Source code for

#!/usr/bin/env python
# -*- coding: utf-8 -*-
r""" - edit occupancy or bfactor in PDB file.

Example:: --occupancy --select A:1-40,B:1-22 \
                                    --set-to 0 \
                                    19_Bujnicki_Human_4_rpr_n0-000001.pdb --occupancy \
                                     --select A:1-2 \
                                     --select-atoms P+C4\' \
                                     --set-to 10 \
                                     -o test_data/3w3s_homologymodel_out.PD
                                     --set-not-selected-to 8


from __future__ import print_function
import re
import string
import argparse

from Bio import PDB
from Bio.PDB import PDBIO
from Bio.PDB.Atom import PDBConstructionWarning

import sys
import warnings
warnings.simplefilter('ignore', PDBConstructionWarning)

[docs] def edit_occupancy_of_pdb(txt, pdb, pdb_out, bfactor, occupancy, set_to, set_not_selected_to, select_atoms, v=False): """Change ouccupancy or bfactor of pdb file. Load the structure, and first set everything to be `set_not_selected_to` and then set selected to `sel_to`. Args: txt (str): A:1-10, selection, what to change pdb (str): filename to read as an input pdb_out (str): filename to save an output bfactor (bool): if edit bfactor occupancy (bool): if edit occupancy set_to (float): set to this value, if within selection set_not_selected_to (float): set to this value, if not within selection select_atoms (str): P, P+C4\\', use + as a separator v (bool): be verbose Returns: bool: if OK, save an output to pdb_out .. warning:: this function requires BioPython """ struc = PDB.PDBParser().get_structure('struc', pdb) # first loop to set everything to set_not_selected_to if set_not_selected_to: for s in struc: for c in s: for r in c: for a in r: if bfactor: a.set_bfactor(set_not_selected_to) if occupancy: a.set_occupancy(set_not_selected_to) # parser selected txt = txt.replace(' ', '') l = re.split('[,:;]', txt) if v: print(txt) print(l) # second loop to set_to for selected for i in l: # ['A', '1-10', '15', '25-30', 'B', '1-10'] if i in string.ascii_letters: if v: print('chain', i) chain_curr = i continue if '-' in i: start, ends = i.split('-') if v: print(start, ends) if int(start) > int(ends): print('Error: range start > end ' + i, file=sys.stderr) return False index = list(range(int(start), int(ends)+1)) else: index = [int(i)] for i in index: if v: print(index) try: atoms = struc[0][chain_curr][i] except KeyError: if i == chain_curr: print('Error: Chain ' + chain_curr + ' not found in the PDB structure', file=sys.stderr) else: print('Error: Residue ' + chain_curr + ':' + str(i) + ' found in the PDB structure', file=sys.stderr) return False for a in atoms: # if run it for all atoms if not select_atoms: if bfactor: a.set_bfactor(set_to) if occupancy: a.set_occupancy(set_to) else: # if select_atoms if '+' in select_atoms: # only for striping atom names select_atoms_list = [x.strip() for x in select_atoms.split('+')] else: select_atoms_list = select_atoms if in select_atoms_list: if bfactor: a.set_bfactor(set_to) if occupancy: a.set_occupancy(set_to) io = PDBIO() io.set_structure(struc) print('Saved ', pdb_out) return True
def get_parser(): """Get parser.""" p = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) group = p.add_mutually_exclusive_group(required=True) group.add_argument('--bfactor', action='store_true', help="set bfactor") group.add_argument('--occupancy', action='store_true', help="set occupancy") p.add_argument('--select', help='get chain, e.g A:1-10, works also for multiple chains' 'e.g A:1-40,B:1-22') p.add_argument('--set-to', help='set value to, default is 1', default=1) p.add_argument('--set-not-selected-to', help='set value to, default is 0', default=0) p.add_argument('-o', '--output', help='file output') p.add_argument('--verbose', action='store_true', help="be verbose") p.add_argument('--select-atoms', help="select only given atoms" "can be only one atom, e.g. P" "or more, use \\' for prims, e.g. P+C4\\'") p.add_argument('file', help='file') return p # main if __name__ == '__main__': parser = get_parser() args = parser.parse_args() if not args.output: args.output = args.file.replace('.pdb', '_out.pdb') edit_occupancy_of_pdb(, args.file, args.output, args.bfactor, args.occupancy, float(args.set_to), float(args.set_not_selected_to), args.select_atoms, args.verbose)