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#!/usr/bin/env python |
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# -*- coding: utf-8 -*- |
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""" |
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""" |
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from __future__ import print_function |
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import argparse |
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from icecream import ic |
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import sys |
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ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr)) |
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ic.configureOutput(prefix='> ') |
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from rna_tools.rna_tools_lib import edit_pdb, add_header, get_version |
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import os |
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def convert_cif_to_pdb(cif_file, add_header_to_output=True, version='', verbose=True, |
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split_conflicting_chains=True, output_path=None): |
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"""Convert an mmCIF file into one or more PDB files. |
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Returns a list of generated PDB filenames. When a direct conversion fails |
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(e.g. multi-character chain ids) the chains are split into separate models |
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following the legacy CLI behavior. |
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""" |
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from Bio.PDB import MMCIFParser, PDBIO |
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def _prepend_header(pdb_file, remarks=None): |
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if not add_header_to_output and not remarks: |
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return |
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new_content = '' |
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if add_header_to_output: |
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new_content += add_header(version) + '\n' |
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if remarks: |
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new_content += '\n'.join(remarks) + '\n' |
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with open(pdb_file, 'r') as fh: |
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new_content += fh.read() |
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with open(pdb_file, 'w') as fh: |
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fh.write(new_content) |
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if output_path and split_conflicting_chains: |
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raise ValueError('output_path is only supported when split_conflicting_chains is False') |
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outputs = [] |
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parser = MMCIFParser() |
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structure = parser.get_structure("structure_id", cif_file) |
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pdb_file = output_path or cif_file.replace('.cif', '_fCIF.pdb') |
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io = PDBIO() |
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io.set_structure(structure) |
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try: |
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io.save(pdb_file) |
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_prepend_header(pdb_file) |
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outputs.append(pdb_file) |
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if verbose: |
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print(f'saved: {pdb_file}') |
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return outputs |
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except Exception: |
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if verbose: |
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print('Warning: some of the chains in this mmCIF file have multi-character ids.') |
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from Bio.PDB.MMCIFParser import MMCIFParser |
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from Bio.PDB import Structure, Model, PDBIO |
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def has_high_rna_content(chain, threshold=0.8): |
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rna_nucleotides = ['A', 'C', 'G', 'U', 'X'] |
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total_residues = 0 |
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rna_residues = 0 |
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for residue in chain: |
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total_residues += 1 |
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if residue.get_resname().strip() in rna_nucleotides: |
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rna_residues += 1 |
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if total_residues == 0: |
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return False |
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return (rna_residues / total_residues) >= threshold |
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parser = MMCIFParser() |
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structure = parser.get_structure("structure", cif_file) |
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if not split_conflicting_chains: |
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import string |
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letters = list(string.ascii_uppercase + string.ascii_lowercase + string.digits) |
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letter_iter = iter(letters) |
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for model in structure: |
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for chain in model: |
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try: |
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chain.id = next(letter_iter) |
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except StopIteration: |
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raise RuntimeError('Too many chains to assign unique single-letter IDs in %s' % cif_file) |
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io = PDBIO() |
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io.set_structure(structure) |
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io.save(pdb_file) |
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_prepend_header(pdb_file) |
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outputs.append(pdb_file) |
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if verbose: |
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print(f'saved: {pdb_file} (renamed chain ids)') |
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return outputs |
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import string |
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letters = list(string.ascii_uppercase) |
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for model in structure: |
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for chain in model: |
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if has_high_rna_content(chain): |
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new_structure = Structure.Structure("new_structure") |
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new_model = Model.Model(0) |
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new_structure.add(new_model) |
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chain_id_new = letters.pop(0) |
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chain_id = chain.get_id() |
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atom_count = 0 |
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for residue in chain: |
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for atom in residue: |
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atom_count += 1 |
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remarks = [f'REMARK rna chain {chain.id} -> {chain_id_new}'] |
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pdb_file = cif_file.replace('.cif', f'_{chain_id}_n{chain_id_new}_fCIF.pdb') |
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if verbose: |
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print(f'rna chain {chain.id} -> {chain_id_new} {pdb_file} # of atoms: {atom_count}') |
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chain.id = chain_id_new |
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new_model.add(chain) |
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io = PDBIO() |
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io.set_structure(new_structure) |
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io.save(pdb_file) |
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_prepend_header(pdb_file, remarks) |
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outputs.append(pdb_file) |
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return outputs |
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View Code Duplication |
def get_parser(): |
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parser = argparse.ArgumentParser( |
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description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) |
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version = os.path.basename(os.path.dirname(os.path.abspath(__file__))), get_version(__file__) |
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version = version[1].strip() |
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parser = argparse.ArgumentParser( |
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description=__doc__, formatter_class=argparse.RawTextHelpFormatter) |
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parser.add_argument('--version', help='', action='version', version=version) |
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parser.add_argument("-v", "--verbose", |
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action="store_true", help="be verbose") |
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parser.add_argument('--no-hr', help='do not insert the header into files', |
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action='store_true') |
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parser.add_argument("file", help="", default="", nargs='+') |
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return parser, version |
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if __name__ == '__main__': |
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parser, version = get_parser() |
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args = parser.parse_args() |
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if list != type(args.file): |
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args.file = [args.file] |
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for cif_file in args.file: |
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convert_cif_to_pdb( |
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cif_file, |
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add_header_to_output=not args.no_hr, |
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version=version, |
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verbose=True, |
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) |
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mmagnus /
rna-tools
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