Mercurial > repos > bgruening > ctb_rdkit_descriptors
changeset 3:8922aa062403 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
| author | bgruening |
|---|---|
| date | Wed, 16 Oct 2019 07:25:29 -0400 |
| parents | 81233a9053f5 |
| children | fcc88ab4f1d3 |
| files | sdf_to_tab.py test-data/CID_3037.tab test-data/ligand.sdf test-data/ligand.tab test-data/rdkit_descriptors_result1.csv test-data/sucos_cluster.sdf |
| diffstat | 6 files changed, 2056 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sdf_to_tab.py Wed Oct 16 07:25:29 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()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_3037.tab Wed Oct 16 07:25:29 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.sdf Wed Oct 16 07:25:29 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 +> <MODEL> +1 + +> <REMARK> + 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 + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.9 + +> <RMSD_LB> +0.000 + +> <RMSD_UB> +0.000 + +$$$$ +pose2 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 30.7330 -43.6060 76.3350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.2340 -43.7750 76.2880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0410 -43.2270 77.2740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4260 -43.3690 77.2600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.2450 -42.7520 78.3610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.0040 -44.0990 76.2100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.2200 -44.6770 75.1980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.8090 -45.4740 74.0590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8400 -44.4960 75.2690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.4270 -44.2630 76.1860 N 0 0 0 0 0 0 0 0 0 0 0 0 + 36.8070 -45.0000 76.7160 H 0 0 0 0 0 0 0 0 0 0 0 0 + 37.2860 -43.4900 75.4970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.0290 -42.3860 75.0350 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.6520 -44.0730 75.2620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.7120 -44.8940 74.1230 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5590 -46.2750 74.4420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 2 3 2 0 0 0 0 + 4 3 1 0 0 0 0 + 4 5 1 0 0 0 0 + 6 4 2 0 0 0 0 + 7 9 2 0 0 0 0 + 7 6 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 2 1 0 0 0 0 + 10 6 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 16 1 0 0 0 0 + 15 14 1 0 0 0 0 +M END +> <MODEL> +2 + +> <REMARK> + VINA RESULT: -4.9 0.118 2.246 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.9 + +> <RMSD_LB> +0.118 + +> <RMSD_UB> +2.246 + +$$$$ +pose3 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 38.0110 -46.2540 74.8060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6410 -45.6700 75.0590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.3810 -44.9390 76.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1300 -44.3850 76.4670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9150 -43.6000 77.7320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1140 -44.5800 75.5190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3400 -45.3070 74.3390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2700 -45.5280 73.2950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6120 -45.8370 74.1410 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8230 -44.0090 75.7650 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.7200 -43.0420 75.6150 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7400 -44.6890 76.1850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7580 -45.8050 76.6870 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4150 -44.0110 75.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3610 -43.2680 74.7800 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.8410 -44.0280 73.6910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 4 2 0 0 0 0 + 7 6 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 7 2 0 0 0 0 + 9 2 1 0 0 0 0 + 10 12 1 0 0 0 0 + 11 10 1 0 0 0 0 + 12 13 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 14 1 0 0 0 0 + 16 15 1 0 0 0 0 +M END +> <MODEL> +3 + +> <REMARK> + VINA RESULT: -4.9 2.960 5.795 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.9 + +> <RMSD_LB> +2.960 + +> <RMSD_UB> +5.795 + +$$$$ +pose4 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 37.9950 -46.2420 74.8040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6310 -45.6410 75.0530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6040 -45.8070 74.1360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3360 -45.2680 74.3380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2650 -45.4860 73.3050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1090 -44.5430 75.5180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1210 -44.3610 76.4750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9070 -43.5920 77.7580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.3670 -44.9230 76.2110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8080 -43.9900 75.7470 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6920 -43.0240 75.5920 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7290 -44.6830 76.1560 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7570 -45.7970 76.6620 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3970 -44.0250 75.9240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3400 -43.3070 74.7170 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.7270 -44.0560 73.6700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 4 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 1 0 0 0 0 + 10 12 1 0 0 0 0 + 11 10 1 0 0 0 0 + 12 13 2 0 0 0 0 + 14 12 1 0 0 0 0 + 15 14 1 0 0 0 0 + 16 15 1 0 0 0 0 +M END +> <MODEL> +4 + +> <REMARK> + VINA RESULT: -4.8 2.958 5.379 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.8 + +> <RMSD_LB> +2.958 + +> <RMSD_UB> +5.379 + +$$$$ +pose5 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 38.0500 -44.6890 74.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6310 -44.7300 74.7250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6330 -45.3790 74.0140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3180 -45.4370 74.4670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2830 -46.1590 73.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0140 -44.8170 75.6890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9980 -44.1580 76.4430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7050 -43.4880 77.7650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.2940 -44.1340 75.9330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6670 -44.8760 76.1740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.4200 -45.6500 76.7300 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7140 -43.9580 75.9320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7570 -43.1100 75.0500 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.5300 -43.9780 76.8600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.1410 -42.6970 77.2850 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.9190 -42.2320 78.3850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 4 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 12 14 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <MODEL> +5 + +> <REMARK> + VINA RESULT: -4.5 2.763 5.379 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.5 + +> <RMSD_LB> +2.763 + +> <RMSD_UB> +5.379 + +$$$$ +pose6 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 33.2740 -46.1140 73.3890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2350 -45.2530 74.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0270 -44.8930 75.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9590 -44.1040 76.3530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.6150 -43.7500 76.9300 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1640 -43.6750 76.9310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4080 -44.0260 76.3810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.7220 -43.5880 76.9830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4060 -44.8150 75.2340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1120 -42.8710 78.1150 N 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0600 -43.3400 78.9790 H 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1290 -41.5260 78.1420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9030 -40.7970 77.1840 O 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4950 -40.8990 79.4590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3180 -39.7680 79.3210 O 0 0 0 0 0 0 0 0 0 0 0 0 + 35.5320 -39.8880 80.0580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 9 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 6 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 2 0 0 0 0 + 10 12 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 14 1 0 0 0 0 + 13 12 2 0 0 0 0 + 15 14 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <MODEL> +6 + +> <REMARK> + VINA RESULT: -4.4 3.106 4.850 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.4 + +> <RMSD_LB> +3.106 + +> <RMSD_UB> +4.850 + +$$$$ +pose7 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 37.4790 -45.2240 74.1750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.1180 -45.0510 74.8080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.9750 -44.3800 76.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7340 -44.2020 76.6200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.6480 -43.4610 77.9270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.6030 -44.7210 75.9710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.7050 -45.3990 74.7460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.5070 -45.9630 74.0190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9750 -45.5460 74.1940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.3180 -44.5390 76.5770 N 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9880 -45.2570 77.1640 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.5250 -43.4650 76.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.6380 -42.6370 75.5140 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4470 -43.2750 77.4400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4060 -41.9700 77.9600 O 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3500 -41.7760 79.0110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 6 10 1 0 0 0 0 + 6 4 2 0 0 0 0 + 7 6 1 0 0 0 0 + 8 7 1 0 0 0 0 + 9 7 2 0 0 0 0 + 9 2 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 10 1 0 0 0 0 + 12 14 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 15 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <MODEL> +7 + +> <REMARK> + VINA RESULT: -4.4 2.847 5.816 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.4 + +> <RMSD_LB> +2.847 + +> <RMSD_UB> +5.816 + +$$$$ +pose8 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 29.2690 -46.5680 70.6110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.9950 -45.8610 71.7330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.2800 -46.2360 72.0950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9750 -45.6010 73.1210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.3680 -46.0550 73.4620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3390 -44.5460 73.7940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0420 -44.1320 73.4510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3330 -42.9960 74.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.4010 -44.8100 72.4170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0440 -43.8770 74.8450 N 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6940 -43.1840 74.5860 H 0 0 0 0 0 0 0 0 0 0 0 0 + 31.8900 -44.1170 76.1600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3600 -45.1120 76.6390 O 0 0 0 0 0 0 0 0 0 0 0 0 + 32.3840 -43.0420 77.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0560 -41.7460 76.6550 O 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0630 -40.8000 77.7210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 2 9 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 6 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 6 1 0 0 0 0 + 7 8 1 0 0 0 0 + 9 7 2 0 0 0 0 + 10 12 1 0 0 0 0 + 11 10 1 0 0 0 0 + 12 13 2 0 0 0 0 + 12 14 1 0 0 0 0 + 15 14 1 0 0 0 0 + 15 16 1 0 0 0 0 +M END +> <MODEL> +8 + +> <REMARK> + VINA RESULT: -4.3 3.964 5.892 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.3 + +> <RMSD_LB> +3.964 + +> <RMSD_UB> +5.892 + +$$$$ +pose9 + OpenBabel09021916093D + + 16 16 0 0 0 0 0 0 0 0999 V2000 + 36.2810 -45.5880 74.7420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7970 -45.3090 74.6830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0060 -45.8780 73.6960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6360 -45.6430 73.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.8340 -46.2940 72.5230 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0540 -44.8050 74.5810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8200 -44.2170 75.6010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.2240 -43.3170 76.6570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1850 -44.4900 75.6220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.6450 -44.5600 74.5200 N 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0630 -45.1230 75.0810 H 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0510 -43.6230 73.7590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.5710 -43.0480 72.8120 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.6490 -43.2470 74.1530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.7000 -44.2290 73.8180 O 0 0 0 0 0 0 0 0 0 0 0 0 + 27.2950 -44.1460 72.4540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 2 9 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 2 0 0 0 0 + 4 6 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 9 1 0 0 0 0 + 7 8 1 0 0 0 0 + 10 6 1 0 0 0 0 + 10 11 1 0 0 0 0 + 12 14 1 0 0 0 0 + 12 10 1 0 0 0 0 + 13 12 2 0 0 0 0 + 15 14 1 0 0 0 0 + 16 15 1 0 0 0 0 +M END +> <MODEL> +9 + +> <REMARK> + VINA RESULT: -4.3 3.971 6.363 + Name = + 7 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_5 + 2 A between atoms: C_2 and C_12 + 3 A between atoms: C_2 and O_15 + 4 A between atoms: C_3 and O_15 + 5 A between atoms: C_4 and C_7 + 6 A between atoms: C_8 and N_13 + 7 A between atoms: C_9 and C_11 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> <TORSDO> +F 3 + +> <SCORE> +-4.3 + +> <RMSD_LB> +3.971 + +> <RMSD_UB> +6.363 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.tab Wed Oct 16 07:25:29 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdkit_descriptors_result1.csv Wed Oct 16 07:25:29 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sucos_cluster.sdf Wed Oct 16 07:25:29 2019 -0400 @@ -0,0 +1,1384 @@ + + RDKit 3D + + 19 20 0 0 0 0 0 0 0 0999 V2000 + 25.8690 10.6750 17.9260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.7660 11.4770 18.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1650 12.4880 17.8120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1480 13.2570 18.3640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7300 13.0010 19.6620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6190 13.8450 20.2480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3280 11.9670 20.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9000 11.7560 21.6900 O 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1990 10.4520 22.2010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3800 10.3250 23.4930 C 0 0 1 0 0 0 0 0 0 0 0 0 + 22.7510 9.1510 24.2170 O 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5930 11.5910 24.3570 C 0 0 0 0 0 0 0 0 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 +$$$$ + + RDKit 3D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 22.8090 9.2070 24.2800 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4710 10.1080 23.3190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.8900 9.6340 22.1960 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5680 10.5170 21.2440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7580 11.8790 21.3690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3130 12.3920 22.5320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5210 13.7530 22.7260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.0810 14.2110 23.9020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.4470 13.3190 24.8860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.2450 11.9700 24.7110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6750 11.4850 23.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 11 2 1 0 + 11 10 2 0 + 11 6 1 0 +M END +$$$$ + + RDKit 3D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 22.7770 9.1670 24.9740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4280 10.0140 24.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6770 11.3690 24.2670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2930 12.2600 23.2950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6430 11.7880 22.1650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.2220 12.6270 21.1460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.5740 12.1120 20.0440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.3400 10.7540 19.9450 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.7580 9.9010 20.9470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.4090 10.3980 22.0610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7960 9.5320 23.0070 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 10 5 1 0 + 11 10 2 0 + 11 2 1 0 +M END +$$$$ + + RDKit 3D + + 15 16 0 0 0 0 0 0 0 0999 V2000 + 22.4510 9.0090 24.4670 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5180 10.3550 24.1060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9990 11.2350 24.9790 N 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1030 12.5320 24.7160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7060 13.0330 23.4860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1940 12.1570 22.5380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.0810 10.8000 22.8500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5800 9.9040 21.8960 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5550 10.3020 20.4800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9570 10.4800 19.9210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.0930 10.2030 20.6880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.3650 10.3660 20.1600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.5090 10.8070 18.8530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3830 11.0830 18.0860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1090 10.9240 18.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 2 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 1 0 + 10 9 1 0 + 11 10 2 0 + 12 11 1 0 + 13 12 2 0 + 14 13 1 0 + 15 10 1 0 + 15 14 2 0 +M END +$$$$ + + RDKit 3D + + 14 15 0 0 0 0 0 0 0 0999 V2000 + 25.2210 12.3240 18.0720 C 0 0 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C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3270 11.9770 22.7910 C 0 0 1 0 0 0 0 0 0 0 0 0 + 22.7770 11.3400 23.9760 O 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7260 10.0020 23.7830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4730 9.6360 22.5540 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9310 9.1250 24.7980 N 0 0 0 0 0 0 0 0 0 0 0 0 + 27.0780 10.9870 20.5190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.5170 9.9760 21.3750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.7840 9.9640 21.7630 N 0 0 0 0 0 0 0 0 0 0 0 0 + 29.6370 10.8810 21.3400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.2680 11.8600 20.5370 N 0 0 0 0 0 0 0 0 0 0 0 0 + 28.0170 11.9450 20.1110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 2 1 0 + 4 3 2 0 + 5 4 1 0 + 6 5 2 0 + 6 1 1 0 + 7 5 1 6 + 8 7 1 0 + 9 8 1 0 + 10 9 1 0 + 11 10 1 0 + 12 11 1 1 + 12 7 1 0 + 13 12 1 0 + 14 13 1 0 + 15 7 1 0 + 15 14 2 0 + 16 14 1 0 + 17 3 1 0 + 18 17 2 0 + 19 18 1 0 + 20 19 2 0 + 21 20 1 0 + 22 17 1 0 + 22 21 2 0 +M END +$$$$ + + RDKit 3D + + 19 21 0 0 0 0 0 0 0 0999 V2000 + 18.6790 10.8940 21.5160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.8760 9.6220 22.6190 N 0 0 0 0 0 0 0 0 0 0 0 0 + 19.3450 9.6270 21.1760 O 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4790 11.8080 24.2920 S 0 0 0 0 0 0 0 0 0 0 0 0 + 19.5140 11.7630 22.5130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7100 9.2150 24.7670 N 0 0 0 0 0 0 0 0 0 0 0 0 + 20.5550 9.7530 20.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8590 10.7120 20.6250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1020 10.1890 21.0270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.2620 10.3730 20.2980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8630 11.5080 19.3970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5800 10.5280 21.4490 C 0 0 2 0 0 0 0 0 0 0 0 0 + 20.9500 11.9060 21.9290 C 0 0 2 0 0 0 0 0 0 0 0 0 + 21.9600 12.7150 22.7910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3230 10.0930 23.7780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.0040 11.6730 18.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.2010 11.1170 19.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7570 12.0240 18.8700 F 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3200 11.2980 18.4090 F 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 1 0 + 5 1 1 0 + 7 3 1 0 + 9 8 2 0 + 10 9 1 0 + 11 8 1 0 + 12 7 1 0 + 12 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26.4280 11.2380 18.0020 F 0 0 0 0 0 0 0 0 0 0 0 0 + 4 1 1 6 + 4 2 1 0 + 6 4 1 0 + 7 6 1 0 + 7 3 1 0 + 8 5 1 0 + 8 2 2 0 + 8 3 1 0 + 9 4 1 0 + 10 9 2 0 + 11 10 1 0 + 12 11 2 0 + 13 12 1 0 + 14 9 1 0 + 14 13 2 0 + 15 14 1 0 + 16 12 1 0 +M END +$$$$ + + RDKit 3D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 23.8920 10.9750 19.7100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1430 9.6540 19.8400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7820 11.7530 20.9950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6770 9.8870 20.1680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1750 12.7870 22.6090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3660 10.1400 23.6660 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3180 11.9530 21.3510 C 0 0 2 0 0 0 0 0 0 0 0 0 + 21.5250 10.6490 21.4640 C 0 0 2 0 0 0 0 0 0 0 0 0 + 22.7380 9.3100 24.6900 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.9210 9.6990 22.5310 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5620 11.8400 24.1130 S 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 1 1 0 + 4 2 1 0 + 7 3 1 1 + 7 5 1 0 + 8 4 1 6 + 8 7 1 0 + 9 6 1 0 + 10 8 1 0 + 10 6 2 0 + 11 6 1 0 + 11 5 1 0 +M END +$$$$ + + RDKit 3D + + 18 20 0 0 0 0 0 0 0 0999 V2000 + 28.6970 10.5240 20.4750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.9220 11.6800 20.9560 N 0 0 0 0 0 0 0 0 0 0 0 0 + 28.7880 12.6650 21.6350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.0810 12.2010 19.9710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.4190 13.2930 19.2740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.6450 13.8320 18.3200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.4810 13.2870 17.9980 N 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0290 12.1840 18.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7860 11.6150 18.3040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3430 10.5040 18.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1080 9.9180 19.9810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.3250 10.4360 20.3200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8200 11.5870 19.6640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.1160 14.9710 17.6690 N 0 0 0 0 0 0 0 0 0 0 0 0 + 27.3480 16.1150 18.5710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.6660 17.2890 17.6050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.8670 16.9430 16.3140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3130 15.5200 16.5590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 1 0 + 4 2 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 11 10 2 0 + 12 11 1 0 + 13 12 2 0 + 13 8 1 0 + 13 4 1 0 + 14 6 1 0 + 15 14 1 0 + 16 15 1 0 + 17 16 1 0 + 18 14 1 0 + 18 17 1 0 +M END +$$$$