| Previous changeset 14:330514267c57 (2020-11-10) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf |
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modified:
change_title_to_metadata_value.py cheminfolib.py distance_finder.py multi_obgrep.py ob_addh.py ob_filter.py ob_genProp.py ob_remIons.py ob_spectrophore_search.py ob_spectrophore_search.xml remove_protonation_state.py subsearch.py |
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added:
test-data/2_mol.sdf |
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| diff -r 330514267c57 -r f5d7ffbb2d33 change_title_to_metadata_value.py --- a/change_title_to_metadata_value.py Tue Nov 10 20:39:26 2020 +0000 +++ b/change_title_to_metadata_value.py Thu Aug 15 11:03:22 2024 +0000 |
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| @@ -11,6 +11,7 @@ import string from openbabel import openbabel, pybel + openbabel.obErrorLog.StopLogging() @@ -19,14 +20,19 @@ description="Change the title from a molecule file to metadata \ 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() @@ -35,8 +41,11 @@ if args.key in mol.data: mol.title = mol.data[args.key] if args.random: - suffix = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(13)) - mol.title += '__%s' % suffix + suffix = "".join( + random.choice(string.ascii_lowercase + string.digits) + for _ in range(13) + ) + mol.title += "__%s" % suffix output.write(mol) output.close() |
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| diff -r 330514267c57 -r f5d7ffbb2d33 cheminfolib.py --- a/cheminfolib.py Tue Nov 10 20:39:26 2020 +0000 +++ b/cheminfolib.py Thu Aug 15 11:03:22 2024 +0000 |
| [ |
| b'@@ -11,28 +11,32 @@\n import tempfile\n from multiprocessing import Pool\n \n-\n try:\n from galaxy import eggs\n- eggs.require(\'psycopg2\')\n+\n+ eggs.require("psycopg2")\n except ImportError:\n psycopg2 = None\n- print(\'psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB\')\n+ print(\n+ "psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB"\n+ )\n \n try:\n from openbabel import openbabel, pybel\n+\n openbabel.obErrorLog.StopLogging()\n except ImportError:\n openbabel, pybel = None, None\n- print(\'OpenBabel could not be found. A few functions are not available without OpenBabel.\')\n+ print(\n+ "OpenBabel could not be found. A few functions are not available without OpenBabel."\n+ )\n \n \n def CountLines(path):\n- out = subprocess.Popen([\'wc\', \'-l\', path],\n- stdout=subprocess.PIPE,\n- stderr=subprocess.STDOUT\n- ).communicate()[0]\n- return int(out.partition(b\' \')[0])\n+ out = subprocess.Popen(\n+ ["wc", "-l", path], stdout=subprocess.PIPE, stderr=subprocess.STDOUT\n+ ).communicate()[0]\n+ return int(out.partition(b" ")[0])\n \n \n def grep(pattern, file_obj):\n@@ -49,15 +53,15 @@\n for line_counter, line in enumerate(open(filepath)):\n if line_counter > 10000:\n break\n- if line.find(\'$$$$\') != -1:\n- return \'sdf\'\n- elif line.find(\'@<TRIPOS>MOLECULE\') != -1:\n- return \'mol2\'\n- elif line.find(\'ligand id\') != -1:\n- return \'drf\'\n- elif possible_inchi and re.findall(\'^InChI=\', line):\n- return \'inchi\'\n- elif re.findall(r\'^M\\s+END\', line):\n+ if line.find("$$$$") != -1:\n+ return "sdf"\n+ elif line.find("@<TRIPOS>MOLECULE") != -1:\n+ return "mol2"\n+ elif line.find("ligand id") != -1:\n+ return "drf"\n+ elif possible_inchi and re.findall("^InChI=", line):\n+ return "inchi"\n+ elif re.findall(r"^M\\s+END", line):\n mol = True\n # first line is not an InChI, so it can\'t be an InChI file\n possible_inchi = False\n@@ -65,99 +69,128 @@\n if mol:\n # END can occures before $$$$, so and SDF file will\n # be recognised as mol, if you not using this hack\'\n- return \'mol\'\n- return \'smi\'\n+ return "mol"\n+ return "smi"\n \n \n def db_connect(args):\n try:\n- db_conn = psycopg2.connect("dbname=%s user=%s host=%s password=%s" % (args.dbname, args.dbuser, args.dbhost, args.dbpasswd))\n+ db_conn = psycopg2.connect(\n+ "dbname=%s user=%s host=%s password=%s"\n+ % (args.dbname, args.dbuser, args.dbhost, args.dbpasswd)\n+ )\n return db_conn\n except psycopg2.Error:\n- sys.exit(\'Unable to connect to the db\')\n+ sys.exit("Unable to connect to the db")\n \n \n ColumnNames = {\n- \'can_smiles\': \'Canonical SMILES\',\n- \'can\': \'Canonical SMILES\',\n- \'inchi\': \'InChI\',\n- \'inchi_key\': \'InChI key\',\n- \'inchi_key_first\': \'InChI key first\',\n- \'inchi_key_last\': \'InChI key last\',\n- \'molwt\': \'Molecular weight\',\n- \'hbd\': \'Hydrogen-bond donors\',\n- \'donors\': \'Hydrogen-bond donors\',\n- \'hba\': \'Hydrogen-bond acceptors\',\n- \'acceptors\': \'Hydrogen-bond acceptors\',\n- \'rotbonds\': \'Rotatable bonds\',\n- \'logp\': \'logP\',\n- \'psa\': \'Polar surface area\',\n- \'mr\': \'Molecular refractivity\',\n- \'atoms\': \'Number of heavy atoms\',\n- \'rings\': \'Number of rings\',\n- \'set_bits\': \'FP2 bits\',\n- \'id\': \'Internal identifier\',\n- \'tani\': \'Tanimoto coefficient\',\n- \'spectrophore\': \'Spectrophores(TM)\',\n- \'dist_spectrophore\': \'Spectrophores(TM) distance to target\',\n- \'synonym\': \'Entry id\',\n+ "can_smiles": "Canonical SMILES",\n+ "can": "Canonical SMILES",\n+ "inchi": "InChI",\n+ "inchi_key": "InChI key",\n+ "inchi_key_first": "InC'..b'ol)),\n+ "acceptors": len(HBA.findall(mol)),\n+ "psa": calc_desc_dict["TPSA"],\n+ "mr": calc_desc_dict["MR"],\n+ "rotbonds": mol.OBMol.NumRotors(),\n+ "can": mol.write("can")\n+ .split()[0]\n+ .strip(), # tthis one works fine for both zinc and chembl (no ZINC code added after can descriptor string)\n+ "inchi": mol.write("inchi").strip(),\n+ "inchi_key": get_inchikey(mol).strip(),\n+ "rings": len(mol.sssr),\n+ "atoms": mol.OBMol.NumHvyAtoms(),\n+ "spectrophore": OBspectrophore(mol),\n+ }\n \n \n def get_inchikey(mol):\n@@ -206,10 +245,12 @@\n spectrophore = pybel.ob.OBSpectrophore()\n # Parameters: rotation angle = 20, normalization for mean and sd, accuracy = 3.0 A and non-stereospecific cages.\n spectrophore.SetNormalization(spectrophore.NormalizationTowardsZeroMeanAndUnitStd)\n- return \', \'.join(["%.3f" % value for value in spectrophore.GetSpectrophore(mol.OBMol)])\n+ return ", ".join(\n+ ["%.3f" % value for value in spectrophore.GetSpectrophore(mol.OBMol)]\n+ )\n \n \n-def split_library(lib_path, lib_format=\'sdf\', package_size=None):\n+def split_library(lib_path, lib_format="sdf", package_size=None):\n """\n Split a library of compounds. Usage: split_library(lib_path, lib_format, package_size)\n IT currently ONLY WORKS FOR SD-Files\n@@ -217,18 +258,39 @@\n pack = 1\n mol_counter = 0\n \n- outfile = open(\'/%s/%s_pack_%i.%s\' % (\'/\'.join(lib_path.split(\'/\')[:-1]), lib_path.split(\'/\')[-1].split(\'.\')[0], pack, \'sdf\'), \'w\')\n+ outfile = open(\n+ "/%s/%s_pack_%i.%s"\n+ % (\n+ "/".join(lib_path.split("/")[:-1]),\n+ lib_path.split("/")[-1].split(".")[0],\n+ pack,\n+ "sdf",\n+ ),\n+ "w",\n+ )\n \n- for line in open(lib_path, \'r\'):\n+ for line in open(lib_path, "r"):\n outfile.write(line)\n- if line.strip() == \'$$$$\':\n+ if line.strip() == "$$$$":\n mol_counter += 1\n if mol_counter % package_size == 0:\n outfile.close()\n pack += 1\n- outfile = open(\'/%s/%s_pack_%i.%s\' % (\'/\'.join(lib_path.split(\'/\')[:-1]), lib_path.split(\'/\')[-1].split(\'.\')[0], pack, \'sdf\'), \'w\')\n+ outfile = open(\n+ "/%s/%s_pack_%i.%s"\n+ % (\n+ "/".join(lib_path.split("/")[:-1]),\n+ lib_path.split("/")[-1].split(".")[0],\n+ pack,\n+ "sdf",\n+ ),\n+ "w",\n+ )\n if mol_counter * 10 % package_size == 0:\n- print(\'%i molecules parsed, starting pack nr. %i\' % (mol_counter, pack - 1))\n+ print(\n+ "%i molecules parsed, starting pack nr. %i"\n+ % (mol_counter, pack - 1)\n+ )\n outfile.close()\n \n return True\n@@ -242,7 +304,7 @@\n output_files = []\n tfile = tempfile.NamedTemporaryFile(delete=False)\n \n- smiles_handle = open(smiles_file, \'r\')\n+ smiles_handle = open(smiles_file, "r")\n for count, line in enumerate(smiles_handle):\n if count % structures_in_one_file == 0 and count != 0:\n tfile.close()\n@@ -257,16 +319,19 @@\n \n def mp_run(input_path, regex, PROCESSES, function_to_call):\n paths = []\n- [paths.append(compound_file) for compound_file in glob.glob(str(input_path) + str(regex))]\n+ [\n+ paths.append(compound_file)\n+ for compound_file in glob.glob(str(input_path) + str(regex))\n+ ]\n paths.sort()\n \n pool = Pool(processes=PROCESSES)\n- print(\'Process initialized with\', PROCESSES, \'processors\')\n+ print("Process initialized with", PROCESSES, "processors")\n result = pool.map_async(function_to_call, paths)\n result.get()\n \n return paths\n \n \n-if __name__ == \'__main__\':\n+if __name__ == "__main__":\n print(check_filetype(sys.argv[1]))\n' |
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| diff -r 330514267c57 -r f5d7ffbb2d33 distance_finder.py --- a/distance_finder.py Tue Nov 10 20:39:26 2020 +0000 +++ b/distance_finder.py Thu Aug 15 11:03:22 2024 +0000 |
| [ |
| @@ -19,9 +19,8 @@ def log(*args, **kwargs): - """Log output to STDERR - """ - print(*args, file=sys.stderr, ** kwargs) + """Log output to STDERR""" + print(*args, file=sys.stderr, **kwargs) def execute(ligands_sdf, points_file, outfile): @@ -35,7 +34,7 @@ points = [] # read the points - with open(points_file, 'r') as f: + with open(points_file, "r") as f: for line in f.readlines(): line.strip() if line: @@ -45,7 +44,7 @@ log("Read points", p) continue log("Failed to read line:", line) - log('Found', len(points), 'atom points') + log("Found", len(points), "atom points") sdf_writer = pybel.Outputfile("sdf", outfile, overwrite=True) @@ -53,7 +52,7 @@ for mol in pybel.readfile("sdf", ligands_sdf): count += 1 if count % 50000 == 0: - log('Processed', count) + log("Processed", count) try: # print("Processing mol", mol.title) @@ -70,32 +69,42 @@ distances = [] for i in coords: # calculates distance based on cartesian coordinates - distance = math.sqrt((point[0] - i[0])**2 + (point[1] - i[1])**2 + (point[2] - i[2])**2) + distance = math.sqrt( + (point[0] - i[0]) ** 2 + + (point[1] - i[1]) ** 2 + + (point[2] - i[2]) ** 2 + ) distances.append(distance) # log("distance:", distance) min_distance = min(distances) # log('Min:', min_distance) # log(count, p, min_distance) - mol.data['distance' + str(p)] = min_distance + mol.data["distance" + str(p)] = min_distance 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() - log('Wrote', count, 'molecules') + log("Wrote", count, "molecules") def main(): 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") + 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) |
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| diff -r 330514267c57 -r f5d7ffbb2d33 multi_obgrep.py --- a/multi_obgrep.py Tue Nov 10 20:39:26 2020 +0000 +++ b/multi_obgrep.py Thu Aug 15 11:03:22 2024 +0000 |
| [ |
| @@ -15,21 +15,55 @@ 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('-o', '--outfile', required=True, help='Path to the output file.') + 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( + "-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.") - 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.") - parser.add_argument("--only-name", dest="only_name", action="store_true", - 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.") - parser.add_argument("--number-of-matches", dest="number_of_matches", action="store_true", - default=False, help="Print the number of matches.") + 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.", + ) + 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.", + ) + parser.add_argument( + "--only-name", + dest="only_name", + action="store_true", + 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.", + ) + parser.add_argument( + "--number-of-matches", + dest="number_of_matches", + action="store_true", + default=False, + help="Print the number of matches.", + ) return parser.parse_args() @@ -42,25 +76,27 @@ def mp_helper(query, args): """ - Helper function for multiprocessing. - That function is a wrapper around obgrep. + Helper function for multiprocessing. + That function is a wrapper around obgrep. """ cmd_list = [] if args.invert_matches: - cmd_list.append('-v') + cmd_list.append("-v") if args.only_name: - cmd_list.append('-n') + cmd_list.append("-n") if args.full_match: - cmd_list.append('-f') + cmd_list.append("-f") if args.number_of_matches: - cmd_list.append('-c') + cmd_list.append("-c") if args.n_times: - cmd_list.append('-t %s' % str(args.n_times)) + cmd_list.append("-t %s" % str(args.n_times)) 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) + 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 + ) stdout, stderr = child.communicate() return (tmp.name, query) @@ -80,9 +116,9 @@ 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') + res_handle = open(result_file, "rb") shutil.copyfileobj(res_handle, out_handle) res_handle.close() os.remove(result_file) @@ -93,7 +129,7 @@ def __main__(): """ - Multiprocessing obgrep search. + Multiprocessing obgrep search. """ args = parse_command_line() obgrep(args) |
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| diff -r 330514267c57 -r f5d7ffbb2d33 ob_addh.py --- a/ob_addh.py Tue Nov 10 20:39:26 2020 +0000 +++ b/ob_addh.py Thu Aug 15 11:03:22 2024 +0000 |
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| @@ -7,16 +7,28 @@ 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('-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') + 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() @@ -32,7 +44,7 @@ def __main__(): """ - Add hydrogen atoms at a certain pH value + Add hydrogen atoms at a certain pH value """ args = parse_command_line(sys.argv) addh(args) |
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| diff -r 330514267c57 -r f5d7ffbb2d33 ob_filter.py --- a/ob_filter.py Tue Nov 10 20:39:26 2020 +0000 +++ b/ob_filter.py Thu Aug 15 11:03:22 2024 +0000 |
| [ |
| @@ -14,33 +14,36 @@ 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.") + 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 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): + 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 @@ -56,16 +59,30 @@ 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) + 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 = '' + 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) + 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) @@ -76,18 +93,18 @@ return_code = child.returncode if return_code: - sys.stdout.write(stdout.decode('utf-8')) - sys.stderr.write(stderr.decode('utf-8')) + 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')) + 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 mol in pybel.readfile("sdf", args.input): for name in open(args.list_of_names): if mol.title.strip() == name.strip(): outfile.write(mol) @@ -96,21 +113,21 @@ def __main__(): """ - Select compounds with certain properties from a small library + Select compounds with certain properties from a small library """ args = parse_command_line() - if args.filters == '__filter_by_name__': + 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': + 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)) + 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: |
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| diff -r 330514267c57 -r f5d7ffbb2d33 ob_genProp.py --- a/ob_genProp.py Tue Nov 10 20:39:26 2020 +0000 +++ b/ob_genProp.py Thu Aug 15 11:03:22 2024 +0000 |
| [ |
| @@ -10,43 +10,57 @@ import cheminfolib import openbabel from openbabel import pybel + openbabel.obErrorLog.StopLogging() def parse_command_line(argv): parser = argparse.ArgumentParser() - 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('--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') + 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( + "--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': + if args.oformat == "sdf": outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) else: - outfile = open(args.output, 'w') + outfile = open(args.output, "w") 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] + if args.oformat == "sdf": + [ + 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 + Physico-chemical properties are computed and stored as metadata in the sdf output file """ args = parse_command_line(sys.argv) compute_properties(args) |
| b |
| diff -r 330514267c57 -r f5d7ffbb2d33 ob_remIons.py --- a/ob_remIons.py Tue Nov 10 20:39:26 2020 +0000 +++ b/ob_remIons.py Thu Aug 15 11:03:22 2024 +0000 |
| [ |
| @@ -8,37 +8,43 @@ 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('-i', '--input', required=True, help='input file name') - parser.add_argument('-o', '--output', required=True, help='output file name') - parser.add_argument('-idx', default=False, action='store_true', help='should output be an indexed text table? works only for inchi/smiles, otherwise is ignored') + 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") + parser.add_argument( + "-idx", + default=False, + action="store_true", + help="should output be an indexed text table? works only for inchi/smiles, otherwise is ignored", + ) return parser.parse_args() def remove_ions(args): - with open(args.output, 'w') as outfile: + with open(args.output, "w") as outfile: for index, mol in enumerate(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 + if "inchi" in mol.data: + del mol.data["inchi"] # remove inchi cache so modified mol is saved - mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else '\n' + mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else "\n" - if args.idx and args.iformat in ['inchi', 'smi']: - outfile.write(f'{index}\t{mol}') - elif mol != '\n': - outfile.write(f'{mol}') + if args.idx and args.iformat in ["inchi", "smi"]: + outfile.write(f"{index}\t{mol}") + elif mol != "\n": + outfile.write(f"{mol}") def __main__(): """ - Remove any counterion and delete any fragment but the largest one for each molecule. + Remove any counterion and delete any fragment but the largest one for each molecule. """ args = parse_command_line() remove_ions(args) |
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| diff -r 330514267c57 -r f5d7ffbb2d33 ob_spectrophore_search.py --- a/ob_spectrophore_search.py Tue Nov 10 20:39:26 2020 +0000 +++ b/ob_spectrophore_search.py Thu Aug 15 11:03:22 2024 +0000 |
| [ |
| @@ -8,6 +8,7 @@ import numpy as np from openbabel import openbabel, pybel + openbabel.obErrorLog.StopLogging() # TODO get rid of eval() @@ -17,49 +18,94 @@ 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') - parser.add_argument('--library', required=True, help='library of compounds with pre-computed physico-chemical properties, including Spectrophores(TM) in tabular format') - parser.add_argument('-c', '--column', required=True, type=int, help='#column containing the Spectrophores(TM) descriptors in the library file') - parser.add_argument('-o', '--output', required=True, help='output file name') - parser.add_argument('-n', '--normalization', default="ZeroMeanAndUnitStd", choices=['No', 'ZeroMean', 'UnitStd', 'ZeroMeanAndUnitStd'], help='Normalization method') - parser.add_argument('-a', '--accuracy', default="20", choices=['1', '2', '5', '10', '15', '20', '30', '36', '45', '60'], help='Accuracy expressed as angular stepsize') - parser.add_argument('-s', '--stereo', default="No", choices=['No', 'Unique', 'Mirror', 'All'], help='Stereospecificity of the cage') - parser.add_argument('-r', '--resolution', type=float, default="3.0", help='Resolution') + parser.add_argument( + "--target", + required=True, + help="target file name in sdf format with Spectrophores(TM) descriptors stored as meta-data", + ) + parser.add_argument( + "--library", + required=True, + help="library of compounds with pre-computed physico-chemical properties, including Spectrophores(TM) in tabular format", + ) + parser.add_argument( + "-c", + "--column", + required=True, + type=int, + help="#column containing the Spectrophores(TM) descriptors in the library file", + ) + parser.add_argument("-o", "--output", required=True, help="output file name") + parser.add_argument( + "-n", + "--normalization", + default="ZeroMeanAndUnitStd", + choices=["No", "ZeroMean", "UnitStd", "ZeroMeanAndUnitStd"], + help="Normalization method", + ) + parser.add_argument( + "-a", + "--accuracy", + default="20", + choices=["1", "2", "5", "10", "15", "20", "30", "36", "45", "60"], + help="Accuracy expressed as angular stepsize", + ) + parser.add_argument( + "-s", + "--stereo", + default="No", + choices=["No", "Unique", "Mirror", "All"], + help="Stereospecificity of the cage", + ) + parser.add_argument( + "-r", "--resolution", type=float, default="3.0", help="Resolution" + ) return parser.parse_args() def set_parameters(args): - if args.normalization == 'No': + if args.normalization == "No": 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.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'): + 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. + Computation of Spectrophores(TM) distances to a target molecule. """ args = parse_command_line() # This sets up the parameters for the Spectrophore generation. Parameters are set to fit those of our standard parsing tool set_parameters(args) - mol = next(pybel.readfile('sdf', args.target)) - target_spectrophore = mol.data["Spectrophores(TM)"].strip().split(', ') + 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 Compute_Spectrophores_distance(target_spectrophore, args) |
| b |
| diff -r 330514267c57 -r f5d7ffbb2d33 ob_spectrophore_search.xml --- a/ob_spectrophore_search.xml Tue Nov 10 20:39:26 2020 +0000 +++ b/ob_spectrophore_search.xml Thu Aug 15 11:03:22 2024 +0000 |
| b |
| @@ -2,7 +2,7 @@ <description>- similarity search based on 1D chemical features</description> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> <expand macro="requirements"> <requirement type="package" version="1.19.1">numpy</requirement> @@ -90,7 +90,7 @@ Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel. .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf -.. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html +.. _Silicos: https://open-babel.readthedocs.io/en/latest/Fingerprints/spectrophore.html .. |Spectrophores (TM)| unicode:: Spectrophores U+2122 ]]> |
| b |
| diff -r 330514267c57 -r f5d7ffbb2d33 remove_protonation_state.py --- a/remove_protonation_state.py Tue Nov 10 20:39:26 2020 +0000 +++ b/remove_protonation_state.py Thu Aug 15 11:03:22 2024 +0000 |
| [ |
| @@ -7,14 +7,15 @@ 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('-i', '--input', required=True, help='input file name') - parser.add_argument('-o', '--output', required=True, help='output file name') + 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() @@ -22,15 +23,15 @@ 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] - if 'inchi' in mol.data: - del mol.data['inchi'] # remove inchi cache so modified mol is saved + 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. + Remove any protonation state from each atom in each molecule. """ args = parse_command_line() remove_protonation(args) |
| b |
| diff -r 330514267c57 -r f5d7ffbb2d33 subsearch.py --- a/subsearch.py Tue Nov 10 20:39:26 2020 +0000 +++ b/subsearch.py Thu Aug 15 11:03:22 2024 +0000 |
| [ |
| @@ -13,21 +13,34 @@ 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('-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("-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( + "-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() + ) return parser.parse_args() @@ -40,20 +53,28 @@ def mp_helper(query, args): """ - Helper function for multiprocessing. - That function is a wrapper around the following command: - obabel file.fs -s"smarts" -Ooutfile.smi -al 999999999 + Helper function for multiprocessing. + That function is a wrapper around the following command: + obabel file.fs -s"smarts" -Ooutfile.smi -al 999999999 """ - if args.oformat == 'names': - opts = '-osmi -xt' + if args.oformat == "names": + opts = "-osmi -xt" else: - opts = '-o%s' % args.oformat + opts = "-o%s" % args.oformat 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) + 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 @@ -73,14 +94,14 @@ """ Wrapper to retrieve a striped SMILES or SMARTS string from different input formats. """ - if args.iformat in ['smi', 'text', 'tabular']: + if args.iformat in ["smi", "text", "tabular"]: with open(args.infile) as text_file: for line in text_file: - yield line.split('\t')[0].strip() + yield line.split("\t")[0].strip() else: # inchi or sdf files for mol in pybel.readfile(args.iformat, args.infile): - yield mol.write('smiles').split('\t')[0] + yield mol.write("smiles").split("\t")[0] def substructure_search(args): @@ -91,18 +112,18 @@ pool.close() pool.join() - if args.oformat == 'names': - out_handle = open(args.outfile, 'w') + if args.oformat == "names": + 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)) + 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') + res_handle = open(result_file, "rb") shutil.copyfileobj(res_handle, out_handle) res_handle.close() os.remove(result_file) @@ -111,7 +132,7 @@ def __main__(): """ - Multiprocessing Open Babel Substructure Search. + Multiprocessing Open Babel Substructure Search. """ args = parse_command_line() substructure_search(args) |
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| diff -r 330514267c57 -r f5d7ffbb2d33 test-data/2_mol.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_mol.sdf Thu Aug 15 11:03:22 2024 +0000 |
| [ |
| @@ -0,0 +1,66 @@ +CC(=O)Oc1ccccc1C(=O)[O-] InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)/p-1 + OpenBabel08132415422D + + 13 13 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 10 1 0 0 0 0 + 5 6 2 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 2 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 + 11 13 1 0 0 0 0 +M CHG 1 13 -1 +M END +$$$$ +CC(=O)Oc1ccccc1C(=O)[O-] InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)/p-1 + OpenBabel08132415422D + + 13 13 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 10 1 0 0 0 0 + 5 6 2 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 2 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 + 11 13 1 0 0 0 0 +M CHG 1 13 -1 +M END +$$$$ |