data/original/casp12"
seqs, cur = {}, None
for line in open(f"{D}/casp12.seq.txt"):
    line = line.strip()
    if line.startswith(">"): cur = line[1:].split()[0]; seqs[cur] = ""
    elif cur: seqs[cur] += line
files = {os.path.basename(p)[:-4]: p for p in glob.glob(f"{D}/x/**/*.pdb", recursive=True)}
al = Align.PairwiseAligner(mode="local", substitution_matrix=substitution_matrices.load("BLOSUM62"), open_gap_score=-11, extend_gap_score=-1)
def mapping(a, b):
    aln = al.align(a, b)[0]
    return {i: j for (i0, i1), (j0, j1) in zip(*aln.aligned) for i, j in zip(range(i0, i1), range(j0, j1))}
pairs = {"5uvn-A": "T0918", "5sy1-A": "T0863", "5nv4-A": "T0892", "5uw2-A": "T0866", "5fhy-A": "T0886", "5aot-A": "T0900",
         "5j4a-B": "T0869", "5j4a-A": "T0868", "5a7d-L": "T0904", "5j5v-B": "T0862", "5jzr-A": "T0859", "5kkp-A": "T0943",
         "5mqp-A": "T0912", "5d9g-A": "T0864", "5lev-A": "T0945", "5j5v-C": "T0870"}
for cid, t in pairs.items():
    pdb, ch = cid.split("-")
    st = A.load(f"data/original/casp12_pdb/{pdb}.cif.gz")
    seqres, residues = A.chain_info(st, ch)
    m = mapping(seqres, seqs[t])
    ca_pdb = {m[r.label_seq - 1]: r.find_atom("CA", "*").pos for r in residues if r.label_seq - 1 in m and r.find_atom("CA", "*")}
    cst = gemmi.read_structure(files[t])
    ca_casp = {r.seqid.num - 1: r.find_atom("CA", "*").pos for r in cst[0][0] if r.find_atom("CA", "*")}
    common = sorted(set(ca_pdb) & set(ca_casp))
    sup = gemmi.superpose_positions([ca_pdb[k] for k in common], [ca_casp[k] for k in common])
    only_pdb = len(set(ca_pdb) - set(ca_casp)); only_casp = len(set(ca_casp) - set(ca_pdb))
    print(f"{cid:8s} {t}: CA RMSD after superposition {sup.rmsd:6.2f} A over {len(common)} residues | residues only in PDB entry {only_pdb}, only in CASP file {only_casp}")