Mercurial > repos > bgruening > openbabel_remsmall
changeset 13:e94b2920d4e4 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
| author | bgruening |
|---|---|
| date | Mon, 19 Oct 2020 14:44:19 +0000 |
| parents | aebc671bae78 |
| children | d7f0ca1f2669 |
| files | change_title_to_metadata_value.py cheminfolib.py distance_finder.py macros.xml multi_obgrep.py ob_addh.py ob_filter.py ob_genProp.py ob_remIons.py ob_spectrophore_search.py remove_protonation_state.py subsearch.py test-data/na-sal.inchi test-data/na-sal_obrmions.inchi test-data/ob_remove_protonation_state.inchi |
| diffstat | 15 files changed, 279 insertions(+), 240 deletions(-) [+] |
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--- a/change_title_to_metadata_value.py Tue Jul 28 08:38:01 2020 -0400 +++ b/change_title_to_metadata_value.py Mon Oct 19 14:44:19 2020 +0000 @@ -6,29 +6,27 @@ value of a given-id of the same molecule file. """ -import os -import sys import argparse import random import string - from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() + def main(): parser = argparse.ArgumentParser( description="Change the title from a molecule file to metadata \ -value of a given-id of the same molecule file.", + value of a given-id of the same molecule file.", ) - parser.add_argument('--infile', '-i', - required=True, help="path to the input file") - parser.add_argument('--outfile', '-o', - required=True, help="path to the output file") - parser.add_argument('--key', '-k', - required=True, help="the metadata key from the sdf file which should inlcude the new title") - parser.add_argument('--random', '-r', - action="store_true", help="Add random suffix to the title.") + parser.add_argument('--infile', '-i', required=True, + help="path to the input file") + parser.add_argument('--outfile', '-o', required=True, + help="path to the output file") + parser.add_argument('--key', '-k', required=True, + help="the metadata key from the sdf file which should inlcude the new title") + parser.add_argument('--random', '-r', action="store_true", + help="Add random suffix to the title.") args = parser.parse_args() @@ -39,11 +37,10 @@ if args.random: suffix = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(13)) mol.title += '__%s' % suffix - output.write( mol ) + output.write(mol) output.close() if __name__ == "__main__": main() -
--- a/cheminfolib.py Tue Jul 28 08:38:01 2020 -0400 +++ b/cheminfolib.py Mon Oct 19 14:44:19 2020 +0000 @@ -4,31 +4,37 @@ Copyright 2012, Bjoern Gruening and Xavier Lucas """ -import os, sys +import glob +import re +import subprocess +import sys +import tempfile +from multiprocessing import Pool + try: from galaxy import eggs eggs.require('psycopg2') -except: +except ImportError: + psycopg2 = None print('psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB') try: from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() -except: +except ImportError: + openbabel, pybel = None, None print('OpenBabel could not be found. A few functions are not available without OpenBabel.') -from multiprocessing import Pool -import glob, tempfile, re -import subprocess -def CountLines( path ): +def CountLines(path): out = subprocess.Popen(['wc', '-l', path], - stdout=subprocess.PIPE, - stderr=subprocess.STDOUT - ).communicate()[0] + stdout=subprocess.PIPE, + stderr=subprocess.STDOUT + ).communicate()[0] return int(out.partition(b' ')[0]) + def grep(pattern, file_obj): grepper = re.compile(pattern) for line in file_obj: @@ -36,6 +42,7 @@ return True return False + def check_filetype(filepath): mol = False possible_inchi = True @@ -50,76 +57,78 @@ return 'drf' elif possible_inchi and re.findall('^InChI=', line): return 'inchi' - elif re.findall('^M\s+END', line): + elif re.findall(r'^M\s+END', line): mol = True # first line is not an InChI, so it can't be an InChI file possible_inchi = False if mol: - # END can occures before $$$$, so and SDF file will + # END can occures before $$$$, so and SDF file will # be recognised as mol, if you not using this hack' return 'mol' return 'smi' + def db_connect(args): try: - db_conn = psycopg2.connect("dbname=%s user=%s host=%s password=%s" % (args.dbname, args.dbuser, args.dbhost, args.dbpasswd)); + db_conn = psycopg2.connect("dbname=%s user=%s host=%s password=%s" % (args.dbname, args.dbuser, args.dbhost, args.dbpasswd)) return db_conn - except: + except psycopg2.Error: sys.exit('Unable to connect to the db') + ColumnNames = { - 'can_smiles' : 'Canonical SMILES', - 'can' : 'Canonical SMILES', - 'inchi' : 'InChI', - 'inchi_key' : 'InChI key', - 'inchi_key_first' : 'InChI key first', - 'inchi_key_last' : 'InChI key last', - 'molwt' : 'Molecular weight', - 'hbd' : 'Hydrogen-bond donors', - 'donors' : 'Hydrogen-bond donors', - 'hba' : 'Hydrogen-bond acceptors', - 'acceptors' : 'Hydrogen-bond acceptors', - 'rotbonds' : 'Rotatable bonds', - 'logp' : 'logP', - 'psa' : 'Polar surface area', - 'mr' : 'Molecular refractivity', - 'atoms' : 'Number of heavy atoms', - 'rings' : 'Number of rings', - 'set_bits' : 'FP2 bits', - 'id' : 'Internal identifier', - 'tani' : 'Tanimoto coefficient', - 'spectrophore' : 'Spectrophores(TM)', - 'dist_spectrophore' : 'Spectrophores(TM) distance to target', - 'synonym' : 'Entry id', + 'can_smiles': 'Canonical SMILES', + 'can': 'Canonical SMILES', + 'inchi': 'InChI', + 'inchi_key': 'InChI key', + 'inchi_key_first': 'InChI key first', + 'inchi_key_last': 'InChI key last', + 'molwt': 'Molecular weight', + 'hbd': 'Hydrogen-bond donors', + 'donors': 'Hydrogen-bond donors', + 'hba': 'Hydrogen-bond acceptors', + 'acceptors': 'Hydrogen-bond acceptors', + 'rotbonds': 'Rotatable bonds', + 'logp': 'logP', + 'psa': 'Polar surface area', + 'mr': 'Molecular refractivity', + 'atoms': 'Number of heavy atoms', + 'rings': 'Number of rings', + 'set_bits': 'FP2 bits', + 'id': 'Internal identifier', + 'tani': 'Tanimoto coefficient', + 'spectrophore': 'Spectrophores(TM)', + 'dist_spectrophore': 'Spectrophores(TM) distance to target', + 'synonym': 'Entry id', } OBDescriptor = { - 'atoms': ["atoms","Number of atoms"], - 'hatoms': ["hatoms","Number of heavy atoms"], # self defined tag hatoms in plugindefines.txt - 'can_smiles' : ["cansmi","Canonical SMILES"], - 'can_smilesNS' : ["cansmiNS","Canonical SMILES without isotopes or stereo"], - #["abonds","Number of aromatic bonds"], - #["bonds","Number of bonds"], - #["dbonds","Number of double bonds"], - #["formula","Chemical formula"], - 'hba': ["HBA1","Number of Hydrogen Bond Acceptors 1 (JoelLib)"], - 'hba2': ["HBA2","Number of Hydrogen Bond Acceptors 2 (JoelLib)"], - 'hbd': ["HBD","Number of Hydrogen Bond Donors (JoelLib)"], - 'inchi': ["InChI","IUPAC InChI identifier"], - 'inchi_key': ["InChIKey","InChIKey"], - #["L5","Lipinski Rule of Five"], - 'logp': ["logP","octanol/water partition coefficient"], - 'mr': ["MR","molar refractivity"], - 'molwt': ["MW","Molecular Weight filter"], - #["nF","Number of Fluorine Atoms"], - #["s","SMARTS filter"], - #["sbonds","Number of single bonds"], - #["smarts","SMARTS filter"], - #["tbonds","Number of triple bonds"], - #["title","For comparing a molecule's title"], - 'psa': ["TPSA","topological polar surface area"], - 'rotbonds' : ['ROTATABLE_BOND', 'rotatable bonds'], + 'atoms': ["atoms", "Number of atoms"], + 'hatoms': ["hatoms", "Number of heavy atoms"], # self defined tag hatoms in plugindefines.txt + 'can_smiles': ["cansmi", "Canonical SMILES"], + 'can_smilesNS': ["cansmiNS", "Canonical SMILES without isotopes or stereo"], + # ["abonds", "Number of aromatic bonds"], + # ["bonds", "Number of bonds"], + # ["dbonds", "Number of double bonds"], + # ["formula", "Chemical formula"], + 'hba': ["HBA1", "Number of Hydrogen Bond Acceptors 1 (JoelLib)"], + 'hba2': ["HBA2", "Number of Hydrogen Bond Acceptors 2 (JoelLib)"], + 'hbd': ["HBD", "Number of Hydrogen Bond Donors (JoelLib)"], + 'inchi': ["InChI", "IUPAC InChI identifier"], + 'inchi_key': ["InChIKey", "InChIKey"], + # ["L5", "Lipinski Rule of Five"], + 'logp': ["logP", "octanol/water partition coefficient"], + 'mr': ["MR", "molar refractivity"], + 'molwt': ["MW", "Molecular Weight filter"], + # ["nF", "Number of Fluorine Atoms"], + # ["s", "SMARTS filter"], + # ["sbonds", "Number of single bonds"], + # ["smarts", "SMARTS filter"], + # ["tbonds", "Number of triple bonds"], + # ["title", "For comparing a molecule's title"], + 'psa': ["TPSA", "topological polar surface area"], + 'rotbonds': ['ROTATABLE_BOND', 'rotatable bonds'], } @@ -128,9 +137,9 @@ outfile = open(args.output, 'w') requested_fields = (filter(lambda x: x not in ["[", "]", "'"], args.fetch)).split(', ') if args.header: - outfile.write( 'Identifier\t' + '\t'.join( [ColumnNames[key] for key in requested_fields] ) + '\n' ) + outfile.write('Identifier\t' + '\t'.join([ColumnNames[key] for key in requested_fields]) + '\n') for row in rows: - outfile.write( row['synonym'] + '\t' + '\t'.join( [str(row[key]) for key in requested_fields] ) + '\n' ) + outfile.write(row['synonym'] + '\t' + '\t'.join([str(row[key]) for key in requested_fields]) + '\n') elif args.oformat in ['sdf', 'mol2']: outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) @@ -139,103 +148,102 @@ mol = pybel.readstring('sdf', row['mol']) if args.oformat == 'sdf': keys = filter(lambda x: x not in ["[", "]", "'"], args.fetch).split(', ') - mol.data.update( { ColumnNames['synonym'] : row['synonym'] } ) + mol.data.update({ColumnNames['synonym']: row['synonym']}) if 'inchi_key' in keys: - keys = (', '.join(keys).replace( "inchi_key", "inchi_key_first, inchi_key_last" )).split(', ') - [ mol.data.update( { ColumnNames[key] : row[key] } ) for key in keys if key] + keys = (', '.join(keys).replace("inchi_key", "inchi_key_first, inchi_key_last")).split(', ') + [mol.data.update({ColumnNames[key]: row[key]}) for key in keys if key] outfile.write(mol) - except: + except OSError: pass else: outfile = open(args.output, 'w') - outfile.write( '\n'.join( [ '%s\t%s' % (row[args.oformat], row['synonym'] ) for row in rows ] ) ) + outfile.write('\n'.join(['%s\t%s' % (row[args.oformat], row['synonym']) for row in rows])) outfile.close() + def pybel_stop_logging(): openbabel.obErrorLog.StopLogging() + def get_properties_ext(mol): - HBD = pybel.Smarts("[!#6;!H0]") - HBA = pybel.Smarts("[$([$([#8,#16]);!$(*=N~O);" + - "!$(*~N=O);X1,X2]),$([#7;v3;" + - "!$([nH]);!$(*(-a)-a)])]" - ) + HBA = pybel.Smarts(("[$([$([#8,#16]);!$(*=N~O);" + "!$(*~N=O);X1,X2]),$([#7;v3;" + "!$([nH]);!$(*(-a)-a)])]" + )) calc_desc_dict = mol.calcdesc() try: logp = calc_desc_dict['logP'] - except: + except KeyError: logp = calc_desc_dict['LogP'] return {"molwt": mol.molwt, "logp": logp, "donors": len(HBD.findall(mol)), - "acceptors": len(HBA.findall(mol)), + "acceptors": len(HBA.findall(mol)), "psa": calc_desc_dict['TPSA'], "mr": calc_desc_dict['MR'], "rotbonds": mol.OBMol.NumRotors(), - "can": mol.write("can").split()[0].strip(), ### tthis one works fine for both zinc and chembl (no ZINC code added after can descriptor string) + "can": mol.write("can").split()[0].strip(), # tthis one works fine for both zinc and chembl (no ZINC code added after can descriptor string) "inchi": mol.write("inchi").strip(), "inchi_key": get_inchikey(mol).strip(), "rings": len(mol.sssr), "atoms": mol.OBMol.NumHvyAtoms(), - "spectrophore" : OBspectrophore(mol), - } + "spectrophore": OBspectrophore(mol), + } + def get_inchikey(mol): conv = openbabel.OBConversion() conv.SetInAndOutFormats("mol", "inchi") conv.SetOptions("K", conv.OUTOPTIONS) - inchikey = conv.WriteString( mol.OBMol ) + inchikey = conv.WriteString(mol.OBMol) return inchikey + def OBspectrophore(mol): spectrophore = pybel.ob.OBSpectrophore() # Parameters: rotation angle = 20, normalization for mean and sd, accuracy = 3.0 A and non-stereospecific cages. - spectrophore.SetNormalization( spectrophore.NormalizationTowardsZeroMeanAndUnitStd ) - return ', '.join( [ "%.3f" % value for value in spectrophore.GetSpectrophore( mol.OBMol ) ] ) + spectrophore.SetNormalization(spectrophore.NormalizationTowardsZeroMeanAndUnitStd) + return ', '.join(["%.3f" % value for value in spectrophore.GetSpectrophore(mol.OBMol)]) + -def squared_euclidean_distance(a, b): - try: - return ((np.asarray( a ) - np.asarray( b ))**2).sum() - except ValueError: - return 0 - -def split_library( lib_path, lib_format = 'sdf', package_size = None ): +def split_library(lib_path, lib_format='sdf', package_size=None): """ - Split a library of compounds. Usage: split_library( lib_path, lib_format, package_size ) - IT currently ONLY WORKS FOR SD-Files + Split a library of compounds. Usage: split_library(lib_path, lib_format, package_size) + IT currently ONLY WORKS FOR SD-Files """ pack = 1 mol_counter = 0 - outfile = open('/%s/%s_pack_%i.%s' % ( '/'.join(lib_path.split('/')[:-1]), lib_path.split('/')[-1].split('.')[0], pack, 'sdf'), 'w' ) + outfile = open('/%s/%s_pack_%i.%s' % ('/'.join(lib_path.split('/')[:-1]), lib_path.split('/')[-1].split('.')[0], pack, 'sdf'), 'w') for line in open(lib_path, 'r'): - outfile.write( line ) + outfile.write(line) if line.strip() == '$$$$': mol_counter += 1 if mol_counter % package_size == 0: outfile.close() pack += 1 - outfile = open('/%s/%s_pack_%i.%s' % ( '/'.join(lib_path.split('/')[:-1]), lib_path.split('/')[-1].split('.')[0], pack, 'sdf'), 'w' ) - if mol_counter*10 % package_size == 0: - print('%i molecules parsed, starting pack nr. %i' % ( mol_counter, pack - 1 )) + outfile = open('/%s/%s_pack_%i.%s' % ('/'.join(lib_path.split('/')[:-1]), lib_path.split('/')[-1].split('.')[0], pack, 'sdf'), 'w') + if mol_counter * 10 % package_size == 0: + print('%i molecules parsed, starting pack nr. %i' % (mol_counter, pack - 1)) outfile.close() return True -def split_smi_library( smiles_file, structures_in_one_file ): + +def split_smi_library(smiles_file, structures_in_one_file): """ - Split a file with SMILES to several files for multiprocessing usage. - Usage: split_smi_library( smiles_file, 10 ) + Split a file with SMILES to several files for multiprocessing usage. + Usage: split_smi_library(smiles_file, 10) """ output_files = [] tfile = tempfile.NamedTemporaryFile(delete=False) smiles_handle = open(smiles_file, 'r') - for count, line in enumerate( smiles_handle ): + for count, line in enumerate(smiles_handle): if count % structures_in_one_file == 0 and count != 0: tfile.close() output_files.append(tfile.name) @@ -247,9 +255,9 @@ return output_files -def mp_run(input_path, regex, PROCESSES, function_to_call ): +def mp_run(input_path, regex, PROCESSES, function_to_call): paths = [] - [ paths.append(compound_file) for compound_file in glob.glob(str(input_path) + str(regex)) ] + [paths.append(compound_file) for compound_file in glob.glob(str(input_path) + str(regex))] paths.sort() pool = Pool(processes=PROCESSES) @@ -259,6 +267,6 @@ return paths + if __name__ == '__main__': print(check_filetype(sys.argv[1])) -
--- a/distance_finder.py Tue Jul 28 08:38:01 2020 -0400 +++ b/distance_finder.py Mon Oct 19 14:44:19 2020 +0000 @@ -11,7 +11,9 @@ # a property named distance1 where the numeric part is the index (starting from 1) of the points (in that example # there would be properties for distance1, distance2 and distance3. -import argparse, os, sys, math +import argparse +import math +import sys from openbabel import pybel @@ -30,7 +32,6 @@ :return: """ - points = [] # read the points @@ -41,7 +42,7 @@ p = line.split() if len(p) == 3: points.append((float(p[0]), float(p[1]), float(p[2]))) - log("Read points",p) + log("Read points", p) continue log("Failed to read line:", line) log('Found', len(points), 'atom points') @@ -56,7 +57,6 @@ try: # print("Processing mol", mol.title) - clone = pybel.Molecule(mol) clone.removeh() @@ -82,7 +82,7 @@ sdf_writer.write(mol) except Exception as e: - log('Failed to handle molecule: '+ str(e)) + log('Failed to handle molecule: ' + str(e)) continue sdf_writer.close() @@ -93,12 +93,10 @@ global work_dir parser = argparse.ArgumentParser(description='XChem distances - measure distances to particular points') - parser.add_argument('-i', '--input', help="SDF containing the 3D molecules to score)") parser.add_argument('-p', '--points', help="PDB format file with atoms") parser.add_argument('-o', '--outfile', default='output.sdf', help="File name for results") - args = parser.parse_args() log("XChem distances args: ", args)
--- a/macros.xml Tue Jul 28 08:38:01 2020 -0400 +++ b/macros.xml Mon Oct 19 14:44:19 2020 +0000 @@ -18,6 +18,11 @@ help="Valid file types are: SDF, MOL, MOL2, CML, InChI, SMILES, and PDB"/> </xml> + <xml name="infile_all_types_except_inchi"> + <param name="infile" format="sdf,mol,mol2,cml,smi,pdb" type="data" label="Molecular input file" + help="Valid file types are: SDF, MOL, MOL2, CML, SMILES, and PDB"/> + </xml> + <xml name="2D_3D_opts"> <param name="gen2d" type="boolean" truevalue="--gen2d" falsevalue="" checked="false" label="Generate 2D coordinates" help="(--gen2d)" />
--- a/multi_obgrep.py Tue Jul 28 08:38:01 2020 -0400 +++ b/multi_obgrep.py Mon Oct 19 14:44:19 2020 +0000 @@ -4,40 +4,43 @@ Output: Molecule file filtered with obgrep. Copyright 2013, Bjoern Gruening and Xavier Lucas """ -import sys, os import argparse import multiprocessing -import tempfile -import subprocess -import shutil +import os import shlex +import shutil +import subprocess +import tempfile -from openbabel import openbabel, pybel -openbabel.obErrorLog.StopLogging() + def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('-i', '--infile', required=True, help='Molecule file.') - parser.add_argument('-q', '--query', required=True, help='Query file, containing different SMARTS in each line.') + parser.add_argument('-q', '--query', required=True, help='Query file, containing different SMARTS in each line.') parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.') parser.add_argument("--iformat", help="Input format, like smi, sdf, inchi") parser.add_argument("--n-times", dest="n_times", type=int, - default=0, help="Print a molecule only if the pattern occurs # times inside the molecule.") + default=0, help="Print a molecule only if the pattern occurs # times inside the molecule.") parser.add_argument('-p', '--processors', type=int, default=multiprocessing.cpu_count()) parser.add_argument("--invert-matches", dest="invert_matches", action="store_true", - default=False, help="Invert the matching, print non-matching molecules.") + default=False, help="Invert the matching, print non-matching molecules.") parser.add_argument("--only-name", dest="only_name", action="store_true", - default=False, help="Only print the name of the molecules.") + default=False, help="Only print the name of the molecules.") parser.add_argument("--full-match", dest="full_match", action="store_true", - default=False, help="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern.") + default=False, help="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern.") parser.add_argument("--number-of-matches", dest="number_of_matches", action="store_true", - default=False, help="Print the number of matches.") + default=False, help="Print the number of matches.") return parser.parse_args() + results = list() + + def mp_callback(res): results.append(res) -def mp_helper( query, args ): + +def mp_helper(query, args): """ Helper function for multiprocessing. That function is a wrapper around obgrep. @@ -57,44 +60,44 @@ tmp = tempfile.NamedTemporaryFile(delete=False) cmd = 'obgrep %s "%s" %s' % (' '.join(cmd_list), query, args.infile) - child = subprocess.Popen(shlex.split(cmd), - stdout=open(tmp.name, 'w+'), stderr=subprocess.PIPE) + child = subprocess.Popen(shlex.split(cmd), stdout=open(tmp.name, 'w+'), stderr=subprocess.PIPE) stdout, stderr = child.communicate() return (tmp.name, query) -def obgrep( args ): - +def obgrep(args): temp_file = tempfile.NamedTemporaryFile() temp_link = "%s.%s" % (temp_file.name, args.iformat) temp_file.close() os.symlink(args.infile, temp_link) args.infile = temp_link - pool = multiprocessing.Pool( args.processors ) - for query in open( args.query ): + pool = multiprocessing.Pool(args.processors) + for query in open(args.query): pool.apply_async(mp_helper, args=(query.strip(), args), callback=mp_callback) - #mp_callback( mp_helper(query.strip(), args) ) + # mp_callback(mp_helper(query.strip(), args)) pool.close() pool.join() - out_handle = open( args.outfile, 'wb' ) + out_handle = open(args.outfile, 'wb') for result_file, query in results: - res_handle = open(result_file,'rb') - shutil.copyfileobj( res_handle, out_handle ) + res_handle = open(result_file, 'rb') + shutil.copyfileobj(res_handle, out_handle) res_handle.close() - os.remove( result_file ) + os.remove(result_file) out_handle.close() - os.remove( temp_link ) + os.remove(temp_link) + def __main__(): """ Multiprocessing obgrep search. """ args = parse_command_line() - obgrep( args ) + obgrep(args) + -if __name__ == "__main__" : +if __name__ == "__main__": __main__()
--- a/ob_addh.py Tue Jul 28 08:38:01 2020 -0400 +++ b/ob_addh.py Mon Oct 19 14:44:19 2020 +0000 @@ -3,21 +3,23 @@ Input: Molecule file Output: Molecule file with hydrogen atoms added at the target pH. """ -import sys, os import argparse +import sys from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() + def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--iformat', type=str, default='sdf' , help='input file format') + parser.add_argument('--iformat', type=str, default='sdf', help='input file format') parser.add_argument('-i', '--input', type=str, required=True, help='input file name') parser.add_argument('-o', '--output', type=str, required=True, help='output file name') parser.add_argument('--polar', action="store_true", default=False, help='Add hydrogen atoms only to polar atoms') parser.add_argument('--pH', type=float, default="7.4", help='Specify target pH value') return parser.parse_args() + def addh(args): outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) for mol in pybel.readfile(args.iformat, args.input): @@ -27,6 +29,7 @@ outfile.write(mol) outfile.close() + def __main__(): """ Add hydrogen atoms at a certain pH value @@ -34,5 +37,6 @@ args = parse_command_line(sys.argv) addh(args) -if __name__ == "__main__" : + +if __name__ == "__main__": __main__()
--- a/ob_filter.py Tue Jul 28 08:38:01 2020 -0400 +++ b/ob_filter.py Mon Oct 19 14:44:19 2020 +0000 @@ -6,35 +6,32 @@ TODO: AND/OR conditions? """ -import sys, os import argparse +import json +import shlex +import subprocess +import sys + import cheminfolib -import json -import shlex, subprocess - 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', - help="A file with list of molecule names to extract. Every name is in one line.", - required=False, - ) + 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): @@ -53,6 +50,7 @@ outfile.write(mol) outfile.close() + def filter_new_compounds(args, filters): if args.iformat == args.oformat: @@ -70,10 +68,9 @@ 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) + # 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) + child = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = child.communicate() return_code = child.returncode @@ -87,6 +84,7 @@ 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): @@ -95,16 +93,17 @@ 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. @@ -114,7 +113,7 @@ mol = next(pybel.readfile('sdf', args.input)) for key, elem in filters.items(): property = cheminfolib.ColumnNames.get(key, key) - if not property in mol.data: + 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 @@ -124,5 +123,5 @@ filter_new_compounds(args, filters) -if __name__ == "__main__" : +if __name__ == "__main__": __main__()
--- a/ob_genProp.py Tue Jul 28 08:38:01 2020 -0400 +++ b/ob_genProp.py Mon Oct 19 14:44:19 2020 +0000 @@ -4,23 +4,25 @@ Output: Physico-chemical properties are computed and stored as metadata in the sdf output file. Copyright 2012, Bjoern Gruening and Xavier Lucas """ -import sys, os import argparse +import sys + +import cheminfolib import openbabel +from openbabel import pybel openbabel.obErrorLog.StopLogging() -import cheminfolib -from openbabel import pybel def parse_command_line(argv): parser = argparse.ArgumentParser() - parser.add_argument('--iformat', default='sdf' , help='input file format') + parser.add_argument('--iformat', default='sdf', help='input file format') parser.add_argument('-i', '--input', required=True, help='input file name') - parser.add_argument('--oformat', default='sdf', choices = ['sdf', 'table'] , help='output file format') + parser.add_argument('--oformat', default='sdf', choices=['sdf', 'table'], help='output file format') parser.add_argument('--header', type=bool, help='Include the header as the first line of the output table') parser.add_argument('-o', '--output', required=True, help='output file name') return parser.parse_args() + def compute_properties(args): if args.oformat == 'sdf': outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) @@ -29,18 +31,19 @@ if args.header: mol = next(pybel.readfile(args.iformat, args.input)) metadata = cheminfolib.get_properties_ext(mol) - outfile.write( '%s\n' % '\t'.join( [ cheminfolib.ColumnNames[key] for key in metadata ] ) ) + outfile.write('%s\n' % '\t'.join([cheminfolib.ColumnNames[key] for key in metadata])) for mol in pybel.readfile(args.iformat, args.input): if mol.OBMol.NumHvyAtoms() > 5: metadata = cheminfolib.get_properties_ext(mol) if args.oformat == 'sdf': - [ mol.data.update( { cheminfolib.ColumnNames[key] : metadata[key] } ) for key in metadata ] + [mol.data.update({cheminfolib.ColumnNames[key]: metadata[key]}) for key in metadata] outfile.write(mol) else: - outfile.write( '%s\n' % ('\t'.join( [ str(metadata[key]) for key in metadata ] ) ) ) + outfile.write('%s\n' % ('\t'.join([str(metadata[key]) for key in metadata]))) outfile.close() + def __main__(): """ Physico-chemical properties are computed and stored as metadata in the sdf output file @@ -48,5 +51,6 @@ args = parse_command_line(sys.argv) compute_properties(args) -if __name__ == "__main__" : + +if __name__ == "__main__": __main__()
--- a/ob_remIons.py Tue Jul 28 08:38:01 2020 -0400 +++ b/ob_remIons.py Mon Oct 19 14:44:19 2020 +0000 @@ -4,29 +4,33 @@ Output: Molecule file with removed ions and fragments. Copyright 2012, Bjoern Gruening and Xavier Lucas """ -import sys, os import argparse from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() + def parse_command_line(): parser = argparse.ArgumentParser() - parser.add_argument('-iformat', default='sdf' , help='input file format') + parser.add_argument('-iformat', default='sdf', help='input file format') parser.add_argument('-i', '--input', required=True, help='input file name') parser.add_argument('-o', '--output', required=True, help='output file name') return parser.parse_args() + def remove_ions(args): outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) for mol in pybel.readfile(args.iformat, args.input): if mol.OBMol.NumHvyAtoms() > 5: mol.OBMol.StripSalts(0) + if 'inchi' in mol.data: + del mol.data['inchi'] # remove inchi cache so modified mol is saved # Check if new small fragments have been created and remove them if mol.OBMol.NumHvyAtoms() > 5: outfile.write(mol) outfile.close() + def __main__(): """ Remove any counterion and delete any fragment but the largest one for each molecule. @@ -34,5 +38,6 @@ args = parse_command_line() remove_ions(args) -if __name__ == "__main__" : + +if __name__ == "__main__": __main__()
--- a/ob_spectrophore_search.py Tue Jul 28 08:38:01 2020 -0400 +++ b/ob_spectrophore_search.py Mon Oct 19 14:44:19 2020 +0000 @@ -4,18 +4,17 @@ Output: parse the target file using the same protocol used to generate the databases in our servers. Physico-chemical properties are computed and stored as metadata in the sdf output file. Copyright 2012, Bjoern Gruening and Xavier Lucas """ -import sys, os import argparse -import math + import numpy as np - from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() -#TODO get rid of eval() +# TODO get rid of eval() global spectrophore spectrophore = pybel.ob.OBSpectrophore() + def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('--target', required=True, help='target file name in sdf format with Spectrophores(TM) descriptors stored as meta-data') @@ -28,26 +27,29 @@ parser.add_argument('-r', '--resolution', type=float, default="3.0", help='Resolution') return parser.parse_args() + def set_parameters(args): if args.normalization == 'No': - spectrophore.SetNormalization( spectrophore.NoNormalization ) + spectrophore.SetNormalization(spectrophore.NoNormalization) else: - spectrophore.SetNormalization( eval('spectrophore.NormalizationTowards' + args.normalization) ) - spectrophore.SetAccuracy( eval('spectrophore.AngStepSize' + args.accuracy) ) - spectrophore.SetStereo( eval('spectrophore.' + args.stereo + 'StereoSpecificProbes') ) - spectrophore.SetResolution( args.resolution ) + spectrophore.SetNormalization(eval('spectrophore.NormalizationTowards' + args.normalization)) + spectrophore.SetAccuracy(eval('spectrophore.AngStepSize' + args.accuracy)) + spectrophore.SetStereo(eval('spectrophore.' + args.stereo + 'StereoSpecificProbes')) + spectrophore.SetResolution(args.resolution) return True + def Compute_Spectrophores_distance(target_spectrophore, args): outfile = open(args.output, 'w') for mol in open(args.library, 'r'): try: - distance = ( ( np.asarray( target_spectrophore, dtype=float ) - np.asarray( mol.split('\t')[ args.column - 1 ].strip().split(', '), dtype=float) )**2).sum() + distance = ((np.asarray(target_spectrophore, dtype=float) - np.asarray(mol.split('\t')[args.column - 1].strip().split(', '), dtype=float))**2).sum() except ValueError: distance = 0 - outfile.write( '%s\t%f\n' % (mol.strip(), distance ) ) + outfile.write('%s\t%f\n' % (mol.strip(), distance)) outfile.close() + def __main__(): """ Computation of Spectrophores(TM) distances to a target molecule. @@ -59,7 +61,8 @@ mol = next(pybel.readfile('sdf', args.target)) target_spectrophore = mol.data["Spectrophores(TM)"].strip().split(', ') # Compute the paired-distance between every molecule in the library and the target - distances = Compute_Spectrophores_distance(target_spectrophore, args) + Compute_Spectrophores_distance(target_spectrophore, args) + -if __name__ == "__main__" : +if __name__ == "__main__": __main__()
--- a/remove_protonation_state.py Tue Jul 28 08:38:01 2020 -0400 +++ b/remove_protonation_state.py Mon Oct 19 14:44:19 2020 +0000 @@ -4,32 +4,37 @@ Output: Molecule file with removed ions and fragments. Copyright 2013, Bjoern Gruening and Xavier Lucas """ -import sys, os import argparse from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() + def parse_command_line(): parser = argparse.ArgumentParser() - parser.add_argument('--iformat', default='sdf' , help='input file format') + parser.add_argument('--iformat', default='sdf', help='input file format') parser.add_argument('-i', '--input', required=True, help='input file name') parser.add_argument('-o', '--output', required=True, help='output file name') return parser.parse_args() -def remove_protonation( args ): + +def remove_protonation(args): outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) for mol in pybel.readfile(args.iformat, args.input): [atom.OBAtom.SetFormalCharge(0) for atom in mol.atoms] - outfile.write( mol ) + if 'inchi' in mol.data: + del mol.data['inchi'] # remove inchi cache so modified mol is saved + outfile.write(mol) outfile.close() + def __main__(): """ Remove any protonation state from each atom in each molecule. """ args = parse_command_line() - remove_protonation( args ) + remove_protonation(args) + -if __name__ == "__main__" : +if __name__ == "__main__": __main__()
--- a/subsearch.py Tue Jul 28 08:38:01 2020 -0400 +++ b/subsearch.py Mon Oct 19 14:44:19 2020 +0000 @@ -4,36 +4,41 @@ Output: Moleculs filtered with specified substructures. Copyright 2013, Bjoern Gruening and Xavier Lucas """ -import sys, os import argparse import multiprocessing -import tempfile +import os +import shutil import subprocess -import shutil +import sys +import tempfile from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() + def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('-i', '--infile', required=True, help='Molecule file.') parser.add_argument('--iformat', help='Input format.') - parser.add_argument('--fastsearch-index', dest="fastsearch_index", - required=True, help='Path to the openbabel fastsearch index.') + parser.add_argument('--fastsearch-index', dest="fastsearch_index", required=True, + help='Path to the openbabel fastsearch index.') parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.') - parser.add_argument('--oformat', - default='smi', help='Output file format') - parser.add_argument("--max-candidates", dest="max_candidates", type=int, - default=4000, help="The maximum number of candidates.") - parser.add_argument('-p', '--processors', type=int, - default=multiprocessing.cpu_count()) + parser.add_argument('--oformat', default='smi', help='Output file format') + parser.add_argument("--max-candidates", dest="max_candidates", type=int, default=4000, + help="The maximum number of candidates.") + parser.add_argument('-p', '--processors', type=int, + default=multiprocessing.cpu_count()) return parser.parse_args() + results = list() + + def mp_callback(res): results.append(res) -def mp_helper( query, args ): + +def mp_helper(query, args): """ Helper function for multiprocessing. That function is a wrapper around the following command: @@ -48,8 +53,7 @@ tmp = tempfile.NamedTemporaryFile(delete=False) cmd = 'obabel -ifs %s -O %s %s -s%s -al %s' % (args.fastsearch_index, tmp.name, opts, query, args.max_candidates) - child = subprocess.Popen(cmd.split(), - stdout=subprocess.PIPE, stderr=subprocess.PIPE) + child = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = child.communicate() return_code = child.returncode @@ -65,43 +69,43 @@ return (tmp.name, query) -def get_smiles_or_smarts( args ): +def get_smiles_or_smarts(args): """ Wrapper to retrieve a striped SMILES or SMARTS string from different input formats. """ if args.iformat in ['smi', 'text', 'tabular']: - with open( args.infile ) as text_file: + with open(args.infile) as text_file: for line in text_file: yield line.split('\t')[0].strip() else: # inchi or sdf files - for mol in pybel.readfile( args.iformat, args.infile ): + for mol in pybel.readfile(args.iformat, args.infile): yield mol.write('smiles').split('\t')[0] -def substructure_search( args ): - pool = multiprocessing.Pool( args.processors ) - for query in get_smiles_or_smarts( args ): +def substructure_search(args): + pool = multiprocessing.Pool(args.processors) + for query in get_smiles_or_smarts(args): pool.apply_async(mp_helper, args=(query, args), callback=mp_callback) - #mp_callback( mp_helper(query, args) ) + # mp_callback(mp_helper(query, args)) pool.close() pool.join() if args.oformat == 'names': - out_handle = open( args.outfile, 'w' ) + out_handle = open(args.outfile, 'w') for result_file, query in results: with open(result_file) as res_handle: for line in res_handle: - out_handle.write('%s\t%s\n' % ( line.strip(), query )) - os.remove( result_file ) + out_handle.write('%s\t%s\n' % (line.strip(), query)) + os.remove(result_file) out_handle.close() else: - out_handle = open( args.outfile, 'wb' ) + out_handle = open(args.outfile, 'wb') for result_file, query in results: - res_handle = open(result_file,'rb') - shutil.copyfileobj( res_handle, out_handle ) + res_handle = open(result_file, 'rb') + shutil.copyfileobj(res_handle, out_handle) res_handle.close() - os.remove( result_file ) + os.remove(result_file) out_handle.close() @@ -110,7 +114,8 @@ Multiprocessing Open Babel Substructure Search. """ args = parse_command_line() - substructure_search( args ) + substructure_search(args) + -if __name__ == "__main__" : +if __name__ == "__main__": __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/na-sal.inchi Mon Oct 19 14:44:19 2020 +0000 @@ -0,0 +1,1 @@ +InChI=1S/C7H6O3.Na/c8-6-4-2-1-3-5(6)7(9)10;/h1-4,8H,(H,9,10);/q;+1/p-1