| Previous changeset 5:351fbd750a6d (2021-02-17) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f" |
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modified:
dimorphite_dl.py rdkit_descriptors.py sdf_to_tab.py |
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added:
rdconf.py test-data/rdconf_output.sdf test-data/staurosporine.smi |
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| diff -r 351fbd750a6d -r 4beb3e026bbb dimorphite_dl.py --- a/dimorphite_dl.py Wed Feb 17 13:00:12 2021 +0000 +++ b/dimorphite_dl.py Sat Dec 04 16:39:05 2021 +0000 |
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| b'@@ -19,8 +19,9 @@\n """\n \n from __future__ import print_function\n+\n+import argparse\n import os\n-import argparse\n import sys\n \n try:\n@@ -43,11 +44,12 @@\n import rdkit\n from rdkit import Chem\n from rdkit.Chem import AllChem\n-except:\n+except Exception:\n msg = "Dimorphite-DL requires RDKit. See https://www.rdkit.org/"\n print(msg)\n raise Exception(msg)\n \n+\n def main(params=None):\n """The main definition run when you call the script from the commandline.\n \n@@ -84,13 +86,14 @@\n with open(args["output_file"], "w") as file:\n for protonated_smi in Protonate(args):\n file.write(protonated_smi + "\\n")\n- elif "return_as_list" in args and args["return_as_list"] == True:\n+ elif "return_as_list" in args and args["return_as_list"]:\n return list(Protonate(args))\n else:\n # No output file specified. Just print it to the screen.\n for protonated_smi in Protonate(args):\n print(protonated_smi)\n \n+\n class MyParser(argparse.ArgumentParser):\n """Overwrite default parse so it displays help file on error. See\n https://stackoverflow.com/questions/4042452/display-help-message-with-python-argparse-when-script-is-called-without-any-argu"""\n@@ -117,15 +120,18 @@\n if file is None:\n file = sys.stdout\n self._print_message(self.format_help(), file)\n- print("""\n+ print(\n+ """\n examples:\n python dimorphite_dl.py --smiles_file sample_molecules.smi\n python dimorphite_dl.py --smiles "CCC(=O)O" --min_ph -3.0 --max_ph -2.0\n python dimorphite_dl.py --smiles "CCCN" --min_ph -3.0 --max_ph -2.0 --output_file output.smi\n python dimorphite_dl.py --smiles_file sample_molecules.smi --pka_precision 2.0 --label_states\n- python dimorphite_dl.py --test""")\n+ python dimorphite_dl.py --test"""\n+ )\n print("")\n \n+\n class ArgParseFuncs:\n """A namespace for storing functions that are useful for processing\n command-line arguments. To keep things organized."""\n@@ -137,27 +143,57 @@\n :return: A parser object.\n """\n \n- parser = MyParser(description="Dimorphite 1.2: Creates models of " +\n- "appropriately protonated small moleucles. " +\n- "Apache 2.0 License. Copyright 2018 Jacob D. " +\n- "Durrant.")\n- parser.add_argument(\'--min_ph\', metavar=\'MIN\', type=float, default=6.4,\n- help=\'minimum pH to consider (default: 6.4)\')\n- parser.add_argument(\'--max_ph\', metavar=\'MAX\', type=float, default=8.4,\n- help=\'maximum pH to consider (default: 8.4)\')\n- parser.add_argument(\'--pka_precision\', metavar=\'PRE\', type=float, default=1.0,\n- help=\'pKa precision factor (number of standard devations, default: 1.0)\')\n- parser.add_argument(\'--smiles\', metavar=\'SMI\', type=str,\n- help=\'SMILES string to protonate\')\n- parser.add_argument(\'--smiles_file\', metavar="FILE", type=str,\n- help=\'file that contains SMILES strings to protonate\')\n- parser.add_argument(\'--output_file\', metavar="FILE", type=str,\n- help=\'output file to write protonated SMILES (optional)\')\n- parser.add_argument(\'--label_states\', action="store_true",\n- help=\'label protonated SMILES with target state \' + \\\n- \'(i.e., "DEPROTONATED", "PROTONATED", or "BOTH").\')\n- parser.add_argument(\'--test\', action="store_true",\n- help=\'run unit tests (for debugging)\')\n+ parser = MyParser(\n+ description="Dimorphite 1.2: Creates models of "\n+ + "appropriately protonated small moleucles. "\n+ + "Apache 2.0 License. Copyright 2018 Jacob D. "\n+ + "Durrant."\n+ )'..b'put) != num_states:\n+ msg = (\n+ args["smiles"]\n+ + " should have "\n+ + str(num_states)\n+ + " states at at pH "\n+ + str(args["min_ph"])\n+ + ": "\n+ + str(output)\n+ )\n print(msg)\n raise Exception(msg)\n \n- if (len(set([l[0] for l in output]) - set(expected_output)) != 0):\n- msg = args["smiles"] + " is not " + " AND ".join(expected_output) + \\\n- " at pH " + str(args["min_ph"]) + " - " + str(args["max_ph"]) + \\\n- "; it is " + " AND ".join([l[0] for l in output])\n+ if len(set([l[0] for l in output]) - set(expected_output)) != 0:\n+ msg = (\n+ args["smiles"]\n+ + " is not "\n+ + " AND ".join(expected_output)\n+ + " at pH "\n+ + str(args["min_ph"])\n+ + " - "\n+ + str(args["max_ph"])\n+ + "; it is "\n+ + " AND ".join([l[0] for l in output])\n+ )\n print(msg)\n raise Exception(msg)\n \n- if (len(set([l[1] for l in output]) - set(labels)) != 0):\n- msg = args["smiles"] + " not labeled as " + " AND ".join(labels) + \\\n- "; it is " + " AND ".join([l[1] for l in output])\n+ if len(set([l[1] for l in output]) - set(labels)) != 0:\n+ msg = (\n+ args["smiles"]\n+ + " not labeled as "\n+ + " AND ".join(labels)\n+ + "; it is "\n+ + " AND ".join([l[1] for l in output])\n+ )\n print(msg)\n raise Exception(msg)\n \n ph_range = sorted(list(set([args["min_ph"], args["max_ph"]])))\n ph_range_str = "(" + " - ".join("{0:.2f}".format(n) for n in ph_range) + ")"\n- print("(CORRECT) " + ph_range_str.ljust(10) + " " + args["smiles"] + " => " + " AND ".join([l[0] for l in output]))\n+ print(\n+ "(CORRECT) "\n+ + ph_range_str.ljust(10)\n+ + " "\n+ + args["smiles"]\n+ + " => "\n+ + " AND ".join([l[0] for l in output])\n+ )\n+\n \n def run(**kwargs):\n """A helpful, importable function for those who want to call Dimorphite-DL\n@@ -1019,6 +1236,7 @@\n # Run the main function with the specified arguments.\n main(kwargs)\n \n+\n def run_with_mol_list(mol_lst, **kwargs):\n """A helpful, importable function for those who want to call Dimorphite-DL\n from another Python script rather than the command line. Note that this\n@@ -1037,10 +1255,13 @@\n # Do a quick check to make sure the user input makes sense.\n for bad_arg in ["smiles", "smiles_file", "output_file", "test"]:\n if bad_arg in kwargs:\n- msg = "You\'re using Dimorphite-DL\'s run_with_mol_list(mol_lst, " + \\\n- "**kwargs) function, but you also passed the \\"" + \\\n- bad_arg + "\\" argument. Did you mean to use the " + \\\n- "run(**kwargs) function instead?"\n+ msg = (\n+ "You\'re using Dimorphite-DL\'s run_with_mol_list(mol_lst, "\n+ + \'**kwargs) function, but you also passed the "\'\n+ + bad_arg\n+ + \'" argument. Did you mean to use the \'\n+ + "run(**kwargs) function instead?"\n+ )\n print(msg)\n raise Exception(msg)\n \n@@ -1076,9 +1297,15 @@\n m.SetProp(prop, str(val))\n mols.append(m)\n else:\n- UtilFuncs.eprint("WARNING: Could not process molecule with SMILES string " + s + " and properties " + str(props))\n+ UtilFuncs.eprint(\n+ "WARNING: Could not process molecule with SMILES string "\n+ + s\n+ + " and properties "\n+ + str(props)\n+ )\n \n return mols\n \n+\n if __name__ == "__main__":\n main()\n' |
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| diff -r 351fbd750a6d -r 4beb3e026bbb rdconf.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdconf.py Sat Dec 04 16:39:05 2021 +0000 |
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| @@ -0,0 +1,229 @@ +#!/usr/bin/python3 + +import gzip +import os +import sys +from optparse import OptionParser + +from rdkit.Chem import AllChem as Chem + +""" +This script was originally written by David Koes, University of Pittsburgh: +https://github.com/dkoes/rdkit-scripts/blob/master/rdconf.py +It is licensed under the MIT licence. + +Given a smiles file, generate 3D conformers in output sdf. +Energy minimizes and filters conformers to meet energy window and rms constraints. + +Some time ago I compared this to alternative conformer generators and +it was quite competitive (especially after RDKit's UFF implementation +added OOP terms). +""" + + +# convert smiles to sdf +def getRMS(mol, c1, c2): + rms = Chem.GetBestRMS(mol, mol, c1, c2) + return rms + + +parser = OptionParser(usage="Usage: %prog [options] <input>.smi <output>.sdf") +parser.add_option( + "--maxconfs", + dest="maxconfs", + action="store", + help="maximum number of conformers to generate per a molecule (default 20)", + default="20", + type="int", + metavar="CNT", +) +parser.add_option( + "--sample_multiplier", + dest="sample", + action="store", + help="sample N*maxconfs conformers and choose the maxconformers with lowest energy (default 1)", + default="1", + type="float", + metavar="N", +) +parser.add_option( + "--seed", + dest="seed", + action="store", + help="random seed (default 9162006)", + default="9162006", + type="int", + metavar="s", +) +parser.add_option( + "--rms_threshold", + dest="rms", + action="store", + help="filter based on rms (default 0.7)", + default="0.7", + type="float", + metavar="R", +) +parser.add_option( + "--energy_window", + dest="energy", + action="store", + help="filter based on energy difference with lowest energy conformer", + default="10", + type="float", + metavar="E", +) +parser.add_option( + "-v", + "--verbose", + dest="verbose", + action="store_true", + default=False, + help="verbose output", +) +parser.add_option( + "--mmff", + dest="mmff", + action="store_true", + default=False, + help="use MMFF forcefield instead of UFF", +) +parser.add_option( + "--nomin", + dest="nomin", + action="store_true", + default=False, + help="don't perform energy minimization (bad idea)", +) +parser.add_option( + "--etkdg", + dest="etkdg", + action="store_true", + default=False, + help="use new ETKDG knowledge-based method instead of distance geometry", +) + + +(options, args) = parser.parse_args() + +if len(args) < 2: + parser.error("Need input and output") + sys.exit(-1) + +input = args[0] +output = args[1] +smifile = open(input) +if options.verbose: + print("Generating a maximum of", options.maxconfs, "per a mol") + +if options.etkdg and not Chem.ETKDG: + print("ETKDB does not appear to be implemented. Please upgrade RDKit.") + sys.exit(1) + +split = os.path.splitext(output) +if split[1] == ".gz": + outf = gzip.open(output, "wt+") + output = split[0] # strip .gz +else: + outf = open(output, "w+") + + +if os.path.splitext(output)[1] == ".pdb": + sdwriter = Chem.PDBWriter(outf) +else: + sdwriter = Chem.SDWriter(outf) + +if sdwriter is None: + print("Could not open ".output) + sys.exit(-1) + +for line in smifile: + toks = line.split() + smi = toks[0] + name = " ".join(toks[1:]) + + pieces = smi.split(".") + if len(pieces) > 1: + smi = max(pieces, key=len) # take largest component by length + print("Taking largest component: %s\t%s" % (smi, name)) + + mol = Chem.MolFromSmiles(smi) + if mol is not None: + if options.verbose: + print(smi) + try: + Chem.SanitizeMol(mol) + mol = Chem.AddHs(mol) + mol.SetProp("_Name", name) + + if options.etkdg: + cids = Chem.EmbedMultipleConfs( + mol, int(options.sample * options.maxconfs), Chem.ETKDG() + ) + else: + cids = Chem.EmbedMultipleConfs( + mol, int(options.sample * options.maxconfs), randomSeed=options.seed + ) + if options.verbose: + print(len(cids), "conformers found") + cenergy = [] + for conf in cids: + # not passing confID only minimizes the first conformer + if options.nomin: + cenergy.append(conf) + elif options.mmff: + converged = Chem.MMFFOptimizeMolecule(mol, confId=conf) + mp = Chem.MMFFGetMoleculeProperties(mol) + cenergy.append( + Chem.MMFFGetMoleculeForceField( + mol, mp, confId=conf + ).CalcEnergy() + ) + else: + converged = not Chem.UFFOptimizeMolecule(mol, confId=conf) + cenergy.append( + Chem.UFFGetMoleculeForceField(mol, confId=conf).CalcEnergy() + ) + if options.verbose: + print("Convergence of conformer", conf, converged) + + mol = Chem.RemoveHs(mol) + sortedcids = sorted(cids, key=lambda cid: cenergy[cid]) + if len(sortedcids) > 0: + mine = cenergy[sortedcids[0]] + else: + mine = 0 + if options.rms == 0: + cnt = 0 + for conf in sortedcids: + if cnt >= options.maxconfs: + break + if (options.energy < 0) or cenergy[conf] - mine <= options.energy: + sdwriter.write(mol, conf) + cnt += 1 + else: + written = {} + for conf in sortedcids: + if len(written) >= options.maxconfs: + break + # check rmsd + passed = True + for seenconf in written.keys(): + rms = getRMS(mol, seenconf, conf) + if (rms < options.rms) or ( + options.energy > 0 and cenergy[conf] - mine > options.energy + ): + passed = False + break + if passed: + written[conf] = True + sdwriter.write(mol, conf) + except (KeyboardInterrupt, SystemExit): + raise + except Exception as e: + print("Exception", e) + else: + print("ERROR:", smi) + +sdwriter.close() +outf.close() |
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| diff -r 351fbd750a6d -r 4beb3e026bbb rdkit_descriptors.py --- a/rdkit_descriptors.py Wed Feb 17 13:00:12 2021 +0000 +++ b/rdkit_descriptors.py Sat Dec 04 16:39:05 2021 +0000 |
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| @@ -8,7 +8,7 @@ from rdkit.Chem import Descriptors -def get_supplier(infile, format='smiles'): +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. @@ -16,14 +16,20 @@ with open(infile) as handle: for line in handle: line = line.strip() - if format == 'smiles': + 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) + 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]) + mol.SetProp("_Name", line.split("\t")[0]) yield mol @@ -31,9 +37,13 @@ """ 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 = [ + (name, f) + for name, f in inspect.getmembers(Descriptors) + if inspect.isfunction(f) and not name.startswith("_") + ] # some which are not in the official Descriptors module we need to add manually - ret.extend([('FormalCharge', Chem.GetFormalCharge), ('SSSR', Chem.GetSSSR)]) + ret.extend([("FormalCharge", Chem.GetFormalCharge), ("SSSR", Chem.GetSSSR)]) ret.sort() return ret @@ -48,40 +58,54 @@ if __name__ == "__main__": parser = argparse.ArgumentParser() - parser.add_argument('-i', '--infile', required=True, help='Path to the input file.') + 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 is stdout") + parser.add_argument( + "-o", + "--outfile", + type=argparse.FileType("w+"), + default=sys.stdout, + help="path to the result file, default is stdout", + ) - parser.add_argument('-s', '--select', default=None, - help="select a subset of comma-separated descriptors to use") + parser.add_argument( + "-s", + "--select", + default=None, + help="select a subset of comma-separated descriptors to use", + ) - parser.add_argument("--header", dest="header", action="store_true", - default=False, - help="Write header line.") + parser.add_argument( + "--header", + dest="header", + action="store_true", + default=False, + help="Write header line.", + ) args = parser.parse_args() - if args.iformat == 'sdf': + 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') - elif args.iformat == 'pdb': + elif args.iformat == "smi": + supplier = get_supplier(args.infile, format="smiles") + elif args.iformat == "inchi": + supplier = get_supplier(args.infile, format="inchi") + elif args.iformat == "pdb": supplier = [Chem.MolFromPDBFile(args.infile)] - elif args.iformat == 'mol2': + elif args.iformat == "mol2": supplier = [Chem.MolFromMol2File(args.infile)] functions = get_rdkit_descriptor_functions() - if args.select and args.select != 'None': - selected = args.select.split(',') + if args.select and args.select != "None": + selected = args.select.split(",") functions = [(name, f) for name, f in functions if name in selected] if args.header: - args.outfile.write('%s\n' % '\t'.join(['MoleculeID'] + [name for name, f in functions])) + args.outfile.write( + "%s\n" % "\t".join(["MoleculeID"] + [name for name, f in functions]) + ) for mol in supplier: if not mol: @@ -91,4 +115,7 @@ molecule_id = mol.GetProp("_Name") except KeyError: molecule_id = Chem.MolToSmiles(mol) - args.outfile.write("%s\n" % '\t'.join([molecule_id] + [str(round(res, 6)) for name, res in descs])) + args.outfile.write( + "%s\n" + % "\t".join([molecule_id] + [str(round(res, 6)) for name, res in descs]) + ) |
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| diff -r 351fbd750a6d -r 4beb3e026bbb sdf_to_tab.py --- a/sdf_to_tab.py Wed Feb 17 13:00:12 2021 +0000 +++ b/sdf_to_tab.py Sat Dec 04 16:39:05 2021 +0000 |
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| @@ -13,36 +13,55 @@ 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 + 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 + 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['SDFMoleculeName'] = mols[n].GetProp('_Name') + d["SDFMoleculeName"] = mols[n].GetProp("_Name") if vars.smiles: - d['SMILES'] = Chem.MolToSmiles(mols[n], isomericSmiles=False) - d['Index'] = int(n) + 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 = df.astype({"Index": int}).set_index("Index") sorted_cols = sorted(df.columns.values.tolist()) - df.to_csv(vars.out, sep='\t', header=vars.header, columns=sorted_cols) + df.to_csv(vars.out, sep="\t", header=vars.header, columns=sorted_cols) 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.") + 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()) |
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| diff -r 351fbd750a6d -r 4beb3e026bbb test-data/rdconf_output.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdconf_output.sdf Sat Dec 04 16:39:05 2021 +0000 |
| b |
| @@ -0,0 +1,166 @@ +staurosporine + RDKit 3D + + 35 42 0 0 0 0 0 0 0 0999 V2000 + -2.1656 1.4438 -2.0402 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5064 0.5224 -1.0006 C 0 0 1 0 0 0 0 0 0 0 0 0 + -2.5333 0.2902 0.0771 C 0 0 1 0 0 0 0 0 0 0 0 0 + -3.0448 -1.1355 -0.1222 C 0 0 1 0 0 0 0 0 0 0 0 0 + -1.8499 -2.0325 0.1086 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9248 -1.7530 -1.0664 C 0 0 1 0 0 0 0 0 0 0 0 0 + -1.2333 -0.6270 -1.7456 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4794 -1.8256 -0.6986 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2443 -2.8970 -0.6134 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9172 -4.2121 -0.8557 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8835 -5.2113 -0.7023 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.1496 -4.8403 -0.3079 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4981 -3.5086 -0.0573 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5336 -2.5530 -0.2153 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5282 -1.1902 -0.0555 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4701 -0.2506 0.3363 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.1276 1.0747 0.4177 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8462 1.4665 0.1077 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2026 2.7102 0.1107 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7041 3.9456 0.4421 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8338 5.0265 0.3768 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4727 4.8205 -0.0097 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9490 3.5396 -0.3412 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0910 2.4739 -0.2786 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2989 1.1681 -0.5288 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9108 0.5646 -0.2791 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2388 -0.7709 -0.3642 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2788 1.9083 0.8642 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3369 0.9521 1.0170 N 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8631 -0.3694 0.7084 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.6279 -1.3464 0.7907 O 0 0 0 0 0 0 0 0 0 0 0 0 + -4.1928 -1.4531 0.6537 N 0 0 0 0 0 0 0 0 0 0 0 0 + -5.2852 -0.5939 0.2385 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.8857 0.2845 1.3121 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4801 1.0939 2.2570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 6 + 2 3 1 0 + 3 4 1 0 + 4 5 1 0 + 6 5 1 1 + 6 7 1 0 + 6 8 1 0 + 8 9 1 0 + 9 10 2 0 + 10 11 1 0 + 11 12 2 0 + 12 13 1 0 + 13 14 2 0 + 14 15 1 0 + 15 16 2 0 + 16 17 1 0 + 17 18 2 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 + 24 25 1 0 + 25 26 1 0 + 26 27 2 0 + 17 28 1 0 + 28 29 1 0 + 29 30 1 0 + 30 31 2 0 + 4 32 1 1 + 32 33 1 0 + 3 34 1 1 + 34 35 1 0 + 7 2 1 0 + 25 2 1 0 + 27 8 1 0 + 14 9 1 0 + 27 15 1 0 + 30 16 1 0 + 26 18 1 0 + 24 19 1 0 +M END +$$$$ +staurosporine + RDKit 3D + + 35 42 0 0 0 0 0 0 0 0999 V2000 + -2.3068 0.9355 -2.4621 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6484 0.1936 -1.2955 C 0 0 1 0 0 0 0 0 0 0 0 0 + -2.6628 -0.4491 -0.4739 C 0 0 1 0 0 0 0 0 0 0 0 0 + -2.1102 -1.3841 0.5829 C 0 0 1 0 0 0 0 0 0 0 0 0 + -1.3580 -2.4343 -0.1341 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6301 -1.9615 -1.3703 C 0 0 1 0 0 0 0 0 0 0 0 0 + -1.0034 -0.8456 -1.9685 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7323 -1.7671 -0.8854 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6653 -2.7175 -0.8097 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6030 -4.0416 -1.1929 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7336 -4.8209 -0.9993 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.8672 -4.2655 -0.4408 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9097 -2.9234 -0.0599 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7941 -2.1557 -0.2513 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5524 -0.8186 0.0257 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.2591 0.2074 0.5765 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.6138 1.4431 0.6965 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3053 1.6277 0.2726 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4639 2.7123 0.2701 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6421 4.0028 0.7116 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3869 4.9173 0.5986 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5824 4.5165 0.0416 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7175 3.2124 -0.3878 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7245 2.2626 -0.2991 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6365 0.9796 -0.6340 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6078 0.6133 -0.2727 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2251 -0.6244 -0.3999 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5496 2.4028 1.3130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.7624 1.6652 1.5409 N 0 0 0 0 0 0 0 0 0 0 0 0 + 4.5952 0.3088 1.0910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.5219 -0.5061 1.1939 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3679 -0.6619 1.5643 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2073 0.2673 2.2885 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6735 0.2555 0.0846 O 0 0 0 0 0 0 0 0 0 0 0 0 + -4.9519 -0.0773 -0.2685 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 6 + 2 3 1 0 + 3 4 1 0 + 4 5 1 0 + 6 5 1 1 + 6 7 1 0 + 6 8 1 0 + 8 9 1 0 + 9 10 2 0 + 10 11 1 0 + 11 12 2 0 + 12 13 1 0 + 13 14 2 0 + 14 15 1 0 + 15 16 2 0 + 16 17 1 0 + 17 18 2 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 + 24 25 1 0 + 25 26 1 0 + 26 27 2 0 + 17 28 1 0 + 28 29 1 0 + 29 30 1 0 + 30 31 2 0 + 4 32 1 1 + 32 33 1 0 + 3 34 1 1 + 34 35 1 0 + 7 2 1 0 + 25 2 1 0 + 27 8 1 0 + 14 9 1 0 + 27 15 1 0 + 30 16 1 0 + 26 18 1 0 + 24 19 1 0 +M END +$$$$ |
| b |
| diff -r 351fbd750a6d -r 4beb3e026bbb test-data/staurosporine.smi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/staurosporine.smi Sat Dec 04 16:39:05 2021 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +C[C@@]12[C@@H]([C@@H](C[C@@H](O1)N3C4=CC=CC=C4C5=C6C(=C7C8=CC=CC=C8N2C7=C53)CNC6=O)NC)OC staurosporine |