Mercurial > repos > jay > pdaug_peptide_core_functions
view PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.py @ 6:6822d43a5f84 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author | jay |
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date | Sun, 31 Jan 2021 02:17:01 +0000 |
parents | e743e76b8991 |
children |
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import tempfile import pandas as pd import shutil import sys import glob import fragbuilder import openbabel from fragbuilder import peptide import os def read_pep_file(pep_infile): file = open(pep_infile) lines = file.readlines() Index = [] list_pep_name = [] for line in lines: if '>' in line: Index.append(line.strip('\n')) else: line = line.strip('\n') line = line.strip('\r') list_pep_name.append(line.strip('\n')) return list_pep_name def structure_gen(pep_seq, out_dir): if not os.path.exists(os.path.join(out_dir, 'DataFile')): os.makedirs(os.path.join(out_dir, 'DataFile')) b = len(pep_seq) for seq in pep_seq: pep = peptide.Peptide(seq, nterm = "charged", cterm = "neutral") pep.regularize() pep.write_pdb(os.path.join(out_dir, 'DataFile', seq+".pdb")) obConversion = openbabel.OBConversion() obConversion.SetInAndOutFormats("pdb", "sdf") mol = openbabel.OBMol() obConversion.ReadFile(mol, os.path.join(out_dir, 'DataFile', seq+".pdb")) mol.AddHydrogens() def main_process(str_pep_file, out_dir): my_pep = read_pep_file(str_pep_file) structure_gen(my_pep, out_dir) if __name__=="__main__": import argparse parser = argparse.ArgumentParser() parser.add_argument("-p", "--pep", required=True, default=None, help="pep file") parser.add_argument("-o", "--OutDir", required=None, default=os.getcwd(), help="Path to out file") args = parser.parse_args() main_process(args.pep, args.OutDir)