Mercurial > repos > bgruening > openbabel_spectrophore_search
view ob_filter.py @ 14:330514267c57 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author | bgruening |
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date | Tue, 10 Nov 2020 20:39:26 +0000 |
parents | 9ce9f996b941 |
children | f5d7ffbb2d33 |
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#!/usr/bin/env python """ Input: set of molecules with pre-calculated physico-chemical properties Output: set of molecules that pass all the filters Copyright 2012, Bjoern Gruening and Xavier Lucas TODO: AND/OR conditions? """ import argparse import json import shlex import subprocess import sys import cheminfolib from openbabel import pybel cheminfolib.pybel_stop_logging() def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('-i', '--input', help='Input file name') parser.add_argument('-iformat', help='Input file format') parser.add_argument('-oformat', default='smi', help='Output file format') parser.add_argument('-o', '--output', help='Output file name', required=True) parser.add_argument('--filters', help="Specify the filters to apply", required=True) parser.add_argument('--list_of_names', required=False, help="A file with list of molecule names to extract. Every name is in one line.") return parser.parse_args() def filter_precalculated_compounds(args, filters): outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) for mol in pybel.readfile('sdf', args.input): for key, elem in filters.items(): # map the short description to the larger metadata names stored in the sdf file property = cheminfolib.ColumnNames.get(key, key) min = elem[0] max = elem[1] if float(mol.data[property]) >= float(min) and float(mol.data[property]) <= float(max): pass else: # leave the filter loop, because one filter constrained are not satisfied break else: # if the filter loop terminates in a normal way (no break) all filter rules are satisfied, so save the compound outfile.write(mol) outfile.close() def filter_new_compounds(args, filters): if args.iformat == args.oformat: # use the -ocopy option from openbabel to speed up the filtering, additionally no conversion is carried out # http://openbabel.org/docs/dev/FileFormats/Copy_raw_text.html#copy-raw-text cmd = 'obabel -i%s %s -ocopy -O %s --filter' % (args.iformat, args.input, args.output) else: cmd = 'obabel -i%s %s -o%s -O %s --filter' % (args.iformat, args.input, args.oformat, args.output) filter_cmd = '' # OBDescriptor stores a mapping from our desc shortcut to the OB name [0] and a long description [1] for key, elem in filters.items(): ob_descriptor_name = cheminfolib.OBDescriptor[key][0] min = elem[0] max = elem[1] filter_cmd += ' %s>=%s %s<=%s ' % (ob_descriptor_name, min, ob_descriptor_name, max) args = shlex.split('%s "%s"' % (cmd, filter_cmd)) # print '%s "%s"' % (cmd, filter_cmd) # calling openbabel with subprocess and pipe potential errors occuring in openbabel to stdout child = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = child.communicate() return_code = child.returncode if return_code: sys.stdout.write(stdout.decode('utf-8')) sys.stderr.write(stderr.decode('utf-8')) sys.stderr.write("Return error code %i from command:\n" % return_code) sys.stderr.write("%s\n" % cmd) else: sys.stdout.write(stdout.decode('utf-8')) sys.stdout.write(stderr.decode('utf-8')) def filter_by_name(args): outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) for mol in pybel.readfile('sdf', args.input): for name in open(args.list_of_names): if mol.title.strip() == name.strip(): outfile.write(mol) outfile.close() def __main__(): """ Select compounds with certain properties from a small library """ args = parse_command_line() if args.filters == '__filter_by_name__': filter_by_name(args) return # Its a small trick to get the parameters in an easy way from the xml file. # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed. # Also the last loop creates a ',{' that is not an valid jason expression. filters = json.loads((args.filters).replace(' ', '').replace(',}', '}')) if args.iformat == 'sdf': # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering mol = next(pybel.readfile('sdf', args.input)) for key, elem in filters.items(): property = cheminfolib.ColumnNames.get(key, key) if property not in mol.data: break else: # if the for loop finishes in a normal way, we should habe all properties at least in the first molecule # assume it is the same for all other molecules and start the precalculated filtering filter_precalculated_compounds(args, filters) return True filter_new_compounds(args, filters) if __name__ == "__main__": __main__()