Mercurial > repos > bgruening > openbabel_obgrep
diff cheminfolib.py @ 14:985ab0acd514 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
| author | bgruening |
|---|---|
| date | Thu, 15 Aug 2024 11:05:06 +0000 |
| parents | 2912ebf12ef2 |
| children |
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--- a/cheminfolib.py Tue Nov 10 20:32:42 2020 +0000 +++ b/cheminfolib.py Thu Aug 15 11:05:06 2024 +0000 @@ -11,28 +11,32 @@ import tempfile from multiprocessing import Pool - try: from galaxy import eggs - eggs.require('psycopg2') + + eggs.require("psycopg2") except ImportError: psycopg2 = None - print('psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB') + 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 ImportError: openbabel, pybel = None, None - print('OpenBabel could not be found. A few functions are not available without OpenBabel.') + print( + "OpenBabel could not be found. A few functions are not available without OpenBabel." + ) def CountLines(path): - out = subprocess.Popen(['wc', '-l', path], - stdout=subprocess.PIPE, - stderr=subprocess.STDOUT - ).communicate()[0] - return int(out.partition(b' ')[0]) + out = subprocess.Popen( + ["wc", "-l", path], stdout=subprocess.PIPE, stderr=subprocess.STDOUT + ).communicate()[0] + return int(out.partition(b" ")[0]) def grep(pattern, file_obj): @@ -49,15 +53,15 @@ for line_counter, line in enumerate(open(filepath)): if line_counter > 10000: break - if line.find('$$$$') != -1: - return 'sdf' - elif line.find('@<TRIPOS>MOLECULE') != -1: - return 'mol2' - elif line.find('ligand id') != -1: - return 'drf' - elif possible_inchi and re.findall('^InChI=', line): - return 'inchi' - elif re.findall(r'^M\s+END', line): + if line.find("$$$$") != -1: + return "sdf" + elif line.find("@<TRIPOS>MOLECULE") != -1: + return "mol2" + elif line.find("ligand id") != -1: + return "drf" + elif possible_inchi and re.findall("^InChI=", line): + return "inchi" + elif re.findall(r"^M\s+END", line): mol = True # first line is not an InChI, so it can't be an InChI file possible_inchi = False @@ -65,99 +69,128 @@ if mol: # END can occures before $$$$, so and SDF file will # be recognised as mol, if you not using this hack' - return 'mol' - return 'smi' + 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 psycopg2.Error: - sys.exit('Unable to connect to the db') + 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"], + "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"], + "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"], + "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'], + "psa": ["TPSA", "topological polar surface area"], + "rotbonds": ["ROTATABLE_BOND", "rotatable bonds"], } def print_output(args, rows): - if args.oformat == 'table': - outfile = open(args.output, 'w') - requested_fields = (filter(lambda x: x not in ["[", "]", "'"], args.fetch)).split(', ') + if args.oformat == "table": + 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']: + elif args.oformat in ["sdf", "mol2"]: outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) for row in rows: try: - 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']}) - 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] + 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"]}) + 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 + ] outfile.write(mol) 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 = open(args.output, "w") + outfile.write( + "\n".join(["%s\t%s" % (row[args.oformat], row["synonym"]) for row in rows]) + ) outfile.close() @@ -167,31 +200,37 @@ 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'] + logp = calc_desc_dict["logP"] except KeyError: - logp = calc_desc_dict['LogP'] + logp = calc_desc_dict["LogP"] - return {"molwt": mol.molwt, - "logp": logp, - "donors": len(HBD.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) - "inchi": mol.write("inchi").strip(), - "inchi_key": get_inchikey(mol).strip(), - "rings": len(mol.sssr), - "atoms": mol.OBMol.NumHvyAtoms(), - "spectrophore": OBspectrophore(mol), - } + return { + "molwt": mol.molwt, + "logp": logp, + "donors": len(HBD.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) + "inchi": mol.write("inchi").strip(), + "inchi_key": get_inchikey(mol).strip(), + "rings": len(mol.sssr), + "atoms": mol.OBMol.NumHvyAtoms(), + "spectrophore": OBspectrophore(mol), + } def get_inchikey(mol): @@ -206,10 +245,12 @@ 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)]) + return ", ".join( + ["%.3f" % value for value in spectrophore.GetSpectrophore(mol.OBMol)] + ) -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 @@ -217,18 +258,39 @@ 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'): + for line in open(lib_path, "r"): outfile.write(line) - if line.strip() == '$$$$': + if line.strip() == "$$$$": 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') + 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)) + print( + "%i molecules parsed, starting pack nr. %i" + % (mol_counter, pack - 1) + ) outfile.close() return True @@ -242,7 +304,7 @@ output_files = [] tfile = tempfile.NamedTemporaryFile(delete=False) - smiles_handle = open(smiles_file, 'r') + smiles_handle = open(smiles_file, "r") for count, line in enumerate(smiles_handle): if count % structures_in_one_file == 0 and count != 0: tfile.close() @@ -257,16 +319,19 @@ 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) - print('Process initialized with', PROCESSES, 'processors') + print("Process initialized with", PROCESSES, "processors") result = pool.map_async(function_to_call, paths) result.get() return paths -if __name__ == '__main__': +if __name__ == "__main__": print(check_filetype(sys.argv[1]))