Mercurial > repos > bgruening > prepare_ligands_for_docking
changeset 0:06340f46ecb8 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/change_title_to_metadata_value.py Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,43 @@ +#!/usr/bin/env python +# -*- coding: UTF-8 -*- + +""" + Change the title from a molecule file to metadata + value of a given-id of the same molecule file. +""" + +import os +import sys +import argparse +import openbabel +openbabel.obErrorLog.StopLogging() +import pybel + + +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.", + ) + 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") + + args = parser.parse_args() + + output = pybel.Outputfile("sdf", args.outfile, overwrite=True) + + for mol in pybel.readfile("sdf", args.infile): + if args.key in mol.data: + mol.title = mol.data[args.key] + output.write( mol ) + + output.close() + + +if __name__ == "__main__": + main() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cheminfolib.py Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,264 @@ +#!/usr/bin/env python +""" + Small library with cheminformatic functions based on openbabel and pgchem. + Copyright 2012, Bjoern Gruening and Xavier Lucas +""" + +import os, sys + +try: + from galaxy import eggs + eggs.require('psycopg2') +except: + print('psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB') + +try: + import pybel + import openbabel +except: + 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 ): + 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): + grepper = re.compile(pattern) + for line in file_obj: + if grepper.search(line): + return True + return False + +def check_filetype(filepath): + mol = False + possible_inchi = True + for line_counter, line in enumerate(open(filepath)): + if line_counter > 10000: + break + if line.find('$$$$') != -1: + return 'sdf' + elif line.find('@<TRIPOS>MOLECULE') != -1: + return 'mol2' + elif line.find('ligand id') != -1: + return 'drf' + elif possible_inchi and re.findall('^InChI=', line): + return 'inchi' + elif re.findall('^M\s+END', line): + mol = True + # first line is not an InChI, so it can't be an InChI file + possible_inchi = False + + if mol: + # END can occures before $$$$, so and SDF file will + # 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)); + return db_conn + except: + 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', +} + +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'], +} + + +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.header: + 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' ) + + 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] + outfile.write(mol) + except: + pass + else: + outfile = open(args.output, 'w') + 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)])]" + ) + calc_desc_dict = mol.calcdesc() + + try: + logp = calc_desc_dict['logP'] + except: + 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), + } + +def get_inchikey(mol): + conv = openbabel.OBConversion() + conv.SetInAndOutFormats("mol", "inchi") + conv.SetOptions("K", conv.OUTOPTIONS) + 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 ) ] ) + +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 ): + """ + 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' ) + + for line in open(lib_path, 'r'): + 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.close() + + return True + +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 ) + """ + output_files = [] + tfile = tempfile.NamedTemporaryFile(delete=False) + + 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() + output_files.append(tfile.name) + tfile = tempfile.NamedTemporaryFile(delete=False) + tfile.write(line) + tfile.close() + output_files.append(tfile.name) + smiles_handle.close() + return output_files + + +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.sort() + + pool = Pool(processes=PROCESSES) + print('Process initialized with', PROCESSES, 'processors') + result = pool.map_async(function_to_call, paths) + result.get() + + return paths + +if __name__ == '__main__': + print(check_filetype(sys.argv[1])) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,40 @@ +<macros> + <token name="@VERSION@">2.4.2</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.4.1">openbabel</requirement> + <requirement type="package" version="3">python</requirement> + <yield /> + </requirements> + </xml> + + <xml name="output_like_input"> + <data name="outfile" format_source="infile" /> + </xml> + + <xml name="infile_all_types"> + <param name="infile" format="sdf,mol,mol2,cml,inchi,smi,pdb" type="data" label="Molecular input file" + help="Valid file types are: SDF, MOL, MOL2, CML, InChI, 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)" /> + <param name="gen3d" type="boolean" truevalue="--gen3d" falsevalue="" checked="false" + label="Generate 3D coordinates" help="(--gen3d)" /> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> + </stdio> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1186/1758-2946-3-33</citation> + <yield /> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multi_obgrep.py Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,101 @@ +#!/usr/bin/env python +""" + Input: Molecules in SDF, SMILES ... + Output: Molecule file filtered with obgrep. + Copyright 2013, Bjoern Gruening and Xavier Lucas +""" +import sys, os +import argparse +import openbabel +openbabel.obErrorLog.StopLogging() +import pybel +import multiprocessing +import tempfile +import subprocess +import shutil +import shlex + +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("--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.") + return parser.parse_args() + +results = list() +def mp_callback(res): + results.append(res) + +def mp_helper( query, args ): + """ + Helper function for multiprocessing. + That function is a wrapper around obgrep. + """ + + cmd_list = [] + if args.invert_matches: + cmd_list.append('-v') + if args.only_name: + cmd_list.append('-n') + if args.full_match: + cmd_list.append('-f') + if args.number_of_matches: + cmd_list.append('-c') + if 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) + + stdout, stderr = child.communicate() + return (tmp.name, query) + + +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.apply_async(mp_helper, args=(query.strip(), args), callback=mp_callback) + #mp_callback( mp_helper(query.strip(), args) ) + pool.close() + pool.join() + + 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.close() + os.remove( result_file ) + out_handle.close() + + os.remove( temp_link ) + +def __main__(): + """ + Multiprocessing obgrep search. + """ + args = parse_command_line() + obgrep( args ) + +if __name__ == "__main__" : + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ob_addh.py Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,38 @@ +#!/usr/bin/env python +""" + Input: Molecule file + Output: Molecule file with hydrogen atoms added at the target pH. +""" +import sys, os +import argparse +import openbabel +openbabel.obErrorLog.StopLogging() +import pybel + +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') + 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): + if mol.OBMol.NumHvyAtoms() > 5: + mol.removeh() + mol.OBMol.AddHydrogens(args.polar, True, args.pH) + outfile.write(mol) + outfile.close() + +def __main__(): + """ + Add hydrogen atoms at a certain pH value + """ + args = parse_command_line(sys.argv) + addh(args) + +if __name__ == "__main__" : + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ob_filter.py Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,112 @@ +#!/usr/bin/env python +""" + Input: set of molecules with pre-calculated physico-chemical properties + Output: set of molecules that pass all the filters + Copyright 2012, Bjoern Gruening and Xavier Lucas + + TODO: AND/OR conditions? +""" +import sys, os +import argparse +import cheminfolib +import json +import pybel +import shlex, subprocess + +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, + ) + return parser.parse_args() + +def filter_precalculated_compounds(args, filters): + outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) + for mol in pybel.readfile('sdf', args.input): + for key, elem in filters.items(): + # map the short description to the larger metadata names stored in the sdf file + property = cheminfolib.ColumnNames[key] + min = elem[0] + max = elem[1] + if float(mol.data[property]) >= float(min) and float(mol.data[property]) <= float(max): + pass + else: + # leave the filter loop, because one filter constrained are not satisfied + break + else: + # if the filter loop terminates in a normal way (no break) all filter rules are satisfied, so save the compound + outfile.write(mol) + outfile.close() + +def filter_new_compounds(args, filters): + + if args.iformat == args.oformat: + # use the -ocopy option from openbabel to speed up the filtering, additionally no conversion is carried out + # http://openbabel.org/docs/dev/FileFormats/Copy_raw_text.html#copy-raw-text + cmd = 'obabel -i%s %s -ocopy -O %s --filter' % (args.iformat, args.input, args.output) + else: + cmd = 'obabel -i%s %s -o%s -O %s --filter' % (args.iformat, args.input, args.oformat, args.output) + filter_cmd = '' + # OBDescriptor stores a mapping from our desc shortcut to the OB name [0] and a long description [1] + for key, elem in filters.items(): + ob_descriptor_name = cheminfolib.OBDescriptor[key][0] + min = elem[0] + max = elem[1] + filter_cmd += ' %s>=%s %s<=%s ' % (ob_descriptor_name, min, ob_descriptor_name, max) + + args = shlex.split('%s "%s"' % (cmd, filter_cmd)) + #print '%s "%s"' % (cmd, filter_cmd) + # calling openbabel with subprocess and pipe potential errors occuring in openbabel to stdout + child = subprocess.Popen(args, + stdout=subprocess.PIPE, stderr=subprocess.PIPE) + + stdout, stderr = child.communicate() + return_code = child.returncode + + if return_code: + sys.stdout.write(stdout.decode('utf-8')) + sys.stderr.write(stderr.decode('utf-8')) + sys.stderr.write("Return error code %i from command:\n" % return_code) + sys.stderr.write("%s\n" % cmd) + else: + sys.stdout.write(stdout.decode('utf-8')) + sys.stdout.write(stderr.decode('utf-8')) + + +def __main__(): + """ + Select compounds with certain properties from a small library + """ + args = parse_command_line() + # Its a small trick to get the parameters in an easy way from the xml file. + # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed. + # Also the last loop creates a ',{' that is not an valid jason expression. + filters = json.loads((args.filters).replace(' ', '').replace(',}', '}')) + if args.iformat == 'sdf': + # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering + mol = next(pybel.readfile('sdf', args.input)) + for key, elem in filters.items(): + property = cheminfolib.ColumnNames[key] + if not property in mol.data: + break + else: + # if the for loop finishes in a normal way, we should habe all properties at least in the first molecule + # assume it is the same for all other molecules and start the precalculated filtering + filter_precalculated_compounds(args, filters) + return True + filter_new_compounds(args, filters) + + +if __name__ == "__main__" : + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ob_genProp.py Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,52 @@ +#!/usr/bin/env python +""" + Input: Molecular input file. + 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 openbabel +openbabel.obErrorLog.StopLogging() +import pybel +import cheminfolib + + +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') + return parser.parse_args() + +def compute_properties(args): + if args.oformat == 'sdf': + outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) + else: + 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 ] ) ) + + 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 ] + outfile.write(mol) + else: + 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 + """ + args = parse_command_line(sys.argv) + compute_properties(args) + +if __name__ == "__main__" : + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ob_prepare_ligands.xml Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,86 @@ +<tool id="prepare_ligands_for_docking" name="Prepare ligands for docking" version="@VERSION@.0"> + <description>Tool to prepare ligands for docking with tools like Autodock Vina</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ + mkdir output && obabel -i '${ligands.ext}' -o '$oformat' -O 'output/molecule.$oformat' -m '$ligands' $gen3d -p $ph_value + ]]></command> + <inputs> + <param type="data" name="ligands" format="sdf,mol2,inchi,smi" label="The ligands which need to be prepared" help="Input in SDF, MOL2, InChi or SMILES format." /> + <param name="ph_value" type="float" value="7.4" min="0" max="14" label="Specify pH value"/> + <param name="gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" /> + <param name="oformat" type="select" label="Output format" > + <option value="pdb">PDB</option> + <option value="pdbqt">PDBQT</option> + <option value="mol">MOL</option> + <option value="mol2">MOL2</option> + </param> + </inputs> + <outputs> + <collection name="file_outputs" type="list" label="Prepared ligands" > + <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" /> + </collection> + </outputs> + <tests> + <test> + <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/> + <param name="oformat" value="pdbqt"/> + <param name="ph_value" value="7.4"/> + <output_collection name="file_outputs" type="list" count="10"> + <element name="molecule1" file="ob_prepare_ligands1.pdbqt" /> + <element name="molecule2" file="ob_prepare_ligands2.pdbqt" /> + <!-- we check only the first 2 --> + </output_collection> + </test> + <test> + <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/> + <param name="oformat" value="mol2"/> + <param name="ph_value" value="7.4"/> + <output_collection name="file_outputs" type="list" count="10"> + <element name="molecule1" file="ob_prepare_ligands1.mol2" /> + <element name="molecule2" file="ob_prepare_ligands2.mol2" /> + <!-- we check only the first 2 --> + </output_collection> + </test> + <test> + <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/> + <param name="oformat" value="mol"/> + <param name="ph_value" value="7.4"/> + <output_collection name="file_outputs" type="list" count="10"> + <!-- just check the count --> + </output_collection> + </test> + <test> + <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/> + <param name="oformat" value="pdb"/> + <param name="ph_value" value="7.4"/> + <output_collection name="file_outputs" type="list" count="10"> + <!-- just check the count --> + </output_collection> + </test> + </tests> + <help><![CDATA[ +**What it does?** + +This tool uses OpenBabel to convert an input molecule file, typically a SD file, to individual output molecule files in pdbqt, pdb, +mol or mol2 formats. There is one output file for each record in the input. +Protonation is performed at a specified pH and 3D coordinates can optionally be generated. 3D coordinate generation should be used when +the docking program requires 3D structures and the input is not 3D. + +The most typical usage is to process a set of ligands in a SD file that will be docked by VINA. In this case the pdbqt output format should +be used, and the resulting collection of molecules can be used as input by VINA. + +**Input** + +Molecules such as an SD file dataset in history. + +**Output** + +A collection of individual molecule files in the specified format. + + ]]></help> + <expand macro="citations"/> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ob_remIons.py Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,38 @@ +#!/usr/bin/env python +""" + Input: molecular input file. + Output: Molecule file with removed ions and fragments. + Copyright 2012, Bjoern Gruening and Xavier Lucas +""" +import sys, os +import argparse +import openbabel +openbabel.obErrorLog.StopLogging() +import pybel + +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') + 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) + # 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. + """ + args = parse_command_line() + remove_ions(args) + +if __name__ == "__main__" : + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ob_spectrophore_search.py Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,66 @@ +#!/usr/bin/env python +""" + Input: tabular format file with one column storing the unique id for the compounds and any other with the Spectrophores(TM) descriptors. + 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 openbabel +openbabel.obErrorLog.StopLogging() +import pybel +import math +import numpy as np + +#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') + 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': + 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 ) + 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() + except ValueError: + distance = 0 + outfile.write( '%s\t%f\n' % (mol.strip(), distance ) ) + outfile.close() + +def __main__(): + """ + 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(', ') + # Compute the paired-distance between every molecule in the library and the target + distances = Compute_Spectrophores_distance(target_spectrophore, args) + +if __name__ == "__main__" : + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/remove_protonation_state.py Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,35 @@ +#!/usr/bin/env python +""" + Input: molecular input file. + Output: Molecule file with removed ions and fragments. + Copyright 2013, Bjoern Gruening and Xavier Lucas +""" +import sys, os +import argparse +import openbabel +openbabel.obErrorLog.StopLogging() +import pybel + +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') + return parser.parse_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 ) + outfile.close() + +def __main__(): + """ + Remove any protonation state from each atom in each molecule. + """ + args = parse_command_line() + remove_protonation( args ) + +if __name__ == "__main__" : + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/subsearch.py Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,116 @@ +#!/usr/bin/env python +""" + Input: Molecules in SDF, SMILES ... + Output: Moleculs filtered with specified substructures. + Copyright 2013, Bjoern Gruening and Xavier Lucas +""" +import sys, os +import argparse +import openbabel +openbabel.obErrorLog.StopLogging() +import pybel +import multiprocessing +import tempfile +import subprocess +import shutil + +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()) + return parser.parse_args() + +results = list() +def mp_callback(res): + results.append(res) + +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 + """ + + if args.oformat == 'names': + opts = '-osmi -xt' + else: + 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) + + child = subprocess.Popen(cmd.split(), + stdout=subprocess.PIPE, stderr=subprocess.PIPE) + + stdout, stderr = child.communicate() + return_code = child.returncode + + if return_code: + sys.stdout.write(stdout) + sys.stderr.write(stderr) + sys.stderr.write("Return error code %i from command:\n" % return_code) + sys.stderr.write("%s\n" % cmd) + else: + sys.stdout.write(stdout) + sys.stdout.write(stderr) + return (tmp.name, query) + + +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: + 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 ): + yield mol.write('smiles').split('\t')[0] + +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) ) + pool.close() + pool.join() + + 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 )) + os.remove( result_file ) + out_handle.close() + else: + 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.close() + os.remove( result_file ) + out_handle.close() + + +def __main__(): + """ + Multiprocessing Open Babel Substructure Search. + """ + args = parse_command_line() + substructure_search( args ) + +if __name__ == "__main__" : + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_mol.dat Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,2 @@ +CC(=O)OC1=CC=CC=C1C(=O)[O-] +CC(=O)OC1=CC=CC=C1C(=O)[O-]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_mol.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,2 @@ +CC(=O)OC1=CC=CC=C1C(=O)[O-] +CC(=O)OC1=CC=CC=C1C(=O)[O-]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_mol.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,3 @@ +CC(=O)OC1=CC=CC=C1C(=O)[O-] +CC(=O)OC1=CC=CC=C1C(=O)[O-] +C
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/8_mol.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,8 @@ +C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl +C1=COC(=C1)CNC2=CC(=C(C=C2C(=O)O)S(=O)(=O)N)Cl +CO[C@H]1[C@@H](C[C@@H]2CN3CCC4=C([C@H]3C[C@@H]2[C@@H]1C(=O)OC)NC5=C4C=CC(=C5)OC)OC(=O)C6=CC(=C(C(=C6)OC)OC)OC +CO[C@H]1[C@@H](C[C@@H]2CN3CCC4=C([C@H]3C[C@@H]2[C@@H]1C(=O)OC)NC5=C4C=CC(=C5)OC)OC(=O)C6=CC(=C(C(=C6)OC)OC)OC.C1NC2=CC(=C(C=C2S(=O)(=O)N1)S(=O)(=O)N)Cl +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)CC +CCC1(N=C2C=C3C(=NC4=CC=CC=C4N3C5=CC=CC=C5)C=C2N1C6=CC=CC=C6)C +CC(=O)OC1=CC=CC=C1C(=O)[O-] +CC(=O)OC1=CC=CC=C1C(=O)[O-]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID2244_with_spectrophore.sdf Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,193 @@ +2244 + OpenBabel07101216402D + + 21 21 0 0 0 0 0 0 0 0999 V2000 + 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +2244 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +212 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <PUBCHEM_IUPAC_INCHIKEY> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +1.2 + +> <PUBCHEM_EXACT_MASS> +180.042259 + +> <PUBCHEM_MOLECULAR_FORMULA> +C9H8O4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +180.15742 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_CACTVS_TPSA> +63.6 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +180.042259 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +13 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +5 6 8 +5 7 8 +6 8 8 +7 9 8 +8 10 8 +9 10 8 + +> <Hydrogen-bond donors> +1 + +> <InChI key> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <logP> +1.3101 + +> <Polar surface area> +63.6 + +> <Number of heavy atoms> +13 + +> <Molecular weight> +180.15742 + +> <InChI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <Spectrophores(TM)> +-1.454, -1.106, -1.162, 0.285, 0.369, 1.008, 0.144, -0.956, 0.133, 0.883, 1.828, 0.029, -1.312, -1.424, -1.287, -0.644, 0.59, 0.746, -0.127, 0.535, 0.368, 0.93, 1.721, -0.097, -1.591, -0.888, -1.332, 0.013, 0.889, 0.249, -0.343, -0.346, -0.047, 1.471, 1.595, 0.329, -1.101, -1.186, 0.953, 0.953, -0.644, -0.653, -1.136, 1.547, 0.533, -0.262, -0.274, 1.27 + +> <Number of rings> +1 + +> <Canonical SMILES> +CC(=O)Oc1ccccc1C(=O)O + +> <Molecular refractivity> +44.9003 + +> <Hydrogen-bond acceptors> +4 + +> <Rotatable bonds> +3 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244.can Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +CC(=O)Oc1ccccc1C(=O)O 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244.inchi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244.sdf Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,155 @@ +2244 + -OEChem-05151212332D + + 21 21 0 0 0 0 0 0 0999 V2000 + 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +2244 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +212 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <PUBCHEM_IUPAC_INCHIKEY> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +1.2 + +> <PUBCHEM_EXACT_MASS> +180.042259 + +> <PUBCHEM_MOLECULAR_FORMULA> +C9H8O4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +180.15742 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_CACTVS_TPSA> +63.6 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +180.042259 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +13 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +5 6 8 +5 7 8 +6 8 8 +7 9 8 +8 10 8 +9 10 8 + +$$$$ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +O(c1c(cccc1)C(=O)O)C(=O)C 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244_FP2.fps Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,7 @@ +#FPS1 +#num_bits=1021 +#type=OpenBabel-FP2/1 +#software=OpenBabel/2.3.1 +#source=CID_2244.sdf +#date=2012-05-15T16:40:38 +00000010004000c00000020000030000010000000008000000000080000000000400400000000010200a020800000000000042000000000000800002000002000c200800010001010000000002808002208000400000000040080000000100000008000000000002004002000010000000020100080100200808000000000004 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244_FP3.fps Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,7 @@ +#FPS1 +#num_bits=55 +#type=OpenBabel-FP3/1 +#software=OpenBabel/2.3.1 +#source=CID_2244.sdf +#date=2012-05-15T16:59:15 +0400000c50b007 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244_FP4.fps Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,7 @@ +#FPS1 +#num_bits=307 +#type=OpenBabel-FP4/1 +#software=OpenBabel/2.3.1 +#source=CID_2244.sdf +#date=2012-05-15T16:59:22 +010000000000000000009800000000004001000000000000000000000000000000000240402801 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244_addh.can Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +CC(=O)Oc1ccccc1C(=O)[O-] 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_2244_maccs.fps Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,7 @@ +#FPS1 +#num_bits=166 +#type=OpenBabel-MACCS/2 +#software=OpenBabel/2.3.1 +#source=CID_2244.sdf +#date=2012-05-15T17:00:39 +0000000000000000000000010000016480cca2d21e 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_3033.sdf Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,271 @@ +3033 + -OEChem-08231107463D + + 30 31 0 0 0 0 0 0 0999 V2000 + 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 14 1 0 0 0 0 + 2 15 1 0 0 0 0 + 3 16 1 0 0 0 0 + 3 30 1 0 0 0 0 + 4 16 2 0 0 0 0 + 5 7 1 0 0 0 0 + 5 9 1 0 0 0 0 + 5 22 1 0 0 0 0 + 6 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + 6 10 2 0 0 0 0 + 7 11 2 0 0 0 0 + 8 16 1 0 0 0 0 + 8 20 1 0 0 0 0 + 8 21 1 0 0 0 0 + 9 14 2 0 0 0 0 + 9 15 1 0 0 0 0 + 10 12 1 0 0 0 0 + 10 23 1 0 0 0 0 + 11 13 1 0 0 0 0 + 11 24 1 0 0 0 0 + 12 13 2 0 0 0 0 + 12 25 1 0 0 0 0 + 13 26 1 0 0 0 0 + 14 17 1 0 0 0 0 + 15 18 2 0 0 0 0 + 17 19 2 0 0 0 0 + 17 27 1 0 0 0 0 + 18 19 1 0 0 0 0 + 18 28 1 0 0 0 0 + 19 29 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3033 + +> <PUBCHEM_CONFORMER_RMSD> +0.6 + +> <PUBCHEM_CONFORMER_DIVERSEORDER> +1 +20 +18 +39 +29 +42 +38 +35 +30 +25 +33 +28 +32 +36 +26 +24 +40 +11 +27 +37 +7 +41 +10 +19 +43 +8 +6 +16 +44 +23 +34 +14 +15 +31 +9 +13 +17 +21 +22 +5 +12 +2 +3 +4 + +> <PUBCHEM_MMFF94_PARTIAL_CHARGES> +28 +1 -0.18 +10 -0.15 +11 -0.15 +12 -0.15 +13 -0.15 +14 0.18 +15 0.18 +16 0.66 +17 -0.15 +18 -0.15 +19 -0.15 +2 -0.18 +22 0.4 +23 0.15 +24 0.15 +25 0.15 +26 0.15 +27 0.15 +28 0.15 +29 0.15 +3 -0.65 +30 0.5 +4 -0.57 +5 -0.6 +6 -0.14 +7 0.1 +8 0.2 +9 0.1 + +> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> +4 + +> <PUBCHEM_PHARMACOPHORE_FEATURES> +7 +1 3 acceptor +1 4 acceptor +1 5 cation +1 5 donor +3 3 4 16 anion +6 6 7 10 11 12 13 rings +6 9 14 15 17 18 19 rings + +> <PUBCHEM_HEAVY_ATOM_COUNT> +19 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_CONFORMER_ID> +00000BD900000001 + +> <PUBCHEM_MMFF94_ENERGY> +65.6362 + +> <PUBCHEM_FEATURE_SELFOVERLAP> +35.578 + +> <PUBCHEM_SHAPE_FINGERPRINT> +10366900 7 17386020514759110480 +114674 6 16903282898360328323 +11578080 2 17913245089295617604 +11582403 64 14544541357940910356 +11640471 11 18127963303313961600 +12236239 1 18272088352834916308 +12363563 72 18042978579496277287 +12553582 1 18190740839094073615 +12596599 1 18201439237582433270 +12788726 201 18410285909464206003 +13032168 30 18201440238019390274 +13140716 1 18187086113919468457 +13538477 17 18339642338307470464 +13583140 156 17241914119188522922 +13764800 53 17895191172601517065 +13965767 371 17259888045752176376 +14115302 16 18342181093776810149 +14787075 74 17907866106787333628 +15279307 12 18198622322777022915 +15375462 189 18270674264943931347 +15669948 3 18336550511731321249 +16752209 62 18336841852664817743 +16945 1 18188484791351783177 +19433438 48 18059583550169763352 +200 152 18130792217719576158 +20645476 183 18270115859187436189 +20905425 154 17970632883131290416 +21452121 199 18046637711133085653 +21639500 275 16988270998321974524 +22112679 90 18342446063036096292 +23419403 2 17835564502519425292 +23493267 7 18115023138028600728 +23526113 38 16660924516543134566 +23557571 272 17821721762863303772 +23559900 14 17896315990920094510 +23598288 3 18411412925846384519 +23598291 2 18059009613384180254 +238 59 16343141308025475526 +4340502 62 17273677940604857177 +6049 1 17240202131864233360 +6992083 37 18058168521433072460 +7615 1 18201433675414973908 +77492 1 18272651289913926852 +81228 2 17968373550240022809 +9709674 26 17896035610527288590 + +> <PUBCHEM_SHAPE_MULTIPOLES> +378.03 +7.01 +2.75 +1.77 +0.78 +1.58 +0.3 +0.41 +1.94 +-1.08 +1.9 +-8.69 +11.04 +2.58 + +> <PUBCHEM_SHAPE_SELFOVERLAP> +790.335 + +> <PUBCHEM_SHAPE_VOLUME> +214.7 + +> <PUBCHEM_COORDINATE_TYPE> +2 +5 +255 + +$$$$ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CO.smarts Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +CO
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/change_title_on_CID_3033.sdf Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,270 @@ +214.7 + OpenBabel06291213403D + + 30 31 0 0 0 0 0 0 0 0999 V2000 + 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 14 1 0 0 0 0 + 2 15 1 0 0 0 0 + 3 16 1 0 0 0 0 + 3 30 1 0 0 0 0 + 4 16 2 0 0 0 0 + 5 7 1 0 0 0 0 + 5 9 1 0 0 0 0 + 5 22 1 0 0 0 0 + 6 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + 6 10 2 0 0 0 0 + 7 11 2 0 0 0 0 + 8 16 1 0 0 0 0 + 8 20 1 0 0 0 0 + 8 21 1 0 0 0 0 + 9 14 2 0 0 0 0 + 9 15 1 0 0 0 0 + 10 12 1 0 0 0 0 + 10 23 1 0 0 0 0 + 11 13 1 0 0 0 0 + 11 24 1 0 0 0 0 + 12 13 2 0 0 0 0 + 12 25 1 0 0 0 0 + 13 26 1 0 0 0 0 + 14 17 1 0 0 0 0 + 15 18 2 0 0 0 0 + 17 19 2 0 0 0 0 + 17 27 1 0 0 0 0 + 18 19 1 0 0 0 0 + 18 28 1 0 0 0 0 + 19 29 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3033 + +> <PUBCHEM_CONFORMER_RMSD> +0.6 + +> <PUBCHEM_CONFORMER_DIVERSEORDER> +1 +20 +18 +39 +29 +42 +38 +35 +30 +25 +33 +28 +32 +36 +26 +24 +40 +11 +27 +37 +7 +41 +10 +19 +43 +8 +6 +16 +44 +23 +34 +14 +15 +31 +9 +13 +17 +21 +22 +5 +12 +2 +3 +4 + +> <PUBCHEM_MMFF94_PARTIAL_CHARGES> +28 +1 -0.18 +10 -0.15 +11 -0.15 +12 -0.15 +13 -0.15 +14 0.18 +15 0.18 +16 0.66 +17 -0.15 +18 -0.15 +19 -0.15 +2 -0.18 +22 0.4 +23 0.15 +24 0.15 +25 0.15 +26 0.15 +27 0.15 +28 0.15 +29 0.15 +3 -0.65 +30 0.5 +4 -0.57 +5 -0.6 +6 -0.14 +7 0.1 +8 0.2 +9 0.1 + +> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> +4 + +> <PUBCHEM_PHARMACOPHORE_FEATURES> +7 +1 3 acceptor +1 4 acceptor +1 5 cation +1 5 donor +3 3 4 16 anion +6 6 7 10 11 12 13 rings +6 9 14 15 17 18 19 rings + +> <PUBCHEM_HEAVY_ATOM_COUNT> +19 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_CONFORMER_ID> +00000BD900000001 + +> <PUBCHEM_MMFF94_ENERGY> +65.6362 + +> <PUBCHEM_FEATURE_SELFOVERLAP> +35.578 + +> <PUBCHEM_SHAPE_FINGERPRINT> +10366900 7 17386020514759110480 +114674 6 16903282898360328323 +11578080 2 17913245089295617604 +11582403 64 14544541357940910356 +11640471 11 18127963303313961600 +12236239 1 18272088352834916308 +12363563 72 18042978579496277287 +12553582 1 18190740839094073615 +12596599 1 18201439237582433270 +12788726 201 18410285909464206003 +13032168 30 18201440238019390274 +13140716 1 18187086113919468457 +13538477 17 18339642338307470464 +13583140 156 17241914119188522922 +13764800 53 17895191172601517065 +13965767 371 17259888045752176376 +14115302 16 18342181093776810149 +14787075 74 17907866106787333628 +15279307 12 18198622322777022915 +15375462 189 18270674264943931347 +15669948 3 18336550511731321249 +16752209 62 18336841852664817743 +16945 1 18188484791351783177 +19433438 48 18059583550169763352 +200 152 18130792217719576158 +20645476 183 18270115859187436189 +20905425 154 17970632883131290416 +21452121 199 18046637711133085653 +21639500 275 16988270998321974524 +22112679 90 18342446063036096292 +23419403 2 17835564502519425292 +23493267 7 18115023138028600728 +23526113 38 16660924516543134566 +23557571 272 17821721762863303772 +23559900 14 17896315990920094510 +23598288 3 18411412925846384519 +23598291 2 18059009613384180254 +238 59 16343141308025475526 +4340502 62 17273677940604857177 +6049 1 17240202131864233360 +6992083 37 18058168521433072460 +7615 1 18201433675414973908 +77492 1 18272651289913926852 +81228 2 17968373550240022809 +9709674 26 17896035610527288590 + +> <PUBCHEM_SHAPE_MULTIPOLES> +378.03 +7.01 +2.75 +1.77 +0.78 +1.58 +0.3 +0.41 +1.94 +-1.08 +1.9 +-8.69 +11.04 +2.58 + +> <PUBCHEM_SHAPE_SELFOVERLAP> +790.335 + +> <PUBCHEM_SHAPE_VOLUME> +214.7 + +> <PUBCHEM_COORDINATE_TYPE> +2 +5 +255 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lib.tabular Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,9 @@ +Hydrogen-bond donors InChI key logP Polar surface area Number of heavy atoms Molecular weight InChI Spectrophores(TM) Number of rings Canonical SMILES Molecular refractivity Hydrogen-bond acceptors Rotatable bonds +3 JZUFKLXOESDKRF-UHFFFAOYSA-N 2.9774 135.12 17 297.73912 InChI=1S/C7H8ClN3O4S2/c8-4-1-5-7(2-6(4)16(9,12)13)17(14,15)11-3-10-5/h1-2,10-11H,3H2,(H2,9,12,13) nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, -1.245, -1.245, -0.178, -0.178, -0.178, -0.178, -0.178, -0.178, -0.178, 1.956, 1.956, -0.178, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 2 Clc1cc2NCNS(=O)(=O)c2cc1S(=O)(=O)N 67.5768 7 1 +3 ZZUFCTLCJUWOSV-UHFFFAOYSA-N 3.7448 131.01 21 330.74414 InChI=1S/C12H11ClN2O5S/c13-9-5-10(15-6-7-2-1-3-20-7)8(12(16)17)4-11(9)21(14,18)19/h1-5,15H,6H2,(H,16,17)(H2,14,18,19) nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, -2.141, -2.141, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 2 OC(=O)c1cc(c(cc1NCc1ccco1)Cl)S(=O)(=O)N 75.4644 7 5 +1 QEVHRUUCFGRFIF-MDEJGZGSSA-N 4.109 117.78 44 608.6787 InChI=1S/C33H40N2O9/c1-38-19-7-8-20-21-9-10-35-16-18-13-27(44-32(36)17-11-25(39-2)30(41-4)26(12-17)40-3)31(42-5)28(33(37)43-6)22(18)15-24(35)29(21)34-23(20)14-19/h7-8,11-12,14,18,22,24,27-28,31,34H,9-10,13,15-16H2,1-6H3/t18-,22+,24-,27-,28+,31+/m1/s1 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 6 COc1ccc2c(c1)[nH]c1c2CCN2[C@@H]1C[C@H]1[C@@H](C2)C[C@H]([C@@H]([C@H]1C(=O)OC)OC)OC(=O)c1cc(OC)c(c(c1)OC)OC 165.5222 10 10 +4 NJKRHQRIYAWMRO-BQTSRIDJSA-N 7.0864 252.9 61 906.41782 InChI=1S/C33H40N2O9.C7H8ClN3O4S2/c1-38-19-7-8-20-21-9-10-35-16-18-13-27(44-32(36)17-11-25(39-2)30(41-4)26(12-17)40-3)31(42-5)28(33(37)43-6)22(18)15-24(35)29(21)34-23(20)14-19;8-4-1-5-7(2-6(4)16(9,12)13)17(14,15)11-3-10-5/h7-8,11-12,14,18,22,24,27-28,31,34H,9-10,13,15-16H2,1-6H3;1-2,10-11H,3H2,(H2,9,12,13)/t18-,22+,24-,27-,28+,31+;/m1./s1 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 8 Clc1cc2NCNS(=O)(=O)c2cc1S(=O)(=O)N.COc1ccc2c(c1)[nH]c1c2CCN2[C@@H]1C[C@H]1[C@@H](C2)C[C@H]([C@@H]([C@H]1C(=O)OC)OC)OC(=O)c1cc(OC)c(c(c1)OC)OC 233.099 17 11 +0 UOOUPHIKFMZJEA-UHFFFAOYSA-N 6.248 33.42 33 430.54354 InChI=1S/C29H26N4/c1-3-29(4-2)31-25-20-27-24(19-28(25)33(29)22-15-9-6-10-16-22)30-23-17-11-12-18-26(23)32(27)21-13-7-5-8-14-21/h5-20H,3-4H2,1-2H3 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, -2.141, -2.141, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 6 CCC1(CC)N=c2c(N1c1ccccc1)cc1c(c2)n(c2ccccc2)c2c(n1)cccc2 143.054 3 4 +0 YQCDIJPZZOKCLA-UHFFFAOYSA-N 5.8579 33.42 32 416.51696 InChI=1S/C28H24N4/c1-3-28(2)30-24-19-26-23(18-27(24)32(28)21-14-8-5-9-15-21)29-22-16-10-11-17-25(22)31(26)20-12-6-4-7-13-20/h4-19H,3H2,1-2H3 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 6 CCC1(C)N=c2c(N1c1ccccc1)cc1c(c2)n(c2ccccc2)c2c(n1)cccc2 138.247 3 3 +0 BSYNRYMUTXBXSQ-UHFFFAOYSA-M -0.0246 66.43 13 179.14948 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 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 2.141, 2.141, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 1 CC(=O)Oc1ccccc1C(=O)[O-] 42.958 4 3 +0 BSYNRYMUTXBXSQ-UHFFFAOYSA-M -0.0246 66.43 13 179.14948 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 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 2.141, 2.141, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 1 CC(=O)Oc1ccccc1C(=O)[O-] 42.958 4 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/molecule.sdf Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,155 @@ +2244 + -OEChem-05151212332D + + 21 21 0 0 0 0 0 0 0999 V2000 + 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +2244 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +212 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <PUBCHEM_IUPAC_INCHIKEY> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +1.2 + +> <PUBCHEM_EXACT_MASS> +180.042259 + +> <PUBCHEM_MOLECULAR_FORMULA> +C9H8O4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +180.15742 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_CACTVS_TPSA> +63.6 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +180.042259 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +13 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +5 6 8 +5 7 8 +6 8 8 +7 9 8 +8 10 8 +9 10 8 + +$$$$ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_convert_on_CID2244.can Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +CC(=O)Oc1ccccc1C(=O)O 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_convert_on_CID2244.cml Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,49 @@ +<?xml version="1.0"?> +<molecule id="id2244" xmlns="http://www.xml-cml.org/schema"> + <atomArray> + <atom id="a1" elementType="O" x2="3.732000" y2="-0.060000"/> + <atom id="a2" elementType="O" x2="6.330100" y2="1.440000"/> + <atom id="a3" elementType="O" x2="4.598100" y2="1.440000"/> + <atom id="a4" elementType="O" x2="2.866000" y2="-1.560000"/> + <atom id="a5" elementType="C" x2="4.598100" y2="-0.560000"/> + <atom id="a6" elementType="C" x2="5.464100" y2="-0.060000"/> + <atom id="a7" elementType="C" x2="4.598100" y2="-1.560000"/> + <atom id="a8" elementType="C" x2="6.330100" y2="-0.560000"/> + <atom id="a9" elementType="C" x2="5.464100" y2="-2.060000"/> + <atom id="a10" elementType="C" x2="6.330100" y2="-1.560000"/> + <atom id="a11" elementType="C" x2="5.464100" y2="0.940000"/> + <atom id="a12" elementType="C" x2="2.866000" y2="-0.560000"/> + <atom id="a13" elementType="C" x2="2.000000" y2="-0.060000"/> + <atom id="a14" elementType="H" x2="4.061100" y2="-1.870000"/> + <atom id="a15" elementType="H" x2="6.867100" y2="-0.250000"/> + <atom id="a16" elementType="H" x2="5.464100" y2="-2.680000"/> + <atom id="a17" elementType="H" x2="6.867100" y2="-1.870000"/> + <atom id="a18" elementType="H" x2="2.310000" y2="0.476900"/> + <atom id="a19" elementType="H" x2="1.463100" y2="0.250000"/> + <atom id="a20" elementType="H" x2="1.690000" y2="-0.596900"/> + <atom id="a21" elementType="H" x2="6.330100" y2="2.060000"/> + </atomArray> + <bondArray> + <bond atomRefs2="a1 a5" order="1"/> + <bond atomRefs2="a1 a12" order="1"/> + <bond atomRefs2="a2 a11" order="1"/> + <bond atomRefs2="a2 a21" order="1"/> + <bond atomRefs2="a3 a11" order="2"/> + <bond atomRefs2="a4 a12" order="2"/> + <bond atomRefs2="a5 a6" order="1"/> + <bond atomRefs2="a5 a7" order="2"/> + <bond atomRefs2="a6 a8" order="2"/> + <bond atomRefs2="a6 a11" order="1"/> + <bond atomRefs2="a7 a9" order="1"/> + <bond atomRefs2="a7 a14" order="1"/> + <bond atomRefs2="a8 a10" order="1"/> + <bond atomRefs2="a8 a15" order="1"/> + <bond atomRefs2="a9 a10" order="2"/> + <bond atomRefs2="a9 a16" order="1"/> + <bond atomRefs2="a10 a17" order="1"/> + <bond atomRefs2="a12 a13" order="1"/> + <bond atomRefs2="a13 a18" order="1"/> + <bond atomRefs2="a13 a19" order="1"/> + <bond atomRefs2="a13 a20" order="1"/> + </bondArray> +</molecule>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_convert_on_CID2244.inchi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_convert_on_CID2244.pdb Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,46 @@ +COMPND 2244 +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 O UNL 1 3.732 -0.060 0.000 1.00 0.00 O +HETATM 2 O UNL 1 6.330 1.440 0.000 1.00 0.00 O +HETATM 3 O UNL 1 4.598 1.440 0.000 1.00 0.00 O +HETATM 4 O UNL 1 2.866 -1.560 0.000 1.00 0.00 O +HETATM 5 C UNL 1 4.598 -0.560 0.000 1.00 0.00 C +HETATM 6 C UNL 1 5.464 -0.060 0.000 1.00 0.00 C +HETATM 7 C UNL 1 4.598 -1.560 0.000 1.00 0.00 C +HETATM 8 C UNL 1 6.330 -0.560 0.000 1.00 0.00 C +HETATM 9 C UNL 1 5.464 -2.060 0.000 1.00 0.00 C +HETATM 10 C UNL 1 6.330 -1.560 0.000 1.00 0.00 C +HETATM 11 C UNL 1 5.464 0.940 0.000 1.00 0.00 C +HETATM 12 C UNL 1 2.866 -0.560 0.000 1.00 0.00 C +HETATM 13 C UNL 1 2.000 -0.060 0.000 1.00 0.00 C +HETATM 14 H UNL 1 4.061 -1.870 0.000 1.00 0.00 H +HETATM 15 H UNL 1 6.867 -0.250 0.000 1.00 0.00 H +HETATM 16 H UNL 1 5.464 -2.680 0.000 1.00 0.00 H +HETATM 17 H UNL 1 6.867 -1.870 0.000 1.00 0.00 H +HETATM 18 H UNL 1 2.310 0.477 0.000 1.00 0.00 H +HETATM 19 H UNL 1 1.463 0.250 0.000 1.00 0.00 H +HETATM 20 H UNL 1 1.690 -0.597 0.000 1.00 0.00 H +HETATM 21 H UNL 1 6.330 2.060 0.000 1.00 0.00 H +CONECT 1 5 12 +CONECT 2 11 21 +CONECT 3 11 +CONECT 4 12 +CONECT 5 1 6 7 +CONECT 6 5 8 11 +CONECT 7 5 9 14 +CONECT 8 6 10 15 +CONECT 9 7 10 16 +CONECT 10 8 9 17 +CONECT 11 2 3 6 +CONECT 12 1 4 13 +CONECT 13 12 18 19 20 +CONECT 14 7 +CONECT 15 8 +CONECT 16 9 +CONECT 17 10 +CONECT 18 13 +CONECT 19 13 +CONECT 20 13 +CONECT 21 2 +MASTER 0 0 0 0 0 0 0 0 21 0 21 0 +END
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_convert_on_CID2244.sdf Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,154 @@ +2244 + OpenBabel03291606592D + + 21 21 0 0 0 0 0 0 0 0999 V2000 + 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +2244 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +212 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <PUBCHEM_IUPAC_INCHIKEY> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +1.2 + +> <PUBCHEM_EXACT_MASS> +180.042259 + +> <PUBCHEM_MOLECULAR_FORMULA> +C9H8O4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +180.15742 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_CACTVS_TPSA> +63.6 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +180.042259 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +13 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +5 6 8 +5 7 8 +6 8 8 +7 9 8 +8 10 8 +9 10 8 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_convert_on_CID2244.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +CC(=O)Oc1ccccc1C(=O)O 2244
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_filter_on_CID2244.sdf Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,154 @@ +2244 + OpenBabel07101213142D + + 21 21 0 0 0 0 0 0 0 0999 V2000 + 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +2244 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +212 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <PUBCHEM_IUPAC_INCHIKEY> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +1.2 + +> <PUBCHEM_EXACT_MASS> +180.042259 + +> <PUBCHEM_MOLECULAR_FORMULA> +C9H8O4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +180.15742 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_CACTVS_TPSA> +63.6 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +180.042259 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +13 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +5 6 8 +5 7 8 +6 8 8 +7 9 8 +8 10 8 +9 10 8 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_filter_on_CID2244.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +O(c1c(cccc1)C(=O)O)C(=O)C 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_filter_on_CID2244_2.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +O(c1c(cccc1)C(=O)O)C(=O)C 2244
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_genprop_on_CID2244.sdf Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,193 @@ +2244 + OpenBabel05191718512D + + 21 21 0 0 0 0 0 0 0 0999 V2000 + 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +2244 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +212 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <PUBCHEM_IUPAC_INCHIKEY> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +1.2 + +> <PUBCHEM_EXACT_MASS> +180.042259 + +> <PUBCHEM_MOLECULAR_FORMULA> +C9H8O4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +180.15742 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_CACTVS_TPSA> +63.6 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +180.042259 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +13 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +5 6 8 +5 7 8 +6 8 8 +7 9 8 +8 10 8 +9 10 8 + +> <Molecular weight> +180.1574199999999 + +> <logP> +1.3100999999999998 + +> <Hydrogen-bond donors> +1 + +> <Hydrogen-bond acceptors> +4 + +> <Polar surface area> +63.6 + +> <Molecular refractivity> +44.900299999999994 + +> <Rotatable bonds> +3 + +> <Canonical SMILES> +CC(=O)Oc1ccccc1C(=O)O + +> <InChI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <InChI key> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <Number of rings> +1 + +> <Number of heavy atoms> +13 + +> <Spectrophores(TM)> +-1.454, -1.106, -1.162, 0.285, 0.369, 1.008, 0.144, -0.956, 0.133, 0.883, 1.828, 0.029, -1.312, -1.424, -1.287, -0.644, 0.590, 0.746, -0.127, 0.535, 0.368, 0.930, 1.721, -0.097, -1.591, -0.888, -1.332, 0.013, 0.889, 0.249, -0.343, -0.346, -0.047, 1.471, 1.595, 0.329, -1.101, -1.186, 0.953, 0.953, -0.644, -0.653, -1.136, 1.547, 0.533, -0.262, -0.274, 1.270 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_genprop_on_CID2244.tabular Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,2 @@ +Molecular weight logP Hydrogen-bond donors Hydrogen-bond acceptors Polar surface area Molecular refractivity Rotatable bonds Canonical SMILES InChI InChI key Number of rings Number of heavy atoms Spectrophores(TM) +180.1574199999999 1.3100999999999998 1 4 63.6 44.900299999999994 3 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) BSYNRYMUTXBXSQ-UHFFFAOYSA-N 1 13 -1.454, -1.106, -1.162, 0.285, 0.369, 1.008, 0.144, -0.956, 0.133, 0.883, 1.828, 0.029, -1.312, -1.424, -1.287, -0.644, 0.590, 0.746, -0.127, 0.535, 0.368, 0.930, 1.721, -0.097, -1.591, -0.888, -1.332, 0.013, 0.889, 0.249, -0.343, -0.346, -0.047, 1.471, 1.595, 0.329, -1.101, -1.186, 0.953, 0.953, -0.644, -0.653, -1.136, 1.547, 0.533, -0.262, -0.274, 1.270
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_multi_obgrep.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,4 @@ +CC(=O)Oc1ccccc1C(=O)[O-] +CC(=O)Oc1ccccc1C(=O)[O-] +CC(=O)Oc1ccccc1C(=O)[O-] +CC(=O)Oc1ccccc1C(=O)[O-]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_prepare_ligands.sdf Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,759 @@ + + SciTegic01171120562D + + 26 30 0 0 0 0 999 V2000 + -8.6396 0.9568 0.0000 O 0 0 + -7.6023 1.5602 0.0000 C 0 0 + -7.6071 3.0602 0.0000 C 0 0 + -6.3104 3.8143 0.0000 C 0 0 + -5.0090 3.0685 0.0000 C 0 0 + -5.0040 1.5682 0.0000 C 0 0 + -6.3008 0.8143 0.0000 C 0 0 + -3.7006 0.8244 0.0000 C 0 0 + -3.7006 -0.6045 0.0000 N 0 0 + -2.4915 -1.3190 0.0000 C 0 0 + -2.5059 -2.8197 0.0000 N 0 0 + -1.2156 -3.5847 0.0000 C 0 0 + -1.2329 -5.0846 0.0000 C 0 0 + -2.5404 -5.8196 0.0000 O 0 0 + -3.8308 -5.0547 0.0000 C 0 0 + -3.8135 -3.5548 0.0000 C 0 0 + -1.2274 -0.6045 0.0000 C 0 0 + 0.0000 -1.3190 0.0000 O 0 0 + 1.2274 -0.6045 0.0000 C 0 0 + 2.4732 -1.3190 0.0000 N 0 0 + 3.7372 -0.6045 0.0000 C 0 0 + 3.7372 0.8244 0.0000 C 0 0 + 2.4732 1.5389 0.0000 C 0 0 + 1.2274 0.8244 0.0000 C 0 0 + -1.2274 0.8244 0.0000 C 0 0 + -2.4915 1.5389 0.0000 N 0 0 + 1 2 1 0 + 2 3 1 0 + 3 4 2 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_prepare_ligands1.mol2 Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,96 @@ +@<TRIPOS>MOLECULE +***** + 42 46 0 0 0 +SMALL +GASTEIGER + +@<TRIPOS>ATOM + 1 O -8.6396 0.9568 0.0000 O.3 1 UNL1 -0.5067 + 2 C -7.6023 1.5602 0.0000 C.ar 1 UNL1 0.1175 + 3 C -7.6071 3.0602 0.0000 C.ar 1 UNL1 -0.0201 + 4 C -6.3104 3.8143 0.0000 C.ar 1 UNL1 -0.0576 + 5 C -5.0090 3.0685 0.0000 C.ar 1 UNL1 -0.0508 + 6 C -5.0040 1.5682 0.0000 C.ar 1 UNL1 0.0226 + 7 C -6.3008 0.8143 0.0000 C.ar 1 UNL1 -0.0095 + 8 C -3.7006 0.8244 0.0000 C.ar 1 UNL1 0.1627 + 9 N -3.7006 -0.6045 0.0000 N.ar 1 UNL1 -0.2088 + 10 C -2.4915 -1.3190 0.0000 C.ar 1 UNL1 0.1687 + 11 N -2.5059 -2.8197 0.0000 N.pl3 1 UNL1 -0.3078 + 12 C -1.2156 -3.5847 0.0000 C.3 1 UNL1 0.0371 + 13 C -1.2329 -5.0846 0.0000 C.3 1 UNL1 0.0634 + 14 O -2.5404 -5.8196 0.0000 O.3 1 UNL1 -0.3767 + 15 C -3.8308 -5.0547 0.0000 C.3 1 UNL1 0.0634 + 16 C -3.8135 -3.5548 0.0000 C.3 1 UNL1 0.0371 + 17 C -1.2274 -0.6045 0.0000 C.ar 1 UNL1 0.1961 + 18 O 0.0000 -1.3190 0.0000 O.2 1 UNL1 -0.4317 + 19 C 1.2274 -0.6045 0.0000 C.ar 1 UNL1 0.2301 + 20 N 2.4732 -1.3190 0.0000 N.ar 1 UNL1 -0.2204 + 21 C 3.7372 -0.6045 0.0000 C.ar 1 UNL1 0.0314 + 22 C 3.7372 0.8244 0.0000 C.ar 1 UNL1 -0.0427 + 23 C 2.4732 1.5389 0.0000 C.ar 1 UNL1 -0.0459 + 24 C 1.2274 0.8244 0.0000 C.ar 1 UNL1 0.0660 + 25 C -1.2274 0.8244 0.0000 C.ar 1 UNL1 0.1241 + 26 N -2.4915 1.5389 0.0000 N.ar 1 UNL1 -0.2233 + 27 H -9.4526 1.4227 0.0000 H 1 UNL1 0.2921 + 28 H -8.5025 3.5734 0.0000 H 1 UNL1 0.0654 + 29 H -6.3137 4.8463 0.0000 H 1 UNL1 0.0619 + 30 H -4.1170 3.5874 0.0000 H 1 UNL1 0.0625 + 31 H -6.2976 -0.2177 0.0000 H 1 UNL1 0.0661 + 32 H -0.2828 -3.0604 0.0000 H 1 UNL1 0.0487 + 33 H -0.2952 -4.1304 0.0000 H 1 UNL1 0.0487 + 34 H -0.3125 -5.6302 0.0000 H 1 UNL1 0.0575 + 35 H -1.2452 -6.1545 0.0000 H 1 UNL1 0.0575 + 36 H -4.7635 -5.5790 0.0000 H 1 UNL1 0.0575 + 37 H -4.7512 -4.5091 0.0000 H 1 UNL1 0.0575 + 38 H -4.7339 -3.0092 0.0000 H 1 UNL1 0.0487 + 39 H -3.8012 -2.4849 0.0000 H 1 UNL1 0.0487 + 40 H 4.6286 -1.1246 0.0000 H 1 UNL1 0.0831 + 41 H 4.6286 1.3445 0.0000 H 1 UNL1 0.0633 + 42 H 2.4700 2.5709 0.0000 H 1 UNL1 0.0626 +@<TRIPOS>BOND + 1 1 2 1 + 2 2 3 ar + 3 3 4 ar + 4 4 5 ar + 5 5 6 ar + 6 6 7 ar + 7 2 7 ar + 8 6 8 1 + 9 8 9 ar + 10 9 10 ar + 11 10 11 1 + 12 11 12 1 + 13 12 13 1 + 14 13 14 1 + 15 14 15 1 + 16 15 16 1 + 17 11 16 1 + 18 10 17 ar + 19 17 18 ar + 20 18 19 ar + 21 19 20 ar + 22 20 21 ar + 23 21 22 ar + 24 22 23 ar + 25 23 24 ar + 26 19 24 ar + 27 24 25 ar + 28 17 25 ar + 29 25 26 ar + 30 8 26 ar + 31 1 27 1 + 32 3 28 1 + 33 4 29 1 + 34 5 30 1 + 35 7 31 1 + 36 12 32 1 + 37 12 33 1 + 38 13 34 1 + 39 13 35 1 + 40 15 36 1 + 41 15 37 1 + 42 16 38 1 + 43 16 39 1 + 44 21 40 1 + 45 22 41 1 + 46 23 42 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_prepare_ligands1.pdbqt Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,41 @@ +REMARK Name = +REMARK 2 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: O_1 and C_2 +REMARK 2 A between atoms: C_6 and C_8 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 -3.701 0.824 0.000 0.00 0.00 +0.163 A +ATOM 2 N UNL 1 -2.491 1.539 0.000 0.00 0.00 -0.223 NA +ATOM 3 C UNL 1 -1.227 0.824 0.000 0.00 0.00 +0.124 A +ATOM 4 C UNL 1 -1.227 -0.605 0.000 0.00 0.00 +0.196 A +ATOM 5 O UNL 1 0.000 -1.319 0.000 0.00 0.00 -0.432 OA +ATOM 6 C UNL 1 1.227 -0.605 0.000 0.00 0.00 +0.230 A +ATOM 7 N UNL 1 2.473 -1.319 0.000 0.00 0.00 -0.220 NA +ATOM 8 C UNL 1 3.737 -0.605 0.000 0.00 0.00 +0.114 A +ATOM 9 C UNL 1 3.737 0.824 0.000 0.00 0.00 +0.021 A +ATOM 10 C UNL 1 2.473 1.539 0.000 0.00 0.00 +0.017 A +ATOM 11 C UNL 1 -2.491 -1.319 0.000 0.00 0.00 +0.169 A +ATOM 12 N UNL 1 -2.506 -2.820 0.000 0.00 0.00 -0.308 N +ATOM 13 C UNL 1 -3.813 -3.555 0.000 0.00 0.00 +0.134 C +ATOM 14 C UNL 1 -3.831 -5.055 0.000 0.00 0.00 +0.178 C +ATOM 15 O UNL 1 -2.540 -5.820 0.000 0.00 0.00 -0.377 OA +ATOM 16 C UNL 1 -1.233 -5.085 0.000 0.00 0.00 +0.178 C +ATOM 17 C UNL 1 -1.216 -3.585 0.000 0.00 0.00 +0.134 C +ATOM 18 C UNL 1 1.227 0.824 0.000 0.00 0.00 +0.066 A +ATOM 19 N UNL 1 -3.701 -0.605 0.000 0.00 0.00 -0.209 NA +ENDROOT +BRANCH 1 22 +ATOM 20 C UNL 1 -7.602 1.560 0.000 0.00 0.00 +0.118 A +ATOM 21 C UNL 1 -6.301 0.814 0.000 0.00 0.00 +0.057 A +ATOM 22 C UNL 1 -5.004 1.568 0.000 0.00 0.00 +0.023 A +ATOM 23 C UNL 1 -5.009 3.068 0.000 0.00 0.00 +0.012 A +ATOM 24 C UNL 1 -6.310 3.814 0.000 0.00 0.00 +0.004 A +ATOM 25 C UNL 1 -7.607 3.060 0.000 0.00 0.00 +0.045 A +BRANCH 20 26 +ATOM 26 O UNL 1 -8.640 0.957 0.000 0.00 0.00 -0.507 OA +ATOM 27 H UNL 1 -9.453 1.423 0.000 0.00 0.00 +0.292 HD +ENDBRANCH 20 26 +ENDBRANCH 1 22 +TORSDOF 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_prepare_ligands2.mol2 Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,162 @@ +@<TRIPOS>MOLECULE +***** + 73 81 0 0 0 +SMALL +GASTEIGER + +@<TRIPOS>ATOM + 1 C -4.7204 3.3431 0.0000 C.3 1 UNL1 0.0371 + 2 O -4.1471 2.2890 0.0000 O.3 1 UNL1 -0.3732 + 3 C -2.6500 2.2500 0.0000 C.3 1 UNL1 0.1246 + 4 C -1.8100 3.5000 0.0000 C.3 1 UNL1 0.0607 + 5 C -0.2400 3.5200 0.0000 C.3 1 UNL1 0.0140 + 6 C 0.5000 2.1800 0.0000 C.3 1 UNL1 0.1404 + 7 O -1.0600 2.1800 0.0000 O.3 1 UNL1 -0.3282 + 8 C -1.8300 0.9300 0.0000 C.3 1 UNL1 0.1744 + 9 C -3.0300 0.9300 0.0000 C.3 1 UNL1 -0.0136 + 10 N -0.9800 -0.7800 0.0000 N.ar 1 UNL1 -0.3070 + 11 C -2.1300 -1.4600 0.0000 C.ar 1 UNL1 0.0527 + 12 C -3.3200 -0.7600 0.0000 C.ar 1 UNL1 -0.0375 + 13 C -4.5500 -1.4800 0.0000 C.ar 1 UNL1 -0.0598 + 14 C -4.5800 -2.7700 0.0000 C.ar 1 UNL1 -0.0611 + 15 C -3.3400 -3.4700 0.0000 C.ar 1 UNL1 -0.0520 + 16 C -2.1300 -2.7900 0.0000 C.ar 1 UNL1 0.0081 + 17 C 0.2400 -2.7700 0.0000 C.ar 1 UNL1 0.0151 + 18 C 1.4300 -3.4700 0.0000 C.ar 1 UNL1 -0.0078 + 19 C 1.7600 -4.9700 0.0000 C.3 1 UNL1 0.0385 + 20 N 3.2600 -5.0800 0.0000 N.am 1 UNL1 -0.3072 + 21 C 3.8500 -3.6300 0.0000 C.2 1 UNL1 0.2453 + 22 O 4.9971 -3.2777 0.0000 O.2 1 UNL1 -0.2702 + 23 C 2.6600 -2.7500 0.0000 C.ar 1 UNL1 0.0518 + 24 C 2.6800 -1.4600 0.0000 C.ar 1 UNL1 0.0221 + 25 C 3.7900 0.5600 0.0000 C.ar 1 UNL1 0.0085 + 26 C 4.9600 1.2800 0.0000 C.ar 1 UNL1 -0.0520 + 27 C 4.9600 2.6300 0.0000 C.ar 1 UNL1 -0.0611 + 28 C 3.8100 3.2900 0.0000 C.ar 1 UNL1 -0.0598 + 29 C 2.6400 2.5900 0.0000 C.ar 1 UNL1 -0.0375 + 30 C 2.6400 1.2400 0.0000 C.ar 1 UNL1 0.0524 + 31 N 1.4900 0.5400 0.0000 N.ar 1 UNL1 -0.3115 + 32 C 1.4500 -0.7600 0.0000 C.ar 1 UNL1 0.0774 + 33 C 0.2400 -1.4400 0.0000 C.ar 1 UNL1 0.0772 + 34 N -2.5511 4.8030 0.0000 N.am 1 UNL1 -0.2947 + 35 C -1.9442 5.8382 0.0000 C.3 1 UNL1 0.0039 + 36 C -4.0519 4.8135 0.0000 C.2 1 UNL1 0.2467 + 37 O -4.6588 3.7783 0.0000 O.2 1 UNL1 -0.2700 + 38 C -4.7941 6.1180 0.0000 C.ar 1 UNL1 0.0369 + 39 C -6.2940 6.1306 0.0000 C.ar 1 UNL1 -0.0496 + 40 C -7.0331 7.4359 0.0000 C.ar 1 UNL1 -0.0610 + 41 C -6.2722 8.7286 0.0000 C.ar 1 UNL1 -0.0617 + 42 C -4.7723 8.7160 0.0000 C.ar 1 UNL1 -0.0610 + 43 C -4.0332 7.4108 0.0000 C.ar 1 UNL1 -0.0496 + 44 H -4.1620 4.2558 0.0000 H 1 UNL1 0.0524 + 45 H -5.7901 3.3703 0.0000 H 1 UNL1 0.0524 + 46 H -5.2316 4.2831 0.0000 H 1 UNL1 0.0524 + 47 H -3.1408 3.2008 0.0000 H 1 UNL1 0.0663 + 48 H -2.8793 3.5399 0.0000 H 1 UNL1 0.0529 + 49 H 0.2979 4.4450 0.0000 H 1 UNL1 0.0328 + 50 H 0.8299 3.5081 0.0000 H 1 UNL1 0.0328 + 51 H -0.4215 2.7238 0.0000 H 1 UNL1 0.0839 + 52 H -3.5650 1.8566 0.0000 H 1 UNL1 0.0277 + 53 H -3.5650 0.0034 0.0000 H 1 UNL1 0.0277 + 54 H -4.1000 0.9300 0.0000 H 1 UNL1 0.0277 + 55 H -3.3189 0.2720 0.0000 H 1 UNL1 0.0638 + 56 H -5.4393 -0.9563 0.0000 H 1 UNL1 0.0618 + 57 H -5.4772 -3.2799 0.0000 H 1 UNL1 0.0618 + 58 H -3.3410 -4.5020 0.0000 H 1 UNL1 0.0624 + 59 H 1.0595 -5.7788 0.0000 H 1 UNL1 0.0512 + 60 H 2.1687 -5.9589 0.0000 H 1 UNL1 0.0512 + 61 H 3.7793 -5.9164 0.0000 H 1 UNL1 0.1493 + 62 H 5.8609 0.7766 0.0000 H 1 UNL1 0.0624 + 63 H 5.8531 3.1472 0.0000 H 1 UNL1 0.0618 + 64 H 3.8006 4.3220 0.0000 H 1 UNL1 0.0618 + 65 H 1.7423 3.0990 0.0000 H 1 UNL1 0.0638 + 66 H -0.8742 5.8311 0.0000 H 1 UNL1 0.0429 + 67 H -2.4730 6.7684 0.0000 H 1 UNL1 0.0429 + 68 H -1.4030 6.7613 0.0000 H 1 UNL1 0.0429 + 69 H -6.8175 5.2412 0.0000 H 1 UNL1 0.0625 + 70 H -8.0651 7.4446 0.0000 H 1 UNL1 0.0618 + 71 H -6.7807 9.6266 0.0000 H 1 UNL1 0.0618 + 72 H -4.2488 9.6054 0.0000 H 1 UNL1 0.0618 + 73 H -3.0012 7.4022 0.0000 H 1 UNL1 0.0625 +@<TRIPOS>BOND + 1 1 2 1 + 2 3 2 1 + 3 3 4 1 + 4 4 5 1 + 5 6 5 1 + 6 6 7 1 + 7 7 8 1 + 8 3 8 1 + 9 8 9 1 + 10 8 10 1 + 11 10 11 ar + 12 11 12 ar + 13 12 13 ar + 14 13 14 ar + 15 14 15 ar + 16 15 16 ar + 17 11 16 ar + 18 16 17 ar + 19 17 18 ar + 20 18 19 1 + 21 19 20 1 + 22 20 21 am + 23 21 22 2 + 24 21 23 1 + 25 18 23 ar + 26 23 24 ar + 27 24 25 ar + 28 25 26 ar + 29 26 27 ar + 30 27 28 ar + 31 28 29 ar + 32 29 30 ar + 33 25 30 ar + 34 30 31 ar + 35 6 31 1 + 36 31 32 ar + 37 24 32 ar + 38 32 33 ar + 39 10 33 ar + 40 17 33 ar + 41 4 34 1 + 42 34 35 1 + 43 34 36 am + 44 36 37 2 + 45 36 38 1 + 46 38 39 ar + 47 39 40 ar + 48 40 41 ar + 49 41 42 ar + 50 42 43 ar + 51 38 43 ar + 52 1 44 1 + 53 1 45 1 + 54 1 46 1 + 55 3 47 1 + 56 4 48 1 + 57 5 49 1 + 58 5 50 1 + 59 6 51 1 + 60 9 52 1 + 61 9 53 1 + 62 9 54 1 + 63 12 55 1 + 64 13 56 1 + 65 14 57 1 + 66 15 58 1 + 67 19 59 1 + 68 19 60 1 + 69 20 61 1 + 70 26 62 1 + 71 27 63 1 + 72 28 64 1 + 73 29 65 1 + 74 35 66 1 + 75 35 67 1 + 76 35 68 1 + 77 39 69 1 + 78 40 70 1 + 79 41 71 1 + 80 42 72 1 + 81 43 73 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_prepare_ligands2.pdbqt Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,64 @@ +REMARK Name = +REMARK 6 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_1 and O_2 +REMARK 2 A between atoms: O_2 and C_3 +REMARK 3 A between atoms: C_4 and N_34 +REMARK 4 A between atoms: C_8 and C_9 +REMARK 5 A between atoms: N_34 and C_35 +REMARK 6 A between atoms: C_36 and C_38 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 -2.650 2.250 0.000 0.00 0.00 +0.191 C +ATOM 2 C UNL 1 -1.830 0.930 0.000 0.00 0.00 +0.174 C +ATOM 3 N UNL 1 -0.980 -0.780 0.000 0.00 0.00 -0.307 N +ATOM 4 C UNL 1 0.240 -1.440 0.000 0.00 0.00 +0.077 A +ATOM 5 C UNL 1 0.240 -2.770 0.000 0.00 0.00 +0.015 A +ATOM 6 C UNL 1 1.430 -3.470 0.000 0.00 0.00 -0.008 A +ATOM 7 C UNL 1 2.660 -2.750 0.000 0.00 0.00 +0.052 A +ATOM 8 C UNL 1 2.680 -1.460 0.000 0.00 0.00 +0.022 A +ATOM 9 C UNL 1 3.790 0.560 0.000 0.00 0.00 +0.008 A +ATOM 10 C UNL 1 2.640 1.240 0.000 0.00 0.00 +0.052 A +ATOM 11 N UNL 1 1.490 0.540 0.000 0.00 0.00 -0.311 N +ATOM 12 C UNL 1 0.500 2.180 0.000 0.00 0.00 +0.224 C +ATOM 13 C UNL 1 -0.240 3.520 0.000 0.00 0.00 +0.080 C +ATOM 14 C UNL 1 2.640 2.590 0.000 0.00 0.00 +0.026 A +ATOM 15 C UNL 1 3.810 3.290 0.000 0.00 0.00 +0.002 A +ATOM 16 C UNL 1 4.960 2.630 0.000 0.00 0.00 +0.001 A +ATOM 17 C UNL 1 4.960 1.280 0.000 0.00 0.00 +0.010 A +ATOM 18 C UNL 1 3.850 -3.630 0.000 0.00 0.00 +0.245 C +ATOM 19 O UNL 1 4.997 -3.278 0.000 0.00 0.00 -0.270 OA +ATOM 20 N UNL 1 3.260 -5.080 0.000 0.00 0.00 -0.307 N +ATOM 21 H UNL 1 3.779 -5.916 0.000 0.00 0.00 +0.149 HD +ATOM 22 C UNL 1 1.760 -4.970 0.000 0.00 0.00 +0.141 C +ATOM 23 C UNL 1 -2.130 -2.790 0.000 0.00 0.00 +0.008 A +ATOM 24 C UNL 1 -3.340 -3.470 0.000 0.00 0.00 +0.010 A +ATOM 25 C UNL 1 -4.580 -2.770 0.000 0.00 0.00 +0.001 A +ATOM 26 C UNL 1 -4.550 -1.480 0.000 0.00 0.00 +0.002 A +ATOM 27 C UNL 1 -3.320 -0.760 0.000 0.00 0.00 +0.026 A +ATOM 28 C UNL 1 1.450 -0.760 0.000 0.00 0.00 +0.077 A +ATOM 29 C UNL 1 -2.130 -1.460 0.000 0.00 0.00 +0.053 A +ATOM 30 C UNL 1 -3.030 0.930 0.000 0.00 0.00 +0.069 C +ATOM 31 O UNL 1 -1.060 2.180 0.000 0.00 0.00 -0.328 OA +ATOM 32 C UNL 1 -1.810 3.500 0.000 0.00 0.00 +0.114 C +ENDROOT +BRANCH 32 33 +ATOM 33 N UNL 1 -2.551 4.803 0.000 0.00 0.00 -0.295 N +ATOM 34 C UNL 1 -4.052 4.814 0.000 0.00 0.00 +0.247 C +ATOM 35 O UNL 1 -4.659 3.778 0.000 0.00 0.00 -0.270 OA +ATOM 36 C UNL 1 -1.944 5.838 0.000 0.00 0.00 +0.132 C +BRANCH 34 37 +ATOM 37 C UNL 1 -4.794 6.118 0.000 0.00 0.00 +0.037 A +ATOM 38 C UNL 1 -4.033 7.411 0.000 0.00 0.00 +0.013 A +ATOM 39 C UNL 1 -4.772 8.716 0.000 0.00 0.00 +0.001 A +ATOM 40 C UNL 1 -6.272 8.729 0.000 0.00 0.00 +0.000 A +ATOM 41 C UNL 1 -7.033 7.436 0.000 0.00 0.00 +0.001 A +ATOM 42 C UNL 1 -6.294 6.131 0.000 0.00 0.00 +0.013 A +ENDBRANCH 34 37 +ENDBRANCH 32 33 +BRANCH 1 44 +ATOM 43 C UNL 1 -4.720 3.343 0.000 0.00 0.00 +0.194 C +ATOM 44 O UNL 1 -4.147 2.289 0.000 0.00 0.00 -0.373 OA +ENDBRANCH 1 44 +TORSDOF 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_remDuplicates_on_2_mol.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,1 @@ +CC(=O)OC1=CC=CC=C1C(=O)[O-]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_remove_protonation_state.sdf Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,154 @@ +2244 + OpenBabel03291607022D + + 21 21 0 0 0 0 0 0 0 0999 V2000 + 3.7320 -0.0600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 1.4400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5981 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 -1.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 0.9400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8660 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0000 -0.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0611 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4641 -2.6800 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.8671 -1.8700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3100 0.4769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4631 0.2500 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6900 -0.5969 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3301 2.0600 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 12 1 0 0 0 0 + 2 11 1 0 0 0 0 + 2 21 1 0 0 0 0 + 3 11 2 0 0 0 0 + 4 12 2 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 8 2 0 0 0 0 + 6 11 1 0 0 0 0 + 7 9 1 0 0 0 0 + 7 14 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 15 1 0 0 0 0 + 9 10 2 0 0 0 0 + 9 16 1 0 0 0 0 + 10 17 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 18 1 0 0 0 0 + 13 19 1 0 0 0 0 + 13 20 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +2244 + +> <PUBCHEM_COMPOUND_CANONICALIZED> +1 + +> <PUBCHEM_CACTVS_COMPLEXITY> +212 + +> <PUBCHEM_CACTVS_HBOND_ACCEPTOR> +4 + +> <PUBCHEM_CACTVS_HBOND_DONOR> +1 + +> <PUBCHEM_CACTVS_ROTATABLE_BOND> +3 + +> <PUBCHEM_CACTVS_SUBSKEYS> +AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA== + +> <PUBCHEM_IUPAC_OPENEYE_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_CAS_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_SYSTEMATIC_NAME> +2-acetyloxybenzoic acid + +> <PUBCHEM_IUPAC_TRADITIONAL_NAME> +2-acetoxybenzoic acid + +> <PUBCHEM_IUPAC_INCHI> +InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) + +> <PUBCHEM_IUPAC_INCHIKEY> +BSYNRYMUTXBXSQ-UHFFFAOYSA-N + +> <PUBCHEM_XLOGP3> +1.2 + +> <PUBCHEM_EXACT_MASS> +180.042259 + +> <PUBCHEM_MOLECULAR_FORMULA> +C9H8O4 + +> <PUBCHEM_MOLECULAR_WEIGHT> +180.15742 + +> <PUBCHEM_OPENEYE_CAN_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_OPENEYE_ISO_SMILES> +CC(=O)OC1=CC=CC=C1C(=O)O + +> <PUBCHEM_CACTVS_TPSA> +63.6 + +> <PUBCHEM_MONOISOTOPIC_WEIGHT> +180.042259 + +> <PUBCHEM_TOTAL_CHARGE> +0 + +> <PUBCHEM_HEAVY_ATOM_COUNT> +13 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_COORDINATE_TYPE> +1 +5 +255 + +> <PUBCHEM_BONDANNOTATIONS> +5 6 8 +5 7 8 +6 8 8 +7 9 8 +8 10 8 +9 10 8 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_spectrophore_search.tabular Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,9 @@ +Hydrogen-bond donors InChI key logP Polar surface area Number of heavy atoms Molecular weight InChI Spectrophores(TM) Number of rings Canonical SMILES Molecular refractivity Hydrogen-bond acceptors Rotatable bonds 0.000000 +3 JZUFKLXOESDKRF-UHFFFAOYSA-N 2.9774 135.12 17 297.73912 InChI=1S/C7H8ClN3O4S2/c8-4-1-5-7(2-6(4)16(9,12)13)17(14,15)11-3-10-5/h1-2,10-11H,3H2,(H2,9,12,13) nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, -1.245, -1.245, -0.178, -0.178, -0.178, -0.178, -0.178, -0.178, -0.178, 1.956, 1.956, -0.178, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 2 Clc1cc2NCNS(=O)(=O)c2cc1S(=O)(=O)N 67.5768 7 1 nan +3 ZZUFCTLCJUWOSV-UHFFFAOYSA-N 3.7448 131.01 21 330.74414 InChI=1S/C12H11ClN2O5S/c13-9-5-10(15-6-7-2-1-3-20-7)8(12(16)17)4-11(9)21(14,18)19/h1-5,15H,6H2,(H,16,17)(H2,14,18,19) nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, -2.141, -2.141, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 2 OC(=O)c1cc(c(cc1NCc1ccco1)Cl)S(=O)(=O)N 75.4644 7 5 nan +1 QEVHRUUCFGRFIF-MDEJGZGSSA-N 4.109 117.78 44 608.6787 InChI=1S/C33H40N2O9/c1-38-19-7-8-20-21-9-10-35-16-18-13-27(44-32(36)17-11-25(39-2)30(41-4)26(12-17)40-3)31(42-5)28(33(37)43-6)22(18)15-24(35)29(21)34-23(20)14-19/h7-8,11-12,14,18,22,24,27-28,31,34H,9-10,13,15-16H2,1-6H3/t18-,22+,24-,27-,28+,31+/m1/s1 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 6 COc1ccc2c(c1)[nH]c1c2CCN2[C@@H]1C[C@H]1[C@@H](C2)C[C@H]([C@@H]([C@H]1C(=O)OC)OC)OC(=O)c1cc(OC)c(c(c1)OC)OC 165.5222 10 10 nan +4 NJKRHQRIYAWMRO-BQTSRIDJSA-N 7.0864 252.9 61 906.41782 InChI=1S/C33H40N2O9.C7H8ClN3O4S2/c1-38-19-7-8-20-21-9-10-35-16-18-13-27(44-32(36)17-11-25(39-2)30(41-4)26(12-17)40-3)31(42-5)28(33(37)43-6)22(18)15-24(35)29(21)34-23(20)14-19;8-4-1-5-7(2-6(4)16(9,12)13)17(14,15)11-3-10-5/h7-8,11-12,14,18,22,24,27-28,31,34H,9-10,13,15-16H2,1-6H3;1-2,10-11H,3H2,(H2,9,12,13)/t18-,22+,24-,27-,28+,31+;/m1./s1 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 8 Clc1cc2NCNS(=O)(=O)c2cc1S(=O)(=O)N.COc1ccc2c(c1)[nH]c1c2CCN2[C@@H]1C[C@H]1[C@@H](C2)C[C@H]([C@@H]([C@H]1C(=O)OC)OC)OC(=O)c1cc(OC)c(c(c1)OC)OC 233.099 17 11 nan +0 UOOUPHIKFMZJEA-UHFFFAOYSA-N 6.248 33.42 33 430.54354 InChI=1S/C29H26N4/c1-3-29(4-2)31-25-20-27-24(19-28(25)33(29)22-15-9-6-10-16-22)30-23-17-11-12-18-26(23)32(27)21-13-7-5-8-14-21/h5-20H,3-4H2,1-2H3 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, -2.141, -2.141, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, 0.428, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 6 CCC1(CC)N=c2c(N1c1ccccc1)cc1c(c2)n(c2ccccc2)c2c(n1)cccc2 143.054 3 4 nan +0 YQCDIJPZZOKCLA-UHFFFAOYSA-N 5.8579 33.42 32 416.51696 InChI=1S/C28H24N4/c1-3-28(2)30-24-19-26-23(18-27(24)32(28)21-14-8-5-9-15-21)29-22-16-10-11-17-25(22)31(26)20-12-6-4-7-13-20/h4-19H,3H2,1-2H3 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 6 CCC1(C)N=c2c(N1c1ccccc1)cc1c(c2)n(c2ccccc2)c2c(n1)cccc2 138.247 3 3 nan +0 BSYNRYMUTXBXSQ-UHFFFAOYSA-M -0.0246 66.43 13 179.14948 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 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 2.141, 2.141, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 1 CC(=O)Oc1ccccc1C(=O)[O-] 42.958 4 3 nan +0 BSYNRYMUTXBXSQ-UHFFFAOYSA-M -0.0246 66.43 13 179.14948 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 nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, 2.141, 2.141, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, -0.428, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan 1 CC(=O)Oc1ccccc1C(=O)[O-] 42.958 4 3 nan
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/obgrep_on_8_mol.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,5 @@ +c1coc(c1)CNc1cc(c(cc1C(=O)O)S(=O)(=O)N)Cl +CO[C@H]1[C@@H](C[C@@H]2CN3CCc4c([C@H]3C[C@@H]2[C@@H]1C(=O)OC)[nH]c1c4ccc(c1)OC)OC(=O)c1cc(c(c(c1)OC)OC)OC +CO[C@H]1[C@@H](C[C@@H]2CN3CCc4c([C@H]3C[C@@H]2[C@@H]1C(=O)OC)[nH]c1c4ccc(c1)OC)OC(=O)c1cc(c(c(c1)OC)OC)OC.C1Nc2cc(c(cc2S(=O)(=O)N1)S(=O)(=O)N)Cl +CC(=O)Oc1ccccc1C(=O)[O-] +CC(=O)Oc1ccccc1C(=O)[O-]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/obremsmall_on_3_mol.smi Fri May 10 08:55:09 2019 -0400 @@ -0,0 +1,2 @@ +CC(=O)OC1=CC=CC=C1C(=O)[O-] +CC(=O)OC1=CC=CC=C1C(=O)[O-]