# HG changeset patch # User bgruening # Date 1571225179 14400 # Node ID 06828e0cc8a7a885450439f9ab7089d35a6a660b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c" diff -r 000000000000 -r 06828e0cc8a7 rdkit_descriptors.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdkit_descriptors.py Wed Oct 16 07:26:19 2019 -0400 @@ -0,0 +1,76 @@ +#!/usr/bin/env python + +from rdkit.Chem import Descriptors +from rdkit import Chem +import sys, os, re +import argparse +import inspect + +def get_supplier( infile, format = 'smiles' ): + """ + Returns a generator over a SMILES or InChI file. Every element is of RDKit + molecule and has its original string as _Name property. + """ + with open(infile) as handle: + for line in handle: + line = line.strip() + if format == 'smiles': + mol = Chem.MolFromSmiles( line, sanitize=True ) + elif format == 'inchi': + mol = Chem.inchi.MolFromInchi( line, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False ) + if mol is None: + yield False + else: + mol.SetProp( '_Name', line.split('\t')[0] ) + yield mol + +def get_rdkit_descriptor_functions(): + """ + Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function) + """ + ret = [ (name, f) for name, f in inspect.getmembers( Descriptors ) if inspect.isfunction( f ) and not name.startswith( '_' ) ] + ret.sort() + return ret + + +def descriptors( mol, functions ): + """ + Calculates the descriptors of a given molecule. + """ + for name, function in functions: + yield (name, function( mol )) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('-i', '--infile', required=True, help='Path to the input file.') + parser.add_argument("--iformat", help="Specify the input file format.") + + parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), + default=sys.stdout, help="path to the result file, default it sdtout") + + parser.add_argument("--header", dest="header", action="store_true", + default=False, + help="Write header line.") + + args = parser.parse_args() + + if args.iformat == 'sdf': + supplier = Chem.SDMolSupplier( args.infile ) + elif args.iformat =='smi': + supplier = get_supplier( args.infile, format = 'smiles' ) + elif args.iformat == 'inchi': + supplier = get_supplier( args.infile, format = 'inchi' ) + + functions = get_rdkit_descriptor_functions() + + if args.header: + args.outfile.write( '%s\n' % '\t'.join( ['MoleculeID'] + [name for name, f in functions] ) ) + + for mol in supplier: + if not mol: + continue + descs = descriptors( mol, functions ) + molecule_id = mol.GetProp("_Name") + args.outfile.write( "%s\n" % '\t'.join( [molecule_id]+ [str(round(res, 6)) for name, res in descs] ) ) + diff -r 000000000000 -r 06828e0cc8a7 sdf_to_tab.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sdf_to_tab.py Wed Oct 16 07:26:19 2019 -0400 @@ -0,0 +1,46 @@ +#!/usr/bin/env python3 +import argparse +import pandas as pd +from rdkit import Chem + +def sdf_to_tab(vars): + mols = Chem.SDMolSupplier(vars.inp, sanitize=False) + df = pd.DataFrame() # for output + + for n in range(len(mols)): + if mols[n]: + d = mols[n].GetPropsAsDict() + # filter dict for desired props + if vars.props.strip() == '': # none specified, return all + d = {prop: val for (prop, val) in d.items() if not any(x in str(val) for x in ['\n', '\t'])} # remove items containing newlines or tabs + else: + d = {prop: val for (prop, val) in d.items() if prop in vars.props.replace(' ', '').split(',')} # remove items not requested via CLI + if vars.name: + d['Name'] = mols[n].GetProp('_Name') + if vars.smiles: + d['SMILES'] = Chem.MolToSmiles(mols[n], isomericSmiles=False) + d['Index'] = int(n) + + df = df.append(d, ignore_index=True) + else: + print("Molecule could not be read - skipped.") + + df = df.astype({'Index': int}).set_index('Index') + df.to_csv(vars.out, sep='\t', header=vars.header) + +def main(): + parser = argparse.ArgumentParser(description="Convert SDF to tabular") + parser.add_argument('--inp', '-i', help="The input file", required=True) + parser.add_argument('--out', '-o', help="The output file", required=True) + parser.add_argument('--props', '-p', help="Properties to filter (leave blank for all)", required=True) + parser.add_argument('--header', '-t', action='store_true', + help="Write property name as the first row.") + parser.add_argument('--smiles', '-s', action='store_true', + help="Include SMILES in output.") + parser.add_argument('--name', '-n', action='store_true', + help="Include molecule name in output.") + sdf_to_tab(parser.parse_args()) + + +if __name__ == "__main__": + main() diff -r 000000000000 -r 06828e0cc8a7 sdf_to_tab.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sdf_to_tab.xml Wed Oct 16 07:26:19 2019 -0400 @@ -0,0 +1,113 @@ + + + 2019.03.1 + + into a tabular file using RDKit + + rdkit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + F 3 + + > + -4.9 + + > + 0.000 + + > + 0.000 + +This tool extracts properties for all molecules saved within an input SD-file, using RDKit, and saves them to tabular format. + + +----- + +.. class:: infomark + +**Input** + +An SD-file. The properties to be extracted can also be specified, separated with a comma; for example, SCORE,RMSD_LB,RMSD_UB. + +If the field is left blank, all properties found in the SD-file will be saved, excluding properties with values that contain newline or tab characters, which would disrupt the tabular format. + +----- + +.. class:: infomark + + **Output** + +Tabular file, where each property is shown in a separate column, with compounds found in the SD-file listed in each row:: + + Name RMSD_LB RMSD_UB SCORE + pose1 0.0 0.0 -4.9 + pose2 0.118 2.246 -4.9 + pose3 2.96 5.795 -4.9 + pose4 2.958 5.379 -4.8 + pose5 2.763 5.379 -4.5 + pose6 3.106 4.85 -4.4 + pose7 2.847 5.816 -4.4 + pose8 3.964 5.892 -4.3 + pose9 3.971 6.363 -4.3 + +]]> + + + + @article{rdkit, + author = {Greg Landrum and others}, + title = {RDKit: Open-source cheminformatics}, + url ={http://www.rdkit.org} + } + + diff -r 000000000000 -r 06828e0cc8a7 test-data/CID_3037.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_3037.sdf Wed Oct 16 07:26:19 2019 -0400 @@ -0,0 +1,220 @@ +3037 + -OEChem-08231108593D + + 27 28 0 0 0 0 0 0 0999 V2000 + -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3872 2.8487 -1.0397 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 8 1 0 0 0 0 + 3 26 1 0 0 0 0 + 4 9 1 0 0 0 0 + 4 27 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 1 0 0 0 0 + 5 18 1 0 0 0 0 + 5 19 1 0 0 0 0 + 6 8 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 9 2 0 0 0 0 + 7 11 1 0 0 0 0 + 8 12 1 0 0 0 0 + 9 13 1 0 0 0 0 + 10 14 2 0 0 0 0 + 10 20 1 0 0 0 0 + 11 15 2 0 0 0 0 + 11 21 1 0 0 0 0 + 12 16 2 0 0 0 0 + 12 22 1 0 0 0 0 + 13 17 2 0 0 0 0 + 13 23 1 0 0 0 0 + 14 16 1 0 0 0 0 + 15 17 1 0 0 0 0 + 16 24 1 0 0 0 0 + 17 25 1 0 0 0 0 +M END +> +3037 + +> +0.6 + +> +8 +10 +12 +1 +7 +5 +11 +3 +6 +9 +4 +2 + +> +25 +1 -0.18 +10 -0.15 +11 -0.15 +12 -0.15 +13 -0.15 +14 0.18 +15 0.18 +16 -0.15 +17 -0.15 +2 -0.18 +20 0.15 +21 0.15 +22 0.15 +23 0.15 +24 0.15 +25 0.15 +26 0.45 +27 0.45 +3 -0.53 +4 -0.53 +5 0.29 +6 -0.14 +7 -0.14 +8 0.08 +9 0.08 + +> +2 + +> +4 +1 3 donor +1 4 donor +6 6 8 10 12 14 16 rings +6 7 9 11 13 15 17 rings + +> +17 + +> +0 + +> +0 + +> +0 + +> +0 + +> +0 + +> +1 + +> +5 + +> +00000BDD00000008 + +> +44.6858 + +> +20.297 + +> +10062212 137 18261117369936506423 +104564 63 17986963035811110412 +11458722 120 18339359768245870841 +11471102 22 5472872458301843344 +11578080 2 18190204380446433792 +116883 192 18265608969609498196 +12236239 1 18410856576819659107 +12592029 89 18338223951597366363 +13549 16 18410575084668353682 +13693222 15 6555421915516066822 +13764800 53 14189033175566991199 +14115302 16 18186237320680093898 +14341114 328 10087642619424135543 +14787075 74 9511159855286719151 +14993402 34 18410855451538227223 +15099037 51 18340768233908588503 +15207287 21 15719111361650760302 +15375358 24 15647053767618106914 +15775835 57 18272650117329930317 +16945 1 17906452130063974618 +17834072 14 15936410035134206066 +18186145 218 17132117918276567720 +19422 9 18271525295227750719 +20279233 1 15719389529571237654 +20645476 183 18339080393619327415 +23402539 116 18186809105365620101 +23402655 69 18342736308283284156 +23559900 14 17603590712323212176 +25 1 17561083592297532664 +26918003 58 6266902359448424189 +296302 2 15213020427345972082 +3082319 5 18338798905472319583 +34934 24 18341891845236497020 +633830 44 17703790310130762689 +74978 22 18266740181857992718 +7832392 63 18340206284835898173 +81228 2 15720767252053392762 +9981440 41 17403743242177431832 + +> +341.85 +8.38 +1.9 +1.1 +0.02 +0 +-1.15 +1.94 +-0.01 +0 +-0.39 +-4.15 +0.01 +0 + +> +722.787 + +> +193 + +> +2 +5 +255 + +$$$$ + diff -r 000000000000 -r 06828e0cc8a7 test-data/CID_3037.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_3037.tab Wed Oct 16 07:26:19 2019 -0400 @@ -0,0 +1,2 @@ +Index Name PUBCHEM_ATOM_DEF_STEREO_COUNT PUBCHEM_ATOM_UDEF_STEREO_COUNT PUBCHEM_BOND_DEF_STEREO_COUNT PUBCHEM_BOND_UDEF_STEREO_COUNT PUBCHEM_CACTVS_TAUTO_COUNT PUBCHEM_COMPONENT_COUNT PUBCHEM_COMPOUND_CID PUBCHEM_CONFORMER_ID PUBCHEM_CONFORMER_RMSD PUBCHEM_EFFECTIVE_ROTOR_COUNT PUBCHEM_FEATURE_SELFOVERLAP PUBCHEM_HEAVY_ATOM_COUNT PUBCHEM_ISOTOPIC_ATOM_COUNT PUBCHEM_MMFF94_ENERGY PUBCHEM_SHAPE_SELFOVERLAP PUBCHEM_SHAPE_VOLUME +0 3037 0.0 0.0 0.0 0.0 5.0 1.0 3037.0 00000BDD00000008 0.6 2.0 20.297 17.0 0.0 44.6858 722.787 193.0 diff -r 000000000000 -r 06828e0cc8a7 test-data/ligand.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.sdf Wed Oct 16 07:26:19 2019 -0400 @@ -0,0 +1,612 @@ +pose1 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 30.7270 -43.7450 76.1540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.2320 -43.8770 76.1820 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9030 -44.5770 75.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.2880 -44.7130 75.1870 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9550 -45.4820 74.0800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.0120 -44.1090 76.2270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3700 -43.3850 77.2450 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1200 -42.7180 78.3740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9820 -43.2890 77.1920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.4390 -44.2310 76.2340 N 0 0 0 0 0 0 0 0 0 0 0 0 + 36.8300 -44.9440 76.7890 H 0 0 0 0 0 0 0 0 0 0 0 0 + 37.2890 -43.4500 75.5420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.0090 -42.3660 75.0480 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.6760 -43.9990 75.3480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.7980 -44.7930 74.1950 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.6010 -46.1780 74.4680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 2 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 16 1 0 0 0 0 + 15 14 1 0 0 0 0 +M END +> +1 + +> + VINA RESULT: -4.9 0.000 0.000 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +> +-4.9 + +> +0.000 + +> +0.000 + +$$$$ +pose2 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 30.7330 -43.6060 76.3350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.2340 -43.7750 76.2880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0410 -43.2270 77.2740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4260 -43.3690 77.2600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.2450 -42.7520 78.3610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.0040 -44.0990 76.2100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.2200 -44.6770 75.1980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.8090 -45.4740 74.0590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8400 -44.4960 75.2690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.4270 -44.2630 76.1860 N 0 0 0 0 0 0 0 0 0 0 0 0 + 36.8070 -45.0000 76.7160 H 0 0 0 0 0 0 0 0 0 0 0 0 + 37.2860 -43.4900 75.4970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.0290 -42.3860 75.0350 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.6520 -44.0730 75.2620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.7120 -44.8940 74.1230 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5590 -46.2750 74.4420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 2 3 2 0 0 0 0 + 4 3 1 0 0 0 0 + 4 5 1 0 0 0 0 + 6 4 2 0 0 0 0 + 7 9 2 0 0 0 0 + 7 6 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 2 1 0 0 0 0 + 10 6 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 16 1 0 0 0 0 + 15 14 1 0 0 0 0 +M END +> +2 + +> + VINA RESULT: -4.9 0.118 2.246 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +> +-4.9 + +> +0.118 + +> +2.246 + +$$$$ +pose3 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 38.0110 -46.2540 74.8060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6410 -45.6700 75.0590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.3810 -44.9390 76.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1300 -44.3850 76.4670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9150 -43.6000 77.7320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1140 -44.5800 75.5190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3400 -45.3070 74.3390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2700 -45.5280 73.2950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6120 -45.8370 74.1410 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8230 -44.0090 75.7650 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.7200 -43.0420 75.6150 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7400 -44.6890 76.1850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7580 -45.8050 76.6870 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4150 -44.0110 75.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3610 -43.2680 74.7800 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.8410 -44.0280 73.6910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 4 2 0 0 0 0 + 7 6 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 7 2 0 0 0 0 + 9 2 1 0 0 0 0 + 10 12 1 0 0 0 0 + 11 10 1 0 0 0 0 + 12 13 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 14 1 0 0 0 0 + 16 15 1 0 0 0 0 +M END +> +3 + +> + VINA RESULT: -4.9 2.960 5.795 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +> +-4.9 + +> +2.960 + +> +5.795 + +$$$$ +pose4 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 37.9950 -46.2420 74.8040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6310 -45.6410 75.0530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6040 -45.8070 74.1360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3360 -45.2680 74.3380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2650 -45.4860 73.3050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1090 -44.5430 75.5180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1210 -44.3610 76.4750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9070 -43.5920 77.7580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.3670 -44.9230 76.2110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8080 -43.9900 75.7470 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6920 -43.0240 75.5920 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7290 -44.6830 76.1560 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7570 -45.7970 76.6620 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3970 -44.0250 75.9240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3400 -43.3070 74.7170 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.7270 -44.0560 73.6700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 4 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 1 0 0 0 0 + 10 12 1 0 0 0 0 + 11 10 1 0 0 0 0 + 12 13 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 14 1 0 0 0 0 + 16 15 1 0 0 0 0 +M END +> +4 + +> + VINA RESULT: -4.8 2.958 5.379 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +> +-4.8 + +> +2.958 + +> +5.379 + +$$$$ +pose5 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 38.0500 -44.6890 74.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6310 -44.7300 74.7250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6330 -45.3790 74.0140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3180 -45.4370 74.4670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2830 -46.1590 73.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0140 -44.8170 75.6890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9980 -44.1580 76.4430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7050 -43.4880 77.7650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.2940 -44.1340 75.9330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6670 -44.8760 76.1740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.4200 -45.6500 76.7300 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7140 -43.9580 75.9320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7570 -43.1100 75.0500 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.5300 -43.9780 76.8600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.1410 -42.6970 77.2850 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.9190 -42.2320 78.3850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 4 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 12 14 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> +5 + +> + VINA RESULT: -4.5 2.763 5.379 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +> +-4.5 + +> +2.763 + +> +5.379 + +$$$$ +pose6 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 33.2740 -46.1140 73.3890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2350 -45.2530 74.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0270 -44.8930 75.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9590 -44.1040 76.3530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.6150 -43.7500 76.9300 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1640 -43.6750 76.9310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4080 -44.0260 76.3810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.7220 -43.5880 76.9830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4060 -44.8150 75.2340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1120 -42.8710 78.1150 N 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0600 -43.3400 78.9790 H 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1290 -41.5260 78.1420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9030 -40.7970 77.1840 O 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4950 -40.8990 79.4590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3180 -39.7680 79.3210 O 0 0 0 0 0 0 0 0 0 0 0 0 + 35.5320 -39.8880 80.0580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 9 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 6 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 2 0 0 0 0 + 10 12 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 14 1 0 0 0 0 + 13 12 2 0 0 0 0 + 15 14 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> +6 + +> + VINA RESULT: -4.4 3.106 4.850 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +> +-4.4 + +> +3.106 + +> +4.850 + +$$$$ +pose7 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 37.4790 -45.2240 74.1750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.1180 -45.0510 74.8080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.9750 -44.3800 76.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7340 -44.2020 76.6200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.6480 -43.4610 77.9270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.6030 -44.7210 75.9710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.7050 -45.3990 74.7460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.5070 -45.9630 74.0190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9750 -45.5460 74.1940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.3180 -44.5390 76.5770 N 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9880 -45.2570 77.1640 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.5250 -43.4650 76.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.6380 -42.6370 75.5140 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4470 -43.2750 77.4400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4060 -41.9700 77.9600 O 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3500 -41.7760 79.0110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 4 2 0 0 0 0 + 7 6 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 7 2 0 0 0 0 + 9 2 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 12 14 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> +7 + +> + VINA RESULT: -4.4 2.847 5.816 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +> +-4.4 + +> +2.847 + +> +5.816 + +$$$$ +pose8 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 29.2690 -46.5680 70.6110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.9950 -45.8610 71.7330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.2800 -46.2360 72.0950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9750 -45.6010 73.1210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.3680 -46.0550 73.4620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3390 -44.5460 73.7940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0420 -44.1320 73.4510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3330 -42.9960 74.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.4010 -44.8100 72.4170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0440 -43.8770 74.8450 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6940 -43.1840 74.5860 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.8900 -44.1170 76.1600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3600 -45.1120 76.6390 O 0 0 0 0 0 0 0 0 0 0 0 0 + 32.3840 -43.0420 77.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0560 -41.7460 76.6550 O 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0630 -40.8000 77.7210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 9 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 6 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 2 0 0 0 0 + 10 12 1 0 0 0 0 + 11 10 1 0 0 0 0 + 12 13 2 0 0 0 0 + 12 14 1 0 0 0 0 + 15 14 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> +8 + +> + VINA RESULT: -4.3 3.964 5.892 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +> +-4.3 + +> +3.964 + +> +5.892 + +$$$$ +pose9 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 36.2810 -45.5880 74.7420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7970 -45.3090 74.6830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0060 -45.8780 73.6960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6360 -45.6430 73.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.8340 -46.2940 72.5230 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0540 -44.8050 74.5810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8200 -44.2170 75.6010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.2240 -43.3170 76.6570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1850 -44.4900 75.6220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.6450 -44.5600 74.5200 N 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0630 -45.1230 75.0810 H 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0510 -43.6230 73.7590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.5710 -43.0480 72.8120 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.6490 -43.2470 74.1530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.7000 -44.2290 73.8180 O 0 0 0 0 0 0 0 0 0 0 0 0 + 27.2950 -44.1460 72.4540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 2 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 10 6 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 14 1 0 0 0 0 + 12 10 1 0 0 0 0 + 13 12 2 0 0 0 0 + 15 14 1 0 0 0 0 + 16 15 1 0 0 0 0 +M END +> +9 + +> + VINA RESULT: -4.3 3.971 6.363 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 3 + +> +-4.3 + +> +3.971 + +> +6.363 + +$$$$ diff -r 000000000000 -r 06828e0cc8a7 test-data/ligand.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.tab Wed Oct 16 07:26:19 2019 -0400 @@ -0,0 +1,10 @@ +Index RMSD_LB RMSD_UB SCORE SMILES +0 0.0 0.0 -4.9 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +1 0.118 2.246 -4.9 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +2 2.96 5.795 -4.9 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +3 2.958 5.379 -4.8 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +4 2.763 5.379 -4.5 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +5 3.106 4.85 -4.4 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +6 2.847 5.816 -4.4 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +7 3.964 5.892 -4.3 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C +8 3.971 6.363 -4.3 [H]N(C(=O)COC)C1C(C)=CC(C)=CC=1C diff -r 000000000000 -r 06828e0cc8a7 test-data/rdkit_descriptors_result1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdkit_descriptors_result1.csv Wed Oct 16 07:26:19 2019 -0400 @@ -0,0 +1,2 @@ +BalabanJ BertzCT Chi0 Chi0n Chi0v Chi1 Chi1n Chi1v Chi2n Chi2v Chi3n Chi3v Chi4n Chi4v EState_VSA1 EState_VSA10 EState_VSA11 EState_VSA2 EState_VSA3 EState_VSA4 EState_VSA5 EState_VSA6 EState_VSA7 EState_VSA8 EState_VSA9 ExactMolWt FpDensityMorgan1 FpDensityMorgan2 FpDensityMorgan3 FractionCSP3 HallKierAlpha HeavyAtomCount HeavyAtomMolWt Ipc Kappa1 Kappa2 Kappa3 LabuteASA MaxAbsEStateIndex MaxAbsPartialCharge MaxEStateIndex MaxPartialCharge MinAbsEStateIndex MinAbsPartialCharge MinEStateIndex MinPartialCharge MolLogP MolMR MolWt NHOHCount NOCount NumAliphaticCarbocycles NumAliphaticHeterocycles NumAliphaticRings NumAromaticCarbocycles NumAromaticHeterocycles NumAromaticRings NumHAcceptors NumHDonors NumHeteroatoms NumRadicalElectrons NumRotatableBonds NumSaturatedCarbocycles NumSaturatedHeterocycles NumSaturatedRings NumValenceElectrons PEOE_VSA1 PEOE_VSA10 PEOE_VSA11 PEOE_VSA12 PEOE_VSA13 PEOE_VSA14 PEOE_VSA2 PEOE_VSA3 PEOE_VSA4 PEOE_VSA5 PEOE_VSA6 PEOE_VSA7 PEOE_VSA8 PEOE_VSA9 RingCount SMR_VSA1 SMR_VSA10 SMR_VSA2 SMR_VSA3 SMR_VSA4 SMR_VSA5 SMR_VSA6 SMR_VSA7 SMR_VSA8 SMR_VSA9 SlogP_VSA1 SlogP_VSA10 SlogP_VSA11 SlogP_VSA12 SlogP_VSA2 SlogP_VSA3 SlogP_VSA4 SlogP_VSA5 SlogP_VSA6 SlogP_VSA7 SlogP_VSA8 SlogP_VSA9 TPSA VSA_EState1 VSA_EState10 VSA_EState2 VSA_EState3 VSA_EState4 VSA_EState5 VSA_EState6 VSA_EState7 VSA_EState8 VSA_EState9 fr_Al_COO fr_Al_OH fr_Al_OH_noTert fr_ArN fr_Ar_COO fr_Ar_N fr_Ar_NH fr_Ar_OH fr_COO fr_COO2 fr_C_O fr_C_O_noCOO fr_C_S fr_HOCCN fr_Imine fr_NH0 fr_NH1 fr_NH2 fr_N_O fr_Ndealkylation1 fr_Ndealkylation2 fr_Nhpyrrole fr_SH fr_aldehyde fr_alkyl_carbamate fr_alkyl_halide fr_allylic_oxid fr_amide fr_amidine fr_aniline fr_aryl_methyl fr_azide fr_azo fr_barbitur fr_benzene fr_benzodiazepine fr_bicyclic fr_diazo fr_dihydropyridine fr_epoxide fr_ester fr_ether fr_furan fr_guanido fr_halogen fr_hdrzine fr_hdrzone fr_imidazole fr_imide fr_isocyan fr_isothiocyan fr_ketone fr_ketone_Topliss fr_lactam fr_lactone fr_methoxy fr_morpholine fr_nitrile fr_nitro fr_nitro_arom fr_nitro_arom_nonortho fr_nitroso fr_oxazole fr_oxime fr_para_hydroxylation fr_phenol fr_phenol_noOrthoHbond fr_phos_acid fr_phos_ester fr_piperdine fr_piperzine fr_priamide fr_prisulfonamd fr_pyridine fr_quatN fr_sulfide fr_sulfonamd fr_sulfone fr_term_acetylene fr_tetrazole fr_thiazole fr_thiocyan fr_thiophene fr_unbrch_alkane fr_urea qed +3037 2.370227579270102 503.6108804181844 12.413849083443592 8.821564533342674 10.333422425379583 8.0585506480638 5.008352593120903 5.764281539139358 3.7228452481073373 4.595716809051308 2.463985083856104 2.934179289431582 1.5965258413271721 1.9859262940770028 0.0 10.213054789681411 0.0 11.49902366656781 27.592991233802653 0.0 12.13273413692322 24.26546827384644 0.0 0.0 23.20187978046503 268.00578492 0.7647058823529411 1.1764705882352942 1.588235294117647 0.07692307692307693 -1.38 17 259.04699999999997 6943.445199590422 12.08686679380967 4.861181105580097 2.8426724700782957 109.048439398113 9.68320845930965 0.5076617533400031 9.68320845930965 0.11870889965789788 0.14701436130007584 0.11870889965789788 0.14701436130007584 -0.5076617533400031 3.9954000000000027 69.03960000000004 269.127 2 2 0 0 0 2 0 2 2 2 4 0 2 0 0 0 88 10.213054789681411 11.49902366656781 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 23.20187978046503 47.52510539416365 16.466088250408664 0.0 2 10.213054789681411 23.20187978046503 0.0 0.0 0.0 6.4208216229260096 0.0 57.5703720216463 0.0 11.49902366656781 0.0 0.0 11.49902366656781 23.20187978046503 10.213054789681411 6.4208216229260096 0.0 11.126902983393991 36.39820241076966 10.045266627482652 0.0 0.0 40.46 0.0 11.70886971249405 0.0 0.0 0.0 0.0 0.0 0.0 0.0 32.01335250972817 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.8647127178367139 diff -r 000000000000 -r 06828e0cc8a7 test-data/rdkit_descriptors_result1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdkit_descriptors_result1.tab Wed Oct 16 07:26:19 2019 -0400 @@ -0,0 +1,2 @@ +MoleculeID BalabanJ BertzCT Chi0 Chi0n Chi0v Chi1 Chi1n Chi1v Chi2n Chi2v Chi3n Chi3v Chi4n Chi4v EState_VSA1 EState_VSA10 EState_VSA11 EState_VSA2 EState_VSA3 EState_VSA4 EState_VSA5 EState_VSA6 EState_VSA7 EState_VSA8 EState_VSA9 ExactMolWt FpDensityMorgan1 FpDensityMorgan2 FpDensityMorgan3 FractionCSP3 HallKierAlpha HeavyAtomCount HeavyAtomMolWt Ipc Kappa1 Kappa2 Kappa3 LabuteASA MaxAbsEStateIndex MaxAbsPartialCharge MaxEStateIndex MaxPartialCharge MinAbsEStateIndex MinAbsPartialCharge MinEStateIndex MinPartialCharge MolLogP MolMR MolWt NHOHCount NOCount NumAliphaticCarbocycles NumAliphaticHeterocycles NumAliphaticRings NumAromaticCarbocycles NumAromaticHeterocycles NumAromaticRings NumHAcceptors NumHDonors NumHeteroatoms NumRadicalElectrons NumRotatableBonds NumSaturatedCarbocycles NumSaturatedHeterocycles NumSaturatedRings NumValenceElectrons PEOE_VSA1 PEOE_VSA10 PEOE_VSA11 PEOE_VSA12 PEOE_VSA13 PEOE_VSA14 PEOE_VSA2 PEOE_VSA3 PEOE_VSA4 PEOE_VSA5 PEOE_VSA6 PEOE_VSA7 PEOE_VSA8 PEOE_VSA9 RingCount SMR_VSA1 SMR_VSA10 SMR_VSA2 SMR_VSA3 SMR_VSA4 SMR_VSA5 SMR_VSA6 SMR_VSA7 SMR_VSA8 SMR_VSA9 SlogP_VSA1 SlogP_VSA10 SlogP_VSA11 SlogP_VSA12 SlogP_VSA2 SlogP_VSA3 SlogP_VSA4 SlogP_VSA5 SlogP_VSA6 SlogP_VSA7 SlogP_VSA8 SlogP_VSA9 TPSA VSA_EState1 VSA_EState10 VSA_EState2 VSA_EState3 VSA_EState4 VSA_EState5 VSA_EState6 VSA_EState7 VSA_EState8 VSA_EState9 fr_Al_COO fr_Al_OH fr_Al_OH_noTert fr_ArN fr_Ar_COO fr_Ar_N fr_Ar_NH fr_Ar_OH fr_COO fr_COO2 fr_C_O fr_C_O_noCOO fr_C_S fr_HOCCN fr_Imine fr_NH0 fr_NH1 fr_NH2 fr_N_O fr_Ndealkylation1 fr_Ndealkylation2 fr_Nhpyrrole fr_SH fr_aldehyde fr_alkyl_carbamate fr_alkyl_halide fr_allylic_oxid fr_amide fr_amidine fr_aniline fr_aryl_methyl fr_azide fr_azo fr_barbitur fr_benzene fr_benzodiazepine fr_bicyclic fr_diazo fr_dihydropyridine fr_epoxide fr_ester fr_ether fr_furan fr_guanido fr_halogen fr_hdrzine fr_hdrzone fr_imidazole fr_imide fr_isocyan fr_isothiocyan fr_ketone fr_ketone_Topliss fr_lactam fr_lactone fr_methoxy fr_morpholine fr_nitrile fr_nitro fr_nitro_arom fr_nitro_arom_nonortho fr_nitroso fr_oxazole fr_oxime fr_para_hydroxylation fr_phenol fr_phenol_noOrthoHbond fr_phos_acid fr_phos_ester fr_piperdine fr_piperzine fr_priamide fr_prisulfonamd fr_pyridine fr_quatN fr_sulfide fr_sulfonamd fr_sulfone fr_term_acetylene fr_tetrazole fr_thiazole fr_thiocyan fr_thiophene fr_unbrch_alkane fr_urea qed +3037 2.370228 503.61088 12.413849 8.821565 10.333422 8.058551 5.008353 5.764282 3.722845 4.595717 2.463985 2.934179 1.596526 1.985926 0.0 10.213055 0.0 11.499024 27.592991 0.0 12.132734 24.265468 0.0 0.0 23.20188 268.005785 0.764706 1.176471 1.588235 0.076923 -1.38 17 259.047 6943.4452 12.086867 4.861181 2.842672 109.048439 9.683208 0.507662 9.683208 0.118709 0.147014 0.118709 0.147014 -0.507662 3.9954 69.0396 269.127 2 2 0 0 0 2 0 2 2 2 4 0 2 0 0 0 88 10.213055 11.499024 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 23.20188 47.525105 16.466088 0.0 2 10.213055 23.20188 0.0 0.0 0.0 6.420822 0.0 57.570372 0.0 11.499024 0.0 0.0 11.499024 23.20188 10.213055 6.420822 0.0 11.126903 36.398202 10.045267 0.0 0.0 40.46 0.0 11.70887 0.0 0.0 0.0 0.0 0.0 0.0 0.0 32.013353 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 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0 0 0 0 + 22.2540 11.3630 25.7760 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5710 12.5910 26.5330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1760 12.4110 28.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.7810 12.0710 28.1350 O 0 0 0 0 0 0 0 0 0 0 0 0 + 20.5060 10.8660 27.4060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.8170 11.0700 25.9210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3600 11.2090 19.8480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 5 1 0 + 8 7 1 0 + 9 8 1 0 + 10 9 1 0 + 10 11 1 1 + 12 10 1 0 + 13 12 1 0 + 14 13 1 0 + 15 14 1 0 + 16 15 1 0 + 17 16 1 0 + 18 17 1 0 + 18 13 1 0 + 19 7 2 0 + 19 2 1 0 +M END +$$$$ + + RDKit 3D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 22.8090 9.2070 24.2800 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4710 10.1080 23.3190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.8900 9.6340 22.1960 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5680 10.5170 21.2440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7580 11.8790 21.3690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3130 12.3920 22.5320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5210 13.7530 22.7260 C 0 0 0 0 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