Mercurial > repos > bgruening > openbabel_structure_distance_finder
changeset 0:c066b5accacf draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/change_title_to_metadata_value.py Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,49 @@ +#!/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 +import random +import string + + +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") + parser.add_argument('--random', '-r', + action="store_true", help="Add random suffix to the 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] + if args.random: + suffix = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(13)) + mol.title += '__%s' % suffix + output.write( mol ) + + output.close() + + +if __name__ == "__main__": + main() +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cheminfolib.py Wed Mar 25 16:47:13 2020 -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/distance_finder.py Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,109 @@ +# Reports distances of ligands to reference points. An example input for the points is: +# +# 5.655 1.497 18.223 +# 1.494 -8.367 18.574 +# 13.034 6.306 25.232 +# +# Data can be space or tab separated but must contain 3 and only 3 numbers for the x, y and z coordinates +# +# That would encode 3 points. +# Each record in the SDF input is read and the closest heavy atom to each of the reference points is recorded as +# a property named distance1 where the numeric part is the index (starting from 1) of the points (in that example +# there would be properties for distance1, distance2 and distance3. + +import argparse, os, sys, math +from openbabel import pybel + + + +def log(*args, **kwargs): + """Log output to STDERR + """ + print(*args, file=sys.stderr, ** kwargs) + + +def execute(ligands_sdf, points_file, outfile): + """ + :param ligands_sdf: A SDF with the 3D molecules to test + :param points_file: A file with the points to consider. + :param outfile: The name of the file for the SDF output + :return: + """ + + + points = [] + + # read the points + with open(points_file, 'r') as f: + for line in f.readlines(): + line.strip() + if line: + p = line.split() + if len(p) == 3: + points.append((float(p[0]), float(p[1]), float(p[2]))) + log("Read points",p) + continue + log("Failed to read line:", line) + log('Found', len(points), 'atom points') + + sdf_writer = pybel.Outputfile("sdf", outfile, overwrite=True) + + count = 0 + for mol in pybel.readfile("sdf", ligands_sdf): + count += 1 + if count % 50000 == 0: + log('Processed', count) + + try: + # print("Processing mol", mol.title) + + clone = pybel.Molecule(mol) + clone.removeh() + + coords = [] + for atom in clone.atoms: + coords.append(atom.coords) + + p = 0 + for point in points: + p += 1 + distances = [] + for i in coords: + # calculates distance based on cartesian coordinates + distance = math.sqrt((point[0] - i[0])**2 + (point[1] - i[1])**2 + (point[2] - i[2])**2) + distances.append(distance) + # log("distance:", distance) + min_distance = min(distances) + # log('Min:', min_distance) + # log(count, p, min_distance) + + mol.data['distance' + str(p)] = min_distance + + sdf_writer.write(mol) + + except Exception as e: + log('Failed to handle molecule: '+ str(e)) + continue + + sdf_writer.close() + log('Wrote', count, 'molecules') + + +def main(): + global work_dir + + parser = argparse.ArgumentParser(description='XChem distances - measure distances to particular points') + + parser.add_argument('-i', '--input', help="SDF containing the 3D molecules to score)") + parser.add_argument('-p', '--points', help="PDB format file with atoms") + parser.add_argument('-o', '--outfile', default='output.sdf', help="File name for results") + + + args = parser.parse_args() + log("XChem distances args: ", args) + + execute(args.input, args.points, args.outfile) + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/distance_finder.xml Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,83 @@ +<tool id="openbabel_structure_distance_finder" name="Determine distance to defined points" version="0.1.0"> + <description>- determine the minimum distances between a molecule and a set of 3D points</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <!-- does not run with obabel 2.4.1 --> + <requirement type="package" version="3.0.0">openbabel</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/distance_finder.py' + -i '$input' + -p $points_file + -o '$output' + ]]></command> + + <configfiles> + <configfile name="points_file">$points</configfile> + </configfiles> + + <inputs> + <param type="data" name="input" format="sdf" label="Ligands to be analysed" help="Input in SDF format" /> + <param type="text" name="points" area="true" label="3D points to consider" help="Points as X, Y, Z coordinates, one point per line"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> + <remove value="'" /> + </valid> + </sanitizer> + </param> + </inputs> + <outputs> + <data format="sdf" name="output" label="The measured ligands"/> + </outputs> + <tests> + <test> + <param name="input" ftype="sdf" value="ligands.sdf"/> + <!-- TODO - work out how to specify multi-line text --> + <param name="points" value="5.655 1.497 18.223" /> + <output name="output" ftype="sdf"> + <assert_contents> + <has_text text="distance1" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +This tool reports distances of ligands to reference points provided as atoms in a PDB file. +It is useful for finding out to what extent a ligand occupies an active site. + +.. class:: infomark + +**Input** + +An SD-file containing 3D molecules. + +The points parameter contains the points to compare to as X, Y and Z coordinates, one point per line. +An example is: + +5.655 1.497 18.223 +1.494 -8.367 18.574 +13.034 6.306 25.232 + +This would encode 3 points. + +Each record in the SDF input is read and the closest heavy atom to each of the points is recorded as +properties in the output SDF. + +.. class:: infomark + +**Output** + +The same SD file as the input but with a series of "distance?" properties added where ? is the index of the points +being compared to. In the example there would be properties for distance1, distance2 and distance3. + + + ]]></help> + <expand macro="citations"/> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,40 @@ +<macros> + <token name="@VERSION@">2.4.2.1</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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,128 @@ +#!/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, + ) + parser.add_argument('--list_of_names', + help="A file with list of molecule names to extract. Every name is in one line.", + required=False, + ) + 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 filter_by_name(args): + outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) + for mol in pybel.readfile('sdf', args.input): + for name in open(args.list_of_names): + if mol.title.strip() == name.strip(): + outfile.write(mol) + outfile.close() + +def __main__(): + """ + Select compounds with certain properties from a small library + """ + args = parse_command_line() + + if args.filters == '__filter_by_name__': + filter_by_name(args) + return + + # Its a small trick to get the parameters in an easy way from the xml file. + # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed. + # Also the last loop creates a ',{' that is not an valid jason expression. + filters = json.loads((args.filters).replace(' ', '').replace(',}', '}')) + if args.iformat == 'sdf': + # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering + mol = next(pybel.readfile('sdf', args.input)) + for key, elem in filters.items(): + property = cheminfolib.ColumnNames[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 Wed Mar 25 16:47:13 2020 -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_remIons.py Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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/filterd_by_name.sdf Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,147 @@ +abc_one + OpenBabel03212013422D + + 26 30 0 0 0 0 0 0 0 0999 V2000 + -8.6396 0.9568 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -7.6023 1.5602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.6071 3.0602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.3104 3.8143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.0090 3.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.0040 1.5682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.3008 0.8143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.7006 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.7006 -0.6045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4915 -1.3190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5059 -2.8197 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2156 -3.5847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2329 -5.0846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5404 -5.8196 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8308 -5.0547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8135 -3.5548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2274 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 -1.3190 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2274 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4732 -1.3190 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7372 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7372 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4732 1.5389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2274 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2274 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4915 1.5389 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 7 2 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 6 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 8 26 2 0 0 0 0 + 9 10 2 0 0 0 0 + 10 11 1 0 0 0 0 + 10 17 1 0 0 0 0 + 11 12 1 0 0 0 0 + 11 16 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 + 17 18 1 0 0 0 0 + 17 25 2 0 0 0 0 + 18 19 1 0 0 0 0 + 19 20 2 0 0 0 0 + 19 24 1 0 0 0 0 + 20 21 1 0 0 0 0 + 21 22 2 0 0 0 0 + 22 23 1 0 0 0 0 + 23 24 2 0 0 0 0 + 24 25 1 0 0 0 0 + 25 26 1 0 0 0 0 +M END +> <mr_id> +4358263 + +> <SMI> +Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2 + +$$$$ +abc_eleven + OpenBabel03212013422D + + 32 35 0 0 1 0 0 0 0 0999 V2000 + 7.1381 -2.1568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0456 -2.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.7409 -1.9129 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6552 -2.9294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1855 -2.6254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7138 -1.2033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5889 0.0182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7889 0.0269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7138 1.2033 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2917 0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0028 1.5132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3155 0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3155 -0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3560 -1.3452 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0028 -1.5132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2917 -0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2542 -4.2907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6559 -5.3308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7448 -4.1226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7580 -5.2264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3978 -6.3710 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.2231 -4.9012 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 9.2380 -6.0068 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.7032 -5.6816 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 + 11.0634 -4.5369 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 11.7181 -6.7872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.1833 -6.4620 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 14.1993 -7.5656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.6630 -7.2376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.1108 -5.8060 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 15.0949 -4.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.6312 -5.0304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 19 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 17 2 0 0 0 0 + 5 6 2 0 0 0 0 + 6 7 1 0 0 0 0 + 6 16 1 0 0 0 0 + 7 8 2 0 0 0 0 + 7 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 16 2 0 0 0 0 + 11 12 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 15 16 1 0 0 0 0 + 17 18 1 0 0 0 0 + 17 19 1 0 0 0 0 + 19 20 1 0 0 0 0 + 20 21 2 0 0 0 0 + 20 22 1 0 0 0 0 + 22 23 1 0 0 0 0 + 23 24 1 0 0 0 0 + 24 25 1 6 0 0 0 + 24 26 1 0 0 0 0 + 26 27 1 0 0 0 0 + 27 28 1 0 0 0 0 + 27 32 1 0 0 0 0 + 28 29 1 0 0 0 0 + 29 30 1 0 0 0 0 + 30 31 1 0 0 0 0 + 31 32 1 0 0 0 0 +M END +> <mr_id> +4362206 + +> <SMI> +Cc1[nH]c(/C=C/2\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lib.tabular Wed Mar 25 16:47:13 2020 -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/ligands.sdf Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,348 @@ +C[C@H](NS(C)(=O)=O)c1ccccn1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 13.1106 0.7550 23.2143 C 0 0 0 0 0 0 + 12.0087 1.7547 22.8361 C 0 0 0 0 0 0 + 11.4071 1.4261 21.5334 N 0 0 0 0 0 0 + 9.9388 0.8337 21.6338 S 0 0 0 0 0 0 + 9.0411 2.3499 21.9038 C 0 0 0 0 0 0 + 9.3678 0.3273 20.3892 O 0 0 0 0 0 0 + 9.6367 0.0497 22.8298 O 0 0 0 0 0 0 + 12.5588 3.1798 22.7273 C 0 0 0 0 0 0 + 12.8091 3.9103 23.8920 C 0 0 0 0 0 0 + 13.2507 5.2279 23.7909 C 0 0 0 0 0 0 + 13.4398 5.7854 22.5337 C 0 0 0 0 0 0 + 13.1881 4.9943 21.4282 C 0 0 0 0 0 0 + 12.7627 3.7170 21.4945 N 0 0 0 0 0 0 + 2 8 1 0 0 0 + 2 3 1 0 0 0 + 2 1 1 0 0 0 + 3 4 1 0 0 0 + 4 5 1 0 0 0 + 4 6 2 0 0 0 + 4 7 2 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +C[C@@H](NS(C)(=O)=O)c1ccccn1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 6.8559 1.7506 21.3142 C 0 0 0 0 0 0 + 7.4019 0.6872 20.3547 C 0 0 0 0 0 0 + 7.4689 1.2291 18.9518 N 0 0 0 0 0 0 + 6.4062 0.5634 17.8113 S 0 0 0 0 0 0 + 4.8453 0.8765 18.6009 C 0 0 0 0 0 0 + 6.4632 1.4005 16.6345 O 0 0 0 0 0 0 + 6.5887 -0.8668 17.7602 O 0 0 0 0 0 0 + 8.6586 -0.0013 20.8698 C 0 0 0 0 0 0 + 9.8290 0.7331 21.0631 C 0 0 0 0 0 0 + 10.9643 0.0817 21.5388 C 0 0 0 0 0 0 + 10.9072 -1.2804 21.8047 C 0 0 0 0 0 0 + 9.7156 -1.9413 21.5709 C 0 0 0 0 0 0 + 8.6053 -1.3390 21.0982 N 0 0 0 0 0 0 + 2 1 1 0 0 0 + 2 3 1 0 0 0 + 2 8 1 0 0 0 + 3 4 1 0 0 0 + 4 5 1 0 0 0 + 4 6 2 0 0 0 + 4 7 2 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +FC(F)(F)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 10 10 0 0 0 0 0 0 0 0999 V2000 + 9.6749 1.3998 21.0525 F 0 0 0 0 0 0 + 10.4122 1.5718 22.1856 C 0 0 0 0 0 0 + 10.7385 2.8940 22.2189 F 0 0 0 0 0 0 + 9.5494 1.3747 23.2216 F 0 0 0 0 0 0 + 11.6206 0.6719 22.2638 C 0 0 0 0 0 0 + 12.7782 1.0724 22.9480 C 0 0 0 0 0 0 + 13.8994 0.2427 22.9901 C 0 0 0 0 0 0 + 13.8750 -0.9970 22.3527 C 0 0 0 0 0 0 + 12.7278 -1.4119 21.6796 C 0 0 0 0 0 0 + 11.6049 -0.5838 21.6354 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 2 4 1 0 0 0 + 2 5 1 0 0 0 + 5 6 2 0 0 0 + 5 10 1 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 + 8 9 1 0 0 0 + 9 10 2 0 0 0 +M END +$$$$ +O=[SH](=O)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 9 9 0 0 0 0 0 0 0 0999 V2000 + 13.5834 1.0389 23.2971 O 0 0 0 0 0 0 + 12.4089 1.7539 22.8402 S 0 0 0 0 0 0 + 11.1134 1.5953 23.4682 O 0 0 0 0 0 0 + 12.7957 3.4745 22.8588 C 0 0 0 0 0 0 + 13.0347 4.1328 21.6517 C 0 0 0 0 0 0 + 13.3512 5.4908 21.6741 C 0 0 0 0 0 0 + 13.4284 6.1723 22.8914 C 0 0 0 0 0 0 + 13.1905 5.5006 24.0928 C 0 0 0 0 0 0 + 12.8736 4.1434 24.0815 C 0 0 0 0 0 0 + 1 2 2 0 0 0 + 2 3 2 0 0 0 + 2 4 1 0 0 0 + 4 5 2 0 0 0 + 4 9 1 0 0 0 + 5 6 1 0 0 0 + 6 7 2 0 0 0 + 7 8 1 0 0 0 + 8 9 2 0 0 0 +M END +$$$$ +CSCCNC(=O)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 5.5458 -1.4150 18.8612 C 0 0 0 0 0 0 + 5.7667 0.2529 18.1959 S 0 0 0 0 0 0 + 7.4715 0.5847 18.7876 C 0 0 0 0 0 0 + 7.5534 0.7884 20.3036 C 0 0 0 0 0 0 + 8.9454 1.0042 20.7146 N 0 0 0 0 0 0 + 9.6402 -0.1322 20.8514 C 0 0 0 0 0 0 + 9.3233 -1.2490 20.4452 O 0 0 0 0 0 0 + 10.9406 -0.0002 21.5911 C 0 0 0 0 0 0 + 11.2868 1.2512 22.1206 C 0 0 0 0 0 0 + 12.4999 1.4280 22.7900 C 0 0 0 0 0 0 + 13.3773 0.3543 22.9381 C 0 0 0 0 0 0 + 13.0426 -0.8964 22.4196 C 0 0 0 0 0 0 + 11.8294 -1.0724 21.7499 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 1 0 0 0 + 4 5 1 0 0 0 + 5 6 1 0 0 0 + 6 7 2 0 0 0 + 6 8 1 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +CCNS(=O)(=O)Cc1cccnc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 13.3598 -1.5609 21.7877 C 0 0 0 0 0 0 + 13.7113 -0.3498 22.6305 C 0 0 0 0 0 0 + 12.7714 0.7692 22.3361 N 0 0 0 0 0 0 + 11.8062 1.1577 23.6906 S 0 0 0 0 0 0 + 10.8599 0.0665 23.8065 O 0 0 0 0 0 0 + 12.7113 1.5035 24.7620 O 0 0 0 0 0 0 + 10.9309 2.6284 23.1295 C 0 0 0 0 0 0 + 11.9375 3.7368 22.9987 C 0 0 0 0 0 0 + 12.7555 3.8614 21.8705 C 0 0 0 0 0 0 + 13.6216 4.9464 21.7613 C 0 0 0 0 0 0 + 13.6489 5.8696 22.7918 C 0 0 0 0 0 0 + 12.8858 5.7762 23.9008 N 0 0 0 0 0 0 + 12.0407 4.7242 23.9742 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 1 0 0 0 + 4 5 2 0 0 0 + 4 6 2 0 0 0 + 4 7 1 0 0 0 + 7 8 1 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +CCc1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 8 8 0 0 0 0 0 0 0 0999 V2000 + 9.3165 -1.3968 21.4474 C 0 0 0 0 0 0 + 10.1701 -1.9537 22.5759 C 0 0 0 0 0 0 + 11.4727 -1.2108 22.7284 C 0 0 0 0 0 0 + 11.5710 -0.1198 23.6025 C 0 0 0 0 0 0 + 12.7795 0.5633 23.7497 C 0 0 0 0 0 0 + 13.8989 0.1675 23.0199 C 0 0 0 0 0 0 + 13.8083 -0.9074 22.1374 C 0 0 0 0 0 0 + 12.6006 -1.5917 21.9895 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 2 0 0 0 + 3 8 1 0 0 0 + 4 5 1 0 0 0 + 5 6 2 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 +M END +$$$$ +CS(=O)(=O)NCCN1CCCC1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 12 12 0 0 0 0 0 0 0 0999 V2000 + 6.8490 0.5139 18.2625 C 0 0 0 0 0 0 + 7.3129 0.1623 19.9428 S 0 0 0 0 0 0 + 7.4343 1.3973 20.6804 O 0 0 0 0 0 0 + 6.5548 -0.9612 20.4458 O 0 0 0 0 0 0 + 8.9263 -0.3881 19.7641 N 0 0 0 0 0 0 + 9.5060 -0.7657 21.0831 C 0 0 0 0 0 0 + 10.8140 -0.0093 21.3638 C 0 0 0 0 0 0 + 11.5742 -0.6154 22.5359 N 0 0 0 0 0 0 + 11.4738 0.2167 23.7970 C 0 0 0 0 0 0 + 12.6714 1.1335 23.7058 C 0 0 0 0 0 0 + 13.7645 0.2387 23.1560 C 0 0 0 0 0 0 + 13.0648 -0.8014 22.2945 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 2 0 0 0 + 2 4 2 0 0 0 + 2 5 1 0 0 0 + 5 6 1 0 0 0 + 6 7 1 0 0 0 + 7 8 1 0 0 0 + 8 9 1 0 0 0 + 8 12 1 0 0 0 + 9 10 1 0 0 0 + 10 11 1 0 0 0 + 11 12 1 0 0 0 +M END +$$$$ +C=Cc1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 8 8 0 0 0 0 0 0 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands_with_title.sdf Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,759 @@ +abc_one + + + 26 30 0 0 0 0 999 V2000 + -8.6396 0.9568 0.0000 O 0 0 + -7.6023 1.5602 0.0000 C 0 0 + -7.6071 3.0602 0.0000 C 0 0 + -6.3104 3.8143 0.0000 C 0 0 + -5.0090 3.0685 0.0000 C 0 0 + -5.0040 1.5682 0.0000 C 0 0 + -6.3008 0.8143 0.0000 C 0 0 + -3.7006 0.8244 0.0000 C 0 0 + -3.7006 -0.6045 0.0000 N 0 0 + -2.4915 -1.3190 0.0000 C 0 0 + -2.5059 -2.8197 0.0000 N 0 0 + -1.2156 -3.5847 0.0000 C 0 0 + -1.2329 -5.0846 0.0000 C 0 0 + -2.5404 -5.8196 0.0000 O 0 0 + -3.8308 -5.0547 0.0000 C 0 0 + -3.8135 -3.5548 0.0000 C 0 0 + -1.2274 -0.6045 0.0000 C 0 0 + 0.0000 -1.3190 0.0000 O 0 0 + 1.2274 -0.6045 0.0000 C 0 0 + 2.4732 -1.3190 0.0000 N 0 0 + 3.7372 -0.6045 0.0000 C 0 0 + 3.7372 0.8244 0.0000 C 0 0 + 2.4732 1.5389 0.0000 C 0 0 + 1.2274 0.8244 0.0000 C 0 0 + -1.2274 0.8244 0.0000 C 0 0 + -2.4915 1.5389 0.0000 N 0 0 + 1 2 1 0 + 2 3 1 0 + 3 4 2 0 + 4 5 1 0 + 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0 + 20 22 2 0 + 22 23 1 0 + 17 23 2 0 + 22 24 1 0 + 24 25 1 0 + 24 26 1 0 + 24 27 1 0 + 12 28 2 0 + 28 29 1 0 + 9 29 2 0 + 7 30 1 0 + 30 31 2 0 + 31 32 1 0 + 5 32 2 0 +M END +> <mr_id> +4255941 + +> <SMI> +CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1 + +$$$$ +abc_ten + + + 35 42 0 0 1 0 999 V2000 + -1.9455 5.8387 0.0000 C 0 0 + -2.5513 4.8029 0.0000 N 0 0 + -1.8100 3.5000 0.0000 C 0 0 2 0 0 0 + -0.2400 3.5200 0.0000 C 0 0 + 0.5000 2.1800 0.0000 C 0 0 1 0 0 0 + -1.0600 2.1800 0.0000 O 0 0 + -1.8300 0.9300 0.0000 C 0 0 1 0 0 0 + -3.0300 0.9300 0.0000 C 0 0 + -2.6500 2.2500 0.0000 C 0 0 2 0 0 0 + -4.1471 2.2892 0.0000 O 0 0 + -4.7748 1.2665 0.0000 C 0 0 + -0.9800 -0.7800 0.0000 N 0 0 + -2.1300 -1.4600 0.0000 C 0 0 + -3.3200 -0.7600 0.0000 C 0 0 + -4.5500 -1.4800 0.0000 C 0 0 + -4.5800 -2.7700 0.0000 C 0 0 + -3.3400 -3.4700 0.0000 C 0 0 + -2.1300 -2.7900 0.0000 C 0 0 + 0.2400 -2.7700 0.0000 C 0 0 + 1.4300 -3.4700 0.0000 C 0 0 + 1.7600 -4.9700 0.0000 C 0 0 + 3.2600 -5.0800 0.0000 N 0 0 + 3.8500 -3.6300 0.0000 C 0 0 + 4.9971 -3.2777 0.0000 O 0 0 + 2.6600 -2.7500 0.0000 C 0 0 + 2.6800 -1.4600 0.0000 C 0 0 + 3.7900 0.5600 0.0000 C 0 0 + 4.9600 1.2800 0.0000 C 0 0 + 4.9600 2.6300 0.0000 C 0 0 + 3.8100 3.2900 0.0000 C 0 0 + 2.6400 2.5900 0.0000 C 0 0 + 2.6400 1.2400 0.0000 C 0 0 + 1.4900 0.5400 0.0000 N 0 0 + 1.4500 -0.7600 0.0000 C 0 0 + 0.2400 -1.4400 0.0000 C 0 0 + 1 2 1 0 + 3 2 1 6 + 3 4 1 0 + 5 4 1 6 + 5 6 1 0 + 6 7 1 0 + 7 8 1 1 + 7 9 1 0 + 3 9 1 0 + 9 10 1 6 + 10 11 1 0 + 7 12 1 0 + 12 13 1 0 + 13 14 1 0 + 14 15 2 0 + 15 16 1 0 + 16 17 2 0 + 17 18 1 0 + 13 18 2 0 + 18 19 1 0 + 19 20 1 0 + 20 21 1 0 + 21 22 1 0 + 22 23 1 0 + 23 24 2 0 + 23 25 1 0 + 20 25 2 0 + 25 26 1 0 + 26 27 1 0 + 27 28 1 0 + 28 29 2 0 + 29 30 1 0 + 30 31 2 0 + 31 32 1 0 + 27 32 2 0 + 32 33 1 0 + 5 33 1 0 + 33 34 1 0 + 26 34 2 0 + 34 35 1 0 + 12 35 1 0 + 19 35 2 0 +M END +> <mr_id> +66 + +> <SMI> +CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35 + +$$$$ +abc_eleven + + + 32 35 0 0 1 0 999 V2000 + 7.1381 -2.1568 0.0000 C 0 0 + 6.0456 -2.6531 0.0000 C 0 0 + 4.7409 -1.9129 0.0000 N 0 0 + 3.6552 -2.9294 0.0000 C 0 0 + 2.1855 -2.6254 0.0000 C 0 0 + 1.7138 -1.2033 0.0000 C 0 0 + 2.5889 0.0182 0.0000 C 0 0 + 3.7889 0.0269 0.0000 O 0 0 + 1.7138 1.2033 0.0000 N 0 0 + 0.2917 0.7475 0.0000 C 0 0 + -1.0028 1.5132 0.0000 C 0 0 + -2.3155 0.7475 0.0000 C 0 0 + -2.3155 -0.7475 0.0000 C 0 0 + -3.3560 -1.3452 0.0000 F 0 0 + -1.0028 -1.5132 0.0000 C 0 0 + 0.2917 -0.7475 0.0000 C 0 0 + 4.2542 -4.2907 0.0000 C 0 0 + 3.6559 -5.3308 0.0000 C 0 0 + 5.7448 -4.1226 0.0000 C 0 0 + 6.7580 -5.2264 0.0000 C 0 0 + 6.3978 -6.3710 0.0000 O 0 0 + 8.2231 -4.9012 0.0000 N 0 0 + 9.2380 -6.0068 0.0000 C 0 0 + 10.7032 -5.6816 0.0000 C 0 0 2 0 0 0 + 11.0634 -4.5369 0.0000 O 0 0 + 11.7181 -6.7872 0.0000 C 0 0 + 13.1833 -6.4620 0.0000 N 0 0 + 14.1993 -7.5656 0.0000 C 0 0 + 15.6630 -7.2376 0.0000 C 0 0 + 16.1108 -5.8060 0.0000 O 0 0 + 15.0949 -4.7024 0.0000 C 0 0 + 13.6312 -5.0304 0.0000 C 0 0 + 1 2 1 0 + 2 3 1 0 + 3 4 1 0 + 4 5 1 0 + 5 6 2 0 + 6 7 1 0 + 7 8 2 0 + 7 9 1 0 + 9 10 1 0 + 10 11 1 0 + 11 12 2 0 + 12 13 1 0 + 13 14 1 0 + 13 15 2 0 + 15 16 1 0 + 6 16 1 0 + 10 16 2 0 + 4 17 2 0 + 17 18 1 0 + 17 19 1 0 + 2 19 2 0 + 19 20 1 0 + 20 21 2 0 + 20 22 1 0 + 22 23 1 0 + 23 24 1 0 + 24 25 1 6 + 24 26 1 0 + 26 27 1 0 + 27 28 1 0 + 28 29 1 0 + 29 30 1 0 + 30 31 1 0 + 31 32 1 0 + 27 32 1 0 +M END +> <mr_id> +4362206 + +> <SMI> +Cc1[nH]c(/C=C/2\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/molecule.sdf Wed Mar 25 16:47:13 2020 -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/name_file.txt Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,2 @@ +abc_one +abc_eleven
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_convert_on_CID2244.can Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_filter_on_CID2244.sdf Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 0 + 4 5 1 0 + 5 6 2 0 + 6 7 1 0 + 2 7 2 0 + 6 8 1 0 + 8 9 1 0 + 9 10 2 0 + 10 11 1 0 + 11 12 1 0 + 12 13 1 0 + 13 14 1 0 + 14 15 1 0 + 15 16 1 0 + 11 16 1 0 + 10 17 1 0 + 17 18 1 0 + 18 19 1 0 + 19 20 2 0 + 20 21 1 0 + 21 22 2 0 + 22 23 1 0 + 23 24 2 0 + 19 24 1 0 + 24 25 1 0 + 17 25 2 0 + 25 26 1 0 + 8 26 2 0 +M END +> <mr_id> +4358263 + +> <SMI> +Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2 + +$$$$ + + SciTegic01171120562D + + 43 51 0 0 1 0 999 V2000 + -4.7204 3.3431 0.0000 C 0 0 + -4.1471 2.2890 0.0000 O 0 0 + -2.6500 2.2500 0.0000 C 0 0 2 0 0 0 + -1.8100 3.5000 0.0000 C 0 0 1 0 0 0 + -0.2400 3.5200 0.0000 C 0 0 + 0.5000 2.1800 0.0000 C 0 0 1 0 0 0 + -1.0600 2.1800 0.0000 O 0 0 + -1.8300 0.9300 0.0000 C 0 0 1 0 0 0 + -3.0300 0.9300 0.0000 C 0 0 + -0.9800 -0.7800 0.0000 N 0 0 + -2.1300 -1.4600 0.0000 C 0 0 + -3.3200 -0.7600 0.0000 C 0 0 + -4.5500 -1.4800 0.0000 C 0 0 + -4.5800 -2.7700 0.0000 C 0 0 + -3.3400 -3.4700 0.0000 C 0 0 + -2.1300 -2.7900 0.0000 C 0 0 + 0.2400 -2.7700 0.0000 C 0 0 + 1.4300 -3.4700 0.0000 C 0 0 + 1.7600 -4.9700 0.0000 C 0 0 + 3.2600 -5.0800 0.0000 N 0 0 + 3.8500 -3.6300 0.0000 C 0 0 + 4.9971 -3.2777 0.0000 O 0 0 + 2.6600 -2.7500 0.0000 C 0 0 + 2.6800 -1.4600 0.0000 C 0 0 + 3.7900 0.5600 0.0000 C 0 0 + 4.9600 1.2800 0.0000 C 0 0 + 4.9600 2.6300 0.0000 C 0 0 + 3.8100 3.2900 0.0000 C 0 0 + 2.6400 2.5900 0.0000 C 0 0 + 2.6400 1.2400 0.0000 C 0 0 + 1.4900 0.5400 0.0000 N 0 0 + 1.4500 -0.7600 0.0000 C 0 0 + 0.2400 -1.4400 0.0000 C 0 0 + -2.5511 4.8030 0.0000 N 0 0 + -1.9442 5.8382 0.0000 C 0 0 + -4.0519 4.8135 0.0000 C 0 0 + -4.6588 3.7783 0.0000 O 0 0 + -4.7941 6.1180 0.0000 C 0 0 + -6.2940 6.1306 0.0000 C 0 0 + -7.0331 7.4359 0.0000 C 0 0 + -6.2722 8.7286 0.0000 C 0 0 + -4.7723 8.7160 0.0000 C 0 0 + -4.0332 7.4108 0.0000 C 0 0 + 1 2 1 0 + 3 2 1 6 + 3 4 1 0 + 4 5 1 0 + 6 5 1 6 + 6 7 1 0 + 7 8 1 0 + 3 8 1 0 + 8 9 1 1 + 8 10 1 0 + 10 11 1 0 + 11 12 1 0 + 12 13 2 0 + 13 14 1 0 + 14 15 2 0 + 15 16 1 0 + 11 16 2 0 + 16 17 1 0 + 17 18 1 0 + 18 19 1 0 + 19 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ob_prepare_ligands1.mol2 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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 Wed Mar 25 16:47:13 2020 -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/obrmions_on_2_mol.smi Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,2 @@ +CC(=O)Oc1ccccc1C(=O)[O-] +CC(=O)Oc1ccccc1C(=O)[O-]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pattern.smarts Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,2 @@ +CC +CO
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split1.pdbqt Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,30 @@ +REMARK Name = +REMARK 3 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_2 and O_4 +REMARK 2 A between atoms: O_4 and C_5 +REMARK 3 A between atoms: C_10 and C_11 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.149 A +ATOM 2 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.038 A +ATOM 3 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.003 A +ATOM 4 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A +ATOM 5 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.004 A +ATOM 6 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.049 A +ENDROOT +BRANCH 6 7 +ATOM 7 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.076 C +ATOM 8 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA +ATOM 9 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA +ENDBRANCH 6 7 +BRANCH 1 10 +ATOM 10 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.424 OA +BRANCH 10 12 +ATOM 11 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.122 C +ATOM 12 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.322 C +ATOM 13 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.250 OA +ENDBRANCH 10 12 +ENDBRANCH 1 10 +TORSDOF 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split2.pdbqt Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,30 @@ +REMARK Name = +REMARK 3 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C_2 and O_4 +REMARK 2 A between atoms: O_4 and C_5 +REMARK 3 A between atoms: C_10 and C_11 +REMARK x y z vdW Elec q Type +REMARK _______ _______ _______ _____ _____ ______ ____ +ROOT +ATOM 1 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.149 A +ATOM 2 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.038 A +ATOM 3 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.003 A +ATOM 4 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.000 A +ATOM 5 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.004 A +ATOM 6 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.049 A +ENDROOT +BRANCH 6 7 +ATOM 7 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.076 C +ATOM 8 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA +ATOM 9 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.544 OA +ENDBRANCH 6 7 +BRANCH 1 10 +ATOM 10 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.424 OA +BRANCH 10 12 +ATOM 11 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.122 C +ATOM 12 C UNL 1 0.000 0.000 0.000 0.00 0.00 +0.322 C +ATOM 13 O UNL 1 0.000 0.000 0.000 0.00 0.00 -0.250 OA +ENDBRANCH 10 12 +ENDBRANCH 1 10 +TORSDOF 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transfs.sdf Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,186 @@ +NC(=NO)NCCc1ccc(S(N)(=O)=O)cc1 + RDKit 3D + + 17 17 0 0 0 0 0 0 0 0999 V2000 + 13.9302 -2.3261 22.5538 N 0 0 0 0 0 0 0 0 0 0 0 0 + 13.7238 -1.7706 23.7651 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.9709 -0.6511 23.8871 N 0 0 0 0 0 0 0 0 0 0 0 0 + 12.3387 0.0187 22.7430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.9859 0.6425 23.1019 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9117 0.4770 22.0521 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.6451 -0.7505 21.4256 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.6682 -0.8525 20.4388 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9346 0.2745 20.0745 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7444 0.1313 18.7757 S 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4465 0.9786 19.4142 N 0 0 0 0 0 0 0 0 0 0 0 0 + 7.2019 0.8863 17.6332 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3224 -1.2458 18.6840 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.1747 1.5057 20.6849 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.1574 1.6019 21.6751 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.2946 -2.3692 24.8521 N 0 0 0 0 0 0 0 0 0 0 0 0 + 14.1962 -1.9686 26.1940 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 + 2 16 2 0 + 3 4 1 0 + 4 5 1 0 + 5 6 1 0 + 6 7 2 0 + 6 15 1 0 + 7 8 1 0 + 8 9 2 0 + 9 10 1 0 + 9 14 1 0 + 10 11 1 0 + 10 12 2 0 + 10 13 2 0 + 14 15 2 0 + 16 17 1 0 +M CHG 1 16 1 +M END +> <CHROM.0> (1) +65.93051459,169.99861208,-59.68475000 + +> <CHROM.1> (1) +145.66221290,-139.37796603,47.03157881,136.25602749,64.42425104,102.07311975 +9.88696665,-0.33137891,21.45559055,-0.16902134,0.67278808,-2.52516849 + +> <Name> (1) +NC(=NO)NCCc1ccc(S(N)(=O)=O)cc1 + +> <RI> (1) +1.41352e+07 + +> <Rbt.Current_Directory> (1) +/data/dnb02/galaxy_db/job_working_directory/007/399/7399639/working + +> <Rbt.Executable> (1) +rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $) + +> <Rbt.Library> (1) +libRbt.so (2013.1, Build901 2013/11/27) + +> <Rbt.Parameter_File> (1) +/usr/local/tools/_conda/envs/__rdock@2013.1-0/share/rdock-2013.1-1/data/scripts/dock.prm + +> <Rbt.Receptor> (1) +receptor.prm + +> <SCORE> (1) +-30.3434 + +> <SCORE.INTER> (1) +-15.8664 + +> <SCORE.INTER.CONST> (1) +1 + +> <SCORE.INTER.POLAR> (1) +-1.12178 + +> <SCORE.INTER.REPUL> (1) +0 + +> <SCORE.INTER.ROT> (1) +5 + +> <SCORE.INTER.VDW> (1) +-22.4523 + +> <SCORE.INTER.norm> (1) +-0.933318 + +> <SCORE.INTRA> (1) +-2.33416 + +> <SCORE.INTRA.DIHEDRAL> (1) +-1.88099 + +> <SCORE.INTRA.DIHEDRAL.0> (1) +10.7462 + +> <SCORE.INTRA.POLAR> (1) +0 + +> <SCORE.INTRA.POLAR.0> (1) +0 + +> <SCORE.INTRA.REPUL> (1) +0 + +> <SCORE.INTRA.REPUL.0> (1) +0 + +> <SCORE.INTRA.VDW> (1) +-1.39366 + +> <SCORE.INTRA.VDW.0> (1) +0.160377 + +> <SCORE.INTRA.norm> (1) +-0.137303 + +> <SCORE.RESTR> (1) + + +> <SCORE.RESTR.norm> (1) +0 + +> <SCORE.SYSTEM> (1) +-12.1428 + +> <SCORE.SYSTEM.CONST> (1) +0 + +> <SCORE.SYSTEM.DIHEDRAL> (1) +0.706521 + +> <SCORE.SYSTEM.POLAR> (1) +-3.2443 + +> <SCORE.SYSTEM.REPUL> (1) +0.676691 + +> <SCORE.SYSTEM.VDW> (1) +-4.8489 + +> <SCORE.SYSTEM.norm> (1) +-0.714283 + +> <SCORE.heavy> (1) +17 + +> <SCORE.norm> (1) +-1.7849 + +> <TransFSReceptor> (1) +receptor + +> <TransFSScore> (1) +0.999997 + +> <Max_SuCOS_Score> (1) +0.44454780182058773 + +> <Max_SuCOS_FeatureMap_Score> (1) +0.19084575451625094 + +> <Max_SuCOS_Protrude_Score> (1) +0.69824984912492449 + +> <Max_SuCOS_Cluster> (1) +dataset_14281034.dat + +> <Max_SuCOS_Index> (1) +11 + +> <Cum_SuCOS_Score> (1) +3.7946511319966216 + +> <Cum_SuCOS_FeatureMap_Score> (1) +0.9189792141377946 + +> <Cum_SuCOS_Protrude_Score> (1) +6.6703230498554467 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transfs_changed_name.sdf Wed Mar 25 16:47:13 2020 -0400 @@ -0,0 +1,186 @@ +NC(=NO)NCCc1ccc(S(N)(=O)=O)cc1__xbrsjqssafh2t + OpenBabel03212010583D + + 17 17 0 0 0 0 0 0 0 0999 V2000 + 13.9302 -2.3261 22.5538 N 0 0 0 0 0 0 0 0 0 0 0 0 + 13.7238 -1.7706 23.7651 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.9709 -0.6511 23.8871 N 0 0 0 0 0 0 0 0 0 0 0 0 + 12.3387 0.0187 22.7430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.9859 0.6425 23.1019 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.9117 0.4770 22.0521 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.6451 -0.7505 21.4256 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.6682 -0.8525 20.4388 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9346 0.2745 20.0745 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7444 0.1313 18.7757 S 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4465 0.9786 19.4142 N 0 0 0 0 0 0 0 0 0 0 0 0 + 7.2019 0.8863 17.6332 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3224 -1.2458 18.6840 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.1747 1.5057 20.6849 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.1574 1.6019 21.6751 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.2946 -2.3692 24.8521 N 0 3 0 0 0 0 0 0 0 0 0 0 + 14.1962 -1.9686 26.1940 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 16 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 6 15 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 2 0 0 0 0 + 9 10 1 0 0 0 0 + 9 14 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 12 2 0 0 0 0 + 10 13 2 0 0 0 0 + 14 15 2 0 0 0 0 + 16 17 1 0 0 0 0 +M CHG 1 16 1 +M END +> <CHROM.0> +65.93051459,169.99861208,-59.68475000 + +> <CHROM.1> +145.66221290,-139.37796603,47.03157881,136.25602749,64.42425104,102.07311975 +9.88696665,-0.33137891,21.45559055,-0.16902134,0.67278808,-2.52516849 + +> <Name> +NC(=NO)NCCc1ccc(S(N)(=O)=O)cc1 + +> <RI> +1.41352e+07 + +> <Rbt.Current_Directory> +/data/dnb02/galaxy_db/job_working_directory/007/399/7399639/working + +> <Rbt.Executable> +rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $) + +> <Rbt.Library> +libRbt.so (2013.1, Build901 2013/11/27) + +> <Rbt.Parameter_File> +/usr/local/tools/_conda/envs/__rdock@2013.1-0/share/rdock-2013.1-1/data/scripts/dock.prm + +> <Rbt.Receptor> +receptor.prm + +> <SCORE> +-30.3434 + +> <SCORE.INTER> +-15.8664 + +> <SCORE.INTER.CONST> +1 + +> <SCORE.INTER.POLAR> +-1.12178 + +> <SCORE.INTER.REPUL> +0 + +> <SCORE.INTER.ROT> +5 + +> <SCORE.INTER.VDW> +-22.4523 + +> <SCORE.INTER.norm> +-0.933318 + +> <SCORE.INTRA> +-2.33416 + +> <SCORE.INTRA.DIHEDRAL> +-1.88099 + +> <SCORE.INTRA.DIHEDRAL.0> +10.7462 + +> <SCORE.INTRA.POLAR> +0 + +> <SCORE.INTRA.POLAR.0> +0 + +> <SCORE.INTRA.REPUL> +0 + +> <SCORE.INTRA.REPUL.0> +0 + +> <SCORE.INTRA.VDW> +-1.39366 + +> <SCORE.INTRA.VDW.0> +0.160377 + +> <SCORE.INTRA.norm> +-0.137303 + +> <SCORE.RESTR> + + +> <SCORE.RESTR.norm> +0 + +> <SCORE.SYSTEM> +-12.1428 + +> <SCORE.SYSTEM.CONST> +0 + +> <SCORE.SYSTEM.DIHEDRAL> +0.706521 + +> <SCORE.SYSTEM.POLAR> +-3.2443 + +> <SCORE.SYSTEM.REPUL> +0.676691 + +> <SCORE.SYSTEM.VDW> +-4.8489 + +> <SCORE.SYSTEM.norm> +-0.714283 + +> <SCORE.heavy> +17 + +> <SCORE.norm> +-1.7849 + +> <TransFSReceptor> +receptor + +> <TransFSScore> +0.999997 + +> <Max_SuCOS_Score> +0.44454780182058773 + +> <Max_SuCOS_FeatureMap_Score> +0.19084575451625094 + +> <Max_SuCOS_Protrude_Score> +0.69824984912492449 + +> <Max_SuCOS_Cluster> +dataset_14281034.dat + +> <Max_SuCOS_Index> +11 + +> <Cum_SuCOS_Score> +3.7946511319966216 + +> <Cum_SuCOS_FeatureMap_Score> +0.9189792141377946 + +> <Cum_SuCOS_Protrude_Score> +6.6703230498554467 + +$$$$