HGNN/read_fasta.py

import os, re
import prody as pr
from tqdm import tqdm
from multiprocessing import Pool


# import subprocess
# os.environ["BABEL_LIBDIR"] = "/home/shenchao/.conda/envs/my2/lib/openbabel/3.1.0"

def write_file(output_file, outline):
    buffer = open(output_file, 'w')
    buffer.write(outline)
    buffer.close()


def lig_rename(infile, outfile):
    ##some peptides may impede the generation of pocket, so rename the ligname first.
    lines = open(infile, 'r').readlines()
    newlines = []
    for line in lines:
        if re.search(r'^HETATM|^ATOM', line):
            newlines.append(line[:17] + "LIG" + line[20:])
        else:
            newlines.append(line)
    write_file(outfile, ''.join(newlines))


def check_mol(infile, outfile):
    # Some metals may have the same ID as ligand, thus making ligand included in the pocket.
    os.system("cat %s | sed '/LIG/d' > %s" % (infile, outfile))


def extract_pocket(protpath,
                   ligpath,
                   cutoff=5.0,
                   protname=None,
                   ligname=None,
                   pdb_pocket_file=None,
                   workdir='.'):
    """
        protpath: the path of protein file (.pdb).
        ligpath: the path of ligand file (.sdf|.mol2|.pdb).
        cutoff: the distance range within the ligand to determine the pocket.
        protname: the name of the protein.
        ligname: the name of the ligand.
        workdir: working directory.
    """
    if protname is None:
        protname = os.path.basename(protpath).split('.')[0]
    if ligname is None:
        ligname = os.path.basename(ligpath).split('.')[0]


    if not re.search(r'.pdb$', ligpath):
        os.system(f"obabel {ligpath} -O {workdir}/{ligname}.pdb")
    else:
        os.system(f"cp {ligpath} {workdir}/{ligname}.pdb")

    xprot = pr.parsePDB(protpath)
    # xlig = pr.parsePDB("%s/%s.pdb"%(workdir, ligname))

    # if (xlig.getResnames() == xlig.getResnames()[0]).all():
    #	lresname = xlig.getResnames()[0]
    # else:
    lig_rename("%s/%s.pdb" % (workdir, ligname), "%s/%s2.pdb" % (workdir, ligname))
    os.remove("%s/%s.pdb" % (workdir, ligname))
    os.rename("%s/%s2.pdb" % (workdir, ligname), "%s/%s.pdb" % (workdir, ligname))
    xlig = pr.parsePDB("%s/%s.pdb" % (workdir, ligname))
    lresname = xlig.getResnames()[0]
    xcom = xlig + xprot

    # select ONLY atoms that belong to the protein
    ret = xcom.select(f'same residue as exwithin %s of resname %s' % (cutoff, lresname))

    pr.writePDB("%s/%s_pocket_%s_temp.pdb" % (workdir, protname, cutoff), ret)
    # ret = pr.parsePDB("%s/%s_pocket_%s.pdb"%(workdir, protname, cutoff))

    check_mol("%s/%s_pocket_%s_temp.pdb" % (workdir, protname, cutoff), pdb_pocket_file)
    os.remove("%s/%s_pocket_%s_temp.pdb" % (workdir, protname, cutoff))


def get_fasta_seq(fasta_file):
    with open(fasta_file) as f:
        lines = []
        for line in f.readlines():
            lines.append(line.strip())
        fasta = "".join(lines[1:])
        return fasta


def read_fasta_from_protein(pdb_file, lig_file, target_id="test", cutoff=5.0, pdb_pocket_file="test_pocket.pdb", fasta_pocket_file="test_pocket.fasta"):
    if not os.path.exists(pdb_file):
        return

    try:
        extract_pocket(pdb_file,
                       lig_file,
                       cutoff=cutoff,
                       protname=target_id,
                       pdb_pocket_file=pdb_pocket_file,
                       ligname=f"{target_id}_ligand")
    except Exception as e:
        print(e)
        return

    os.system(f"./pdb2fasta {pdb_pocket_file} > {fasta_pocket_file}")
    return get_fasta_seq(fasta_pocket_file)


def read_fasta_from_pocket(pocket_pdb_file, fasta_pocket_file="test_pocket.fasta"):
    os.system(f"./pdb2fasta {pocket_pdb_file} > {fasta_pocket_file}")
    return get_fasta_seq(fasta_pocket_file)