| Next changeset 1:8eab6d2b7bdf (2019-10-11) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645" |
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added:
sucos.py sucos_cluster.py sucos_macros.xml sucos_max.py sucos_max.xml test-data/cluster1.sdf test-data/cluster2.sdf test-data/cluster3.sdf test-data/cluster4.sdf test-data/cluster5.sdf test-data/cluster6.sdf test-data/split_1.sdf test-data/split_2.sdf test-data/split_3.sdf test-data/split_4.sdf test-data/sucos_cluster.sdf test-data/sucos_inputs.sdf test-data/sucos_refmol.mol utils.py |
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| diff -r 000000000000 -r bb5365381c8f sucos.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sucos.py Wed Oct 02 12:57:54 2019 -0400 |
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| b'@@ -0,0 +1,202 @@\n+#!/usr/bin/env python\n+"""\n+Basic SuCOS scoring. Allows a set of molecules from a SD file to be overlayed to a reference molecule,\n+with the resulting scores being written as properties in the output SD file.\n+\n+SuCOS is the work of Susan Leung.\n+GitHub: https://github.com/susanhleung/SuCOS\n+Publication: https://doi.org/10.26434/chemrxiv.8100203.v1\n+"""\n+\n+from __future__ import print_function\n+import argparse, os, sys, gzip\n+import numpy as np\n+from rdkit import Chem, rdBase, RDConfig\n+from rdkit.Chem import AllChem, rdShapeHelpers\n+from rdkit.Chem.FeatMaps import FeatMaps\n+import utils\n+\n+\n+### start function definitions #########################################\n+\n+# Setting up the features to use in FeatureMap\n+fdef = AllChem.BuildFeatureFactory(os.path.join(RDConfig.RDDataDir, \'BaseFeatures.fdef\'))\n+\n+fmParams = {}\n+for k in fdef.GetFeatureFamilies():\n+ fparams = FeatMaps.FeatMapParams()\n+ fmParams[k] = fparams\n+\n+keep = (\'Donor\', \'Acceptor\', \'NegIonizable\', \'PosIonizable\', \'ZnBinder\',\n+ \'Aromatic\', \'Hydrophobe\', \'LumpedHydrophobe\')\n+\n+def filterFeature(f):\n+ result = f.GetFamily() in keep\n+ # TODO - nothing ever seems to be filtered. Is this expected?\n+ if not result:\n+ utils.log("Filtered out feature type", f.GetFamily())\n+ return result\n+\n+def getRawFeatures(mol):\n+\n+ rawFeats = fdef.GetFeaturesForMol(mol)\n+ # filter that list down to only include the ones we\'re interested in\n+ filtered = list(filter(filterFeature, rawFeats))\n+ return filtered\n+\n+def get_FeatureMapScore(small_feats, large_feats, tani=False, score_mode=FeatMaps.FeatMapScoreMode.All):\n+ """\n+ Generate the feature map score.\n+\n+ :param small_feats:\n+ :param large_feats:\n+ :param tani:\n+ :return:\n+ """\n+\n+ featLists = []\n+ for rawFeats in [small_feats, large_feats]:\n+ # filter that list down to only include the ones we\'re interested in\n+ featLists.append(rawFeats)\n+ fms = [FeatMaps.FeatMap(feats=x, weights=[1] * len(x), params=fmParams) for x in featLists]\n+ # set the score mode\n+ fms[0].scoreMode = score_mode\n+\n+ try:\n+ if tani:\n+ c = fms[0].ScoreFeats(featLists[1])\n+ A = fms[0].GetNumFeatures()\n+ B = len(featLists[1])\n+ if B != fms[1].GetNumFeatures():\n+ utils.log("Why isn\'t B equal to number of features...?!")\n+ tani_score = float(c) / (A+B-c)\n+ return tani_score\n+ else:\n+ fm_score = fms[0].ScoreFeats(featLists[1]) / min(fms[0].GetNumFeatures(), len(featLists[1]))\n+ return fm_score\n+ except ZeroDivisionError:\n+ utils.log("ZeroDivisionError")\n+ return 0\n+\n+ if tani:\n+ tani_score = float(c) / (A+B-c)\n+ return tani_score\n+ else:\n+ fm_score = fms[0].ScoreFeats(featLists[1]) / min(fms[0].GetNumFeatures(), len(featLists[1]))\n+ return fm_score\n+\n+\n+def get_SucosScore(ref_mol, query_mol, tani=False, ref_features=None, query_features=None, score_mode=FeatMaps.FeatMapScoreMode.All):\n+ """\n+ This is the key function that calculates the SuCOS scores and is expected to be called from other modules.\n+ To improve performance you can pre-calculate the features and pass them in as optional parameters to avoid having\n+ to recalculate them. Use the getRawFeatures function to pre-calculate the features.\n+\n+ :param ref_mol: The reference molecule to compare to\n+ :param query_mol: The molecule to align to the reference\n+ :param tani: Whether to calculate Tanimoto distances\n+ :param ref_features: An optional feature map for the reference molecule, avoiding the need to re-calculate it.\n+ :param query_features: An optional feature map for the query molecule, avoiding the need to re-calculate it.\n+ :return: A tuple of 3 values. 1 the sucos score, 2 the feature map score,\n+ 3 the Tanimoto distance or 1 minus the protrude distance\n+ """\n+\n+ if not ref_features'..b'rs.ShapeTanimotoDist(ref_mol, query_mol))\n+ tani_sim = np.clip(tani_sim, 0, 1)\n+ SuCOS_score = 0.5*fm_score + 0.5*tani_sim\n+ return SuCOS_score, fm_score, tani_sim\n+ else:\n+ protrude_dist = rdShapeHelpers.ShapeProtrudeDist(ref_mol, query_mol, allowReordering=False)\n+ protrude_dist = np.clip(protrude_dist, 0, 1)\n+ protrude_val = 1.0 - protrude_dist\n+ SuCOS_score = 0.5 * fm_score + 0.5 * protrude_val\n+ return SuCOS_score, fm_score, protrude_val\n+\n+def process(refmol_filename, inputs_filename, outputs_filename, refmol_index=None,\n+ refmol_format=None, tani=False, score_mode=FeatMaps.FeatMapScoreMode.All):\n+\n+ ref_mol = utils.read_single_molecule(refmol_filename, index=refmol_index, format=refmol_format)\n+ #utils.log("Reference mol has", ref_mol.GetNumHeavyAtoms(), "heavy atoms")\n+ ref_features = getRawFeatures(ref_mol)\n+\n+ input_file = utils.open_file_for_reading(inputs_filename)\n+ suppl = Chem.ForwardSDMolSupplier(input_file)\n+ output_file = utils.open_file_for_writing(outputs_filename)\n+ writer = Chem.SDWriter(output_file)\n+\n+ count = 0\n+ total = 0\n+ errors = 0\n+ for mol in suppl:\n+ count +=1\n+ if mol is None:\n+ continue\n+ #utils.log("Mol has", str(mol.GetNumHeavyAtoms()), "heavy atoms")\n+ try:\n+ sucos_score, fm_score, val3 = get_SucosScore(ref_mol, mol, tani=tani, ref_features=ref_features, score_mode=score_mode)\n+ mol.SetDoubleProp("SuCOS_Score", sucos_score)\n+ mol.SetDoubleProp("SuCOS_FeatureMap_Score", fm_score)\n+ if tani:\n+ mol.SetDoubleProp("SuCOS_Tanimoto_Score", val3)\n+ else:\n+ mol.SetDoubleProp("SuCOS_Protrude_Score", val3)\n+ utils.log("Scores:", sucos_score, fm_score, val3)\n+ writer.write(mol)\n+ total +=1\n+ except ValueError as e:\n+ errors +=1\n+ utils.log("Molecule", count, "failed to score:", e.message)\n+\n+ input_file.close()\n+ writer.flush()\n+ writer.close()\n+ output_file.close()\n+\n+ utils.log("Completed.", total, "processed, ", count, "succeeded, ", errors, "errors")\n+\n+def parse_score_mode(value):\n+ if value == None or value == \'all\':\n+ return FeatMaps.FeatMapScoreMode.All\n+ elif value == \'closest\':\n+ return FeatMaps.FeatMapScoreMode.Closest\n+ elif value == \'best\':\n+ return FeatMaps.FeatMapScoreMode.Best\n+ else:\n+ raise ValueError(value + " is not a valid scoring mode option")\n+\n+\n+### start main execution #########################################\n+\n+def main():\n+\n+ parser = argparse.ArgumentParser(description=\'SuCOS with RDKit\')\n+ parser.add_argument(\'-i\', \'--input\', help=\'Input file in SDF format. Can be gzipped (*.gz).\')\n+ parser.add_argument(\'-r\', \'--refmol\', help=\'Molecule to compare against in Molfile (.mol) or SDF (.sdf) format\')\n+ parser.add_argument(\'--refmol-format\', help="Format for the reference molecule (mol or sdf). " +\n+ "Only needed if files don\'t have the expected extensions")\n+ parser.add_argument(\'--refmolidx\', help=\'Reference molecule index in SD file if not the first\', type=int, default=1)\n+ parser.add_argument(\'-o\', \'--output\', help=\'Output file in SDF format. Can be gzipped (*.gz).\')\n+ parser.add_argument(\'--tanimoto\', action=\'store_true\', help=\'Include Tanimoto distance in score\')\n+ parser.add_argument(\'--score_mode\', choices=[\'all\', \'closest\', \'best\'],\n+ help="choose the scoring mode for the feature map, default is \'all\'.")\n+\n+ args = parser.parse_args()\n+ utils.log("SuCOS Args: ", args)\n+\n+ score_mode = parse_score_mode(args.score_mode)\n+\n+ process(args.refmol, args.input, args.output, refmol_index=args.refmolidx,\n+ refmol_format=args.refmol_format, tani=args.tanimoto, score_mode=score_mode)\n+\n+\n+if __name__ == "__main__":\n+ main()\n' |
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| diff -r 000000000000 -r bb5365381c8f sucos_cluster.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sucos_cluster.py Wed Oct 02 12:57:54 2019 -0400 |
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| @@ -0,0 +1,134 @@ +#!/usr/bin/env python +""" +Cluster a set of molecules based on their 3D overlays as determined by the SuCOS score. + +This will generate a set of SD files, one for each cluster of molecules (presumably corresponding to a +binding pocket in the protein target). + + +SuCOS is the work of Susan Leung. +GitHub: https://github.com/susanhleung/SuCOS +Publication: https://doi.org/10.26434/chemrxiv.8100203.v1 +""" + +import sucos, utils +import argparse, gzip +from rdkit import Chem +import numpy as np +import pandas as pd +from scipy.cluster.hierarchy import linkage, fcluster + +### start main execution ######################################### + + +def calc_distance_matrix(mols): + """ + Calculate a full distance matrix for the given molecules. Identical molecules get a score of 0.0 with the maximum + distance possible being 1.0. + :param mols: A list of molecules. It must be possible to iterate through this list multiple times + :return: A NxN 2D array of distance scores, with N being the number of molecules in the input + """ + + # TODO - do we need to calculate both sides of the matrix? Tanimoto is supposed to be a symmetric distance measure, + # but the matrix that is generated does not seem to be symmetric. + + mol_fm_tuples = [] + for mol in mols: + features = sucos.getRawFeatures(mol) + mol_fm_tuples.append((mol, features)) + + matrix = [] + for tuple1 in mol_fm_tuples: + tmp = [] + for tuple2 in mol_fm_tuples: + if tuple1[0] == tuple2[0]: + tmp.append(0.0) + else: + #utils.log("Calculating SuCOS between", mol1, mol2) + sucos_score, fm_score, tani_score = sucos.get_SucosScore(tuple1[0], tuple2[0], + tani=True, ref_features=tuple1[1], query_features=tuple2[1]) + tmp.append(1.0 - sucos_score) + matrix.append(tmp) + + + return matrix + + +def cluster(matrix, threshold=0.8): + """ + Cluster the supplied distance matrix returning an array of clusters. + :param matrix: the distance matrix, as calculated with the calc_distance_matrix function. + :param threshold: The clustering cuttoff. The default of 0.8 is a reasonable value to use. + :return: An array of clusters, each cluster being an array of the indices from the matrix. + """ + + indexes = [x for x in range(0, len(matrix))] + cols = [x for x in range(0, len(matrix[0]))] + #utils.log("indexes", indexes) + #utils.log("cols", cols) + df = pd.DataFrame(matrix, columns=cols, index=indexes) + utils.log("DataFrame:", df.shape) + #utils.log(df) + indices = np.triu_indices(df.shape[0], k=1) + #utils.log("Indices:", indices) + t = np.array(df)[indices] + Z = linkage(t, 'average') + lig_clusters = [] + cluster_arr = fcluster(Z, t=threshold, criterion='distance') + for i in range(np.amax(cluster_arr)): + clus = df.columns[np.argwhere(cluster_arr==i+1)] + lig_clusters.append([x[0] for x in clus.tolist()]) + + utils.log("Clusters", lig_clusters) + return lig_clusters + +def write_clusters_to_sdfs(mols, clusters, basename, gzip=False): + """ + Write the molecules to SDF files, 1 file for each cluster. + :param mols The molecules to write: + :param clusters The clusters, as returned by the cluster function: + :param basename The basename for the file name. e.g. if basename is 'output' then files like + output1.sdf, output2.sdf will be written: + :param gzip Whether to gzip the output + :return: + """ + + i = 0 + for cluster in clusters: + i += 1 + filename = basename + str(i) + ".sdf" + if gzip: + filename += ".gz" + utils.log("Writing ", len(cluster), "molecules in cluster", i, "to file", filename) + output_file = utils.open_file_for_writing(filename) + writer = Chem.SDWriter(output_file) + for index in cluster: + mol = mols[index] + writer.write(mol) + writer.flush() + writer.close() + output_file.close() + + + +def main(): + parser = argparse.ArgumentParser(description='Clustering with SuCOS and RDKit') + parser.add_argument('-i', '--input', help='Input file in SDF format. Can be gzipped (*.gz).') + parser.add_argument('-o', '--output', default="cluster", help="Base name for output files in SDF format. " + + "e.g. if value is 'output' then files like output1.sdf, output2.sdf will be created") + parser.add_argument('--gzip', action='store_true', help='Gzip the outputs generating files like output1.sdf.gz, output2.sdf.gz') + parser.add_argument('-t', '--threshold', type=float, default=0.8, help='Clustering threshold') + + args = parser.parse_args() + utils.log("SuCOS Cluster Args: ", args) + + input_file = utils.open_file_for_reading(args.input) + suppl = Chem.ForwardSDMolSupplier(input_file) + mols = list(suppl) + matrix = calc_distance_matrix(mols) + clusters = cluster(matrix, threshold=args.threshold) + write_clusters_to_sdfs(mols, clusters, args.output, gzip=args.gzip) + + +if __name__ == "__main__": + main() \ No newline at end of file |
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| diff -r 000000000000 -r bb5365381c8f sucos_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sucos_macros.xml Wed Oct 02 12:57:54 2019 -0400 |
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| @@ -0,0 +1,19 @@ +<macros> + <xml name="citations"> + <citations> + <citation type="doi">10.26434/chemrxiv.8100203.v1</citation> + <citation type="bibtex"> + @article{rdkit, + author = {Greg Landrum and others}, + title = {RDKit: Open-source cheminformatics}, + url ={http://www.rdkit.org} + }</citation> + </citations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2019.03.2.0">rdkit</requirement> + <yield /> + </requirements> + </xml> +</macros> |
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| diff -r 000000000000 -r bb5365381c8f sucos_max.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sucos_max.py Wed Oct 02 12:57:54 2019 -0400 |
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| @@ -0,0 +1,154 @@ +#!/usr/bin/env python +""" +Assess ligands against a second set of molecules using SuCOS scores. +This is a quite specialised function that is designed to take a set of potential follow up +compounds and compare them to a set of clustered fragment hits to help identify which follow up +ligands best map to the binding space of the hits. + +The clustering of the fragment hits is expected to be performed with the sucos_cluster.py module +and will generate a set of SD files, one for each cluster of hits (presumably corresponding to a +binding pocket in the protein target). + +Each molecule in the input ligands is then compared (using SuCOS) to each hit in the clusters. There + are different modes which determine how the ligand is assessed. + +In mode 'max' the hit with the best SuCOS score is identified. The output is a SD file with each of the ligands, +with these additional fields for each molecule: +Max_SuCOS_Score - the best score +Max_SuCOS_FeatureMap_Score - the feature map score for the hit that has the best SuCOS score +Max_SuCOS_Protrude_Score - the protrude volume for the hit that has the best SuCOS score +Max_SuCOS_Cluster - the name of the cluster SD file that contains the best hit +Max_SuCOS_Index - the index of the best hit in the SD file + +In mode 'cum' the sum of all the scores is calculated and reported as the following properties for each molecule: +Cum_SuCOS_Score property: the sum of the SuCOS scores +Cum_SuCOS_FeatureMap_Score: the sum of the feature map scores +Cum_SuCOS_Protrude_Score: the sum of the protrude volume scores + +If a molecule has no alignment to any of the clustered hits (all alignment scores of zero) then it is not +included in the results. + + +SuCOS is the work of Susan Leung. +GitHub: https://github.com/susanhleung/SuCOS +Publication: https://doi.org/10.26434/chemrxiv.8100203.v1 +""" + +import sucos, utils +import argparse, gzip, os +from rdkit import Chem + + +def process(inputfilename, clusterfilenames, outputfilename, mode): + + all_clusters = {} + for filename in clusterfilenames: + cluster = [] + cluster_file = utils.open_file_for_reading(filename) + suppl = Chem.ForwardSDMolSupplier(cluster_file) + i = 0 + for mol in suppl: + i += 1 + if not mol: + utils.log("WARNING: failed to generate molecule", i, "in cluster", filename) + continue + try: + features = sucos.getRawFeatures(mol) + cluster.append((mol, features)) + except: + utils.log("WARNING: failed to generate features for molecule", i, "in cluster", filename) + + cluster_file.close() + all_clusters[filename] = cluster + + input_file = utils.open_file_for_reading(inputfilename) + suppl = Chem.ForwardSDMolSupplier(input_file) + output_file = utils.open_file_for_writing(outputfilename) + writer = Chem.SDWriter(output_file) + + comparisons = 0 + mol_num = 0 + + for mol in suppl: + mol_num += 1 + if not mol: + utils.log("WARNING: failed to generate molecule", mol_num, "in input") + continue + try: + query_features = sucos.getRawFeatures(mol) + except: + utils.log("WARNING: failed to generate features for molecule", mol_num, "in input") + continue + scores = [0, 0, 0] + for clusterfilename in all_clusters: + cluster = all_clusters[clusterfilename] + index = 0 + for entry in cluster: + hit = entry[0] + ref_features = entry[1] + index += 1 + comparisons += 1 + sucos_score, fm_score, vol_score = sucos.get_SucosScore(hit, mol, + tani=False, ref_features=ref_features, query_features=query_features) + if mode == 'max': + if sucos_score > scores[0]: + scores[0] = sucos_score + scores[1] = fm_score + scores[2] = vol_score + cluster_name = clusterfilename + cluster_index = index + elif mode == 'cum': + scores[0] += sucos_score + scores[1] += fm_score + scores[2] += vol_score + else: + raise ValueError("Invalid mode: " + mode) + + if scores[0] > 0: + if mode == 'max': + cluster_file_name_only = cluster_name.split(os.sep)[-1] + #utils.log("Max SuCOS:", scores[0], "FM:", scores[1], "P:", scores[2],"File:", cluster_file_name_only, "Index:", cluster_index) + mol.SetDoubleProp("Max_SuCOS_Score", scores[0]) + mol.SetDoubleProp("Max_SuCOS_FeatureMap_Score", scores[1]) + mol.SetDoubleProp("Max_SuCOS_Protrude_Score", scores[2]) + mol.SetProp("Max_SuCOS_Cluster", cluster_file_name_only) + mol.SetIntProp("Max_SuCOS_Index", cluster_index) + + else: + #utils.log("Cum SuCOS:", scores[0], "FM:", scores[1], "P:", scores[2]) + mol.SetDoubleProp("Cum_SuCOS_Score", scores[0]) + mol.SetDoubleProp("Cum_SuCOS_FeatureMap_Score", scores[1]) + mol.SetDoubleProp("Cum_SuCOS_Protrude_Score", scores[2]) + + writer.write(mol) + + else: + utils.log("Molecule", mol_num, "did not overlay. Omitting from results") + + + input_file.close() + writer.flush() + writer.close() + output_file.close() + + utils.log("Completed", comparisons, "comparisons") + + +### start main execution ######################################### + +def main(): + parser = argparse.ArgumentParser(description='Max SuCOS scores with RDKit') + parser.add_argument('-i', '--input', help='Input file to score in SDF format. Can be gzipped (*.gz).') + parser.add_argument('-o', '--output', help='Output file in SDF format. Can be gzipped (*.gz).') + parser.add_argument('-m', '--mode', choices=['max', 'cum'], + default='max', help='Score mode: max = best score, cum = sum of all scores') + parser.add_argument('clusters', nargs='*', help="One or more SDF files with the clustered hits") + + args = parser.parse_args() + utils.log("Max SuCOS Args: ", args) + + process(args.input, args.clusters, args.output, args.mode) + + +if __name__ == "__main__": + main() \ No newline at end of file |
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| diff -r 000000000000 -r bb5365381c8f sucos_max.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sucos_max.xml Wed Oct 02 12:57:54 2019 -0400 |
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| @@ -0,0 +1,85 @@ +<tool id="sucos_max_score" name="Max SuCOS score" version="0.1"> + <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description> + <macros> + <import>sucos_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ + python '$__tool_directory__/sucos_max.py' + -i '$input' + -o '$output' + -m $mode + #for $cluster in $clusters + '$cluster' + #end for + ]]></command> + <inputs> + <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." /> + <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." /> + <param name="mode" type="select" value="max" label="Mode"> + <option value="max">Max score</option> + <option value="cum">Cumulative score</option> + </param> + </inputs> + <outputs> + <data format="sdf" name="output" label="The scored ligands"/> + </outputs> + <tests> + <test> + <param name="input" ftype="sdf" value="sucos_cluster.sdf"/> + <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/> + <param name="mode" value="max"/> + <output name="output" ftype="sdf"> + <assert_contents> + <has_text text="Max_SuCOS_Score" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype="sdf" value="sucos_cluster.sdf"/> + <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/> + <param name="mode" value="cum"/> + <output name="output" ftype="sdf"> + <assert_contents> + <has_text text="Cum_SuCOS_Score" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +This tool determines the maximum SuCOS score of ligands, presumed to be potential follow on compounds, compared to a +set of clustered reference compounds, presumed to be fragment screening hits. Each ligand to be scored is compared to +all of the reference compounds with the highest score being recorded, along with the cluster it came from and the index +of the molecule within that cluster. + +The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_. + +.. _GitHub: https://github.com/susanhleung/SuCOS +.. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203 + +.. class:: infomark + +**Input** + +The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and +will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file. + +.. class:: infomark + +**Output** + +The same SD file as the input ligands with a "Max_SuCOS_Score" property added containing the best (maximum) SuCOS score +along with the "Max_SuCOS_FeatureMap_Score" and "Max_SuCOS_Tanimoto_Score" of that comparison. + +In addition, the "Max_SuCOS_Cluster" field shows the name of the cluster file that contained the molecule with this best +score and the "Max_SuCOS_Index" shows the index (first record is index 1) of that molecule in the file. + + ]]></help> + <expand macro="citations"/> +</tool> + |
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| diff -r 000000000000 -r bb5365381c8f test-data/cluster1.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster1.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| @@ -0,0 +1,77 @@ + + RDKit 3D + + 16 18 0 0 0 0 0 0 0 0999 V2000 + 19.9510 12.4320 19.9980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.0820 11.0800 19.7160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.2110 12.9210 21.2780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.4730 10.2080 20.7160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.6070 12.0470 22.2840 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.7310 10.6920 21.9840 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.8690 12.5020 23.5750 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.1210 9.8120 22.9630 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.2630 11.6100 24.5730 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.3860 10.2600 24.2390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5170 12.0970 25.8880 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7700 9.2670 25.1440 N 0 0 0 0 0 0 0 0 0 0 0 0 + 20.6720 13.9160 27.1880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.3000 12.6550 27.9160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7880 13.5100 26.2340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.8880 11.5200 27.1000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 1 1 0 + 4 2 1 0 + 5 3 2 0 + 6 4 2 0 + 6 5 1 0 + 7 5 1 0 + 8 6 1 0 + 9 7 2 0 + 10 8 2 0 + 10 9 1 0 + 11 9 1 0 + 12 10 1 0 + 14 13 1 0 + 15 13 1 0 + 15 11 1 0 + 16 11 1 0 + 16 14 1 0 +M END +$$$$ + + RDKit 3D + + 15 16 0 0 0 0 0 0 0 0999 V2000 + 18.6370 11.5460 19.0470 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 19.3410 11.4910 20.6100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.1300 12.5410 21.5090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.1120 10.3920 20.9640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.7080 12.5060 22.7780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.6710 10.3800 22.2200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.4820 11.4070 23.1080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.4530 9.4460 22.7560 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7320 9.9040 23.9840 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.1510 11.1000 24.2190 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5310 9.1910 24.8790 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.2170 11.9110 25.4550 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.4620 11.2450 26.6090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.0350 11.5770 27.9760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.9480 12.9640 28.2400 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 2 1 0 + 5 3 1 0 + 6 4 2 0 + 7 6 1 0 + 7 5 2 0 + 8 6 1 0 + 9 8 2 0 + 10 9 1 0 + 10 7 1 0 + 11 9 1 0 + 12 10 1 0 + 13 12 1 0 + 14 13 1 0 + 15 14 1 0 +M END +$$$$ |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/cluster2.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster2.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| @@ -0,0 +1,167 @@ + + RDKit 3D + + 10 10 0 0 0 0 0 0 0 0999 V2000 + 24.4730 11.1990 19.8620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.5530 12.0600 20.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.9840 11.0460 18.5670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.8330 10.4330 20.9970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.1360 12.7690 19.0380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.5550 11.7420 17.5050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3160 10.6870 21.0270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.6290 12.6010 17.7470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6740 10.0940 22.2270 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.1850 13.2880 16.6940 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 1 1 0 + 4 1 1 0 + 5 2 1 0 + 6 3 2 0 + 7 4 1 0 + 8 6 1 0 + 8 5 2 0 + 9 7 1 0 + 10 8 1 0 +M END +$$$$ + + RDKit 3D + + 11 11 0 0 0 0 0 0 0 0999 V2000 + 23.8350 12.2020 19.5760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.4520 11.9220 18.2610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0420 12.8700 19.8340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9370 11.8100 20.7250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.2680 12.2940 17.1940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8750 13.2520 18.7790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8350 10.2970 20.9620 C 0 0 1 0 0 0 0 0 0 0 0 0 + 25.4680 12.9560 17.4710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1570 9.7480 21.5040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7030 9.9910 21.9220 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.2630 13.3220 16.4230 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 1 1 0 + 4 1 1 0 + 5 2 1 0 + 6 3 2 0 + 7 4 1 0 + 8 6 1 0 + 8 5 2 0 + 7 9 1 1 + 10 7 1 0 + 11 8 1 0 +M END +$$$$ + + RDKit 3D + + 12 12 0 0 0 0 0 0 0 0999 V2000 + 26.5880 11.6480 19.1670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.9260 11.0670 20.2530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8770 11.8420 17.9690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.0300 12.0720 19.2730 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.5820 10.6900 20.1310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.5420 11.4720 17.8340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.4990 12.4120 16.8870 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.9860 10.8940 19.5000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.8950 10.8910 18.9250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.8700 10.0590 21.2980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8110 11.0000 21.8820 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6380 10.2010 22.3970 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 1 1 0 + 4 1 1 0 + 5 2 1 0 + 6 3 2 0 + 7 3 1 0 + 8 4 1 0 + 9 5 2 0 + 9 6 1 0 + 10 5 1 0 + 11 10 1 0 + 12 11 1 0 +M END +$$$$ + + RDKit 3D + + 16 17 0 0 0 0 0 0 0 0999 V2000 + 26.3090 11.5670 19.1200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.7750 11.8580 19.3620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.5460 10.8930 20.0800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.6820 11.9660 17.9260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.9150 13.1100 20.2510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.4910 10.6030 19.9180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1900 10.6200 19.8540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3290 11.7060 17.6830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3920 12.6330 16.9610 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3630 13.3270 20.6990 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.8080 10.8590 20.6700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.5890 11.0260 18.6540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3960 9.8840 20.9090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.7810 12.1210 21.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.0220 10.5180 21.1760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.2950 9.8120 22.2580 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 1 2 0 + 4 1 1 0 + 5 2 1 0 + 6 2 1 0 + 7 3 1 0 + 8 4 2 0 + 9 4 1 0 + 10 5 1 0 + 11 6 1 0 + 12 7 2 0 + 12 8 1 0 + 13 7 1 0 + 14 11 1 0 + 14 10 1 0 + 15 13 1 0 + 16 15 1 0 +M END +$$$$ + + RDKit 3D + + 18 20 0 0 0 0 0 0 0 0999 V2000 + 28.6970 10.5240 20.4750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.9220 11.6800 20.9560 N 0 0 0 0 0 0 0 0 0 0 0 0 + 28.7880 12.6650 21.6350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.0810 12.2010 19.9710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.4190 13.2930 19.2740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.6450 13.8320 18.3200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.4810 13.2870 17.9980 N 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0290 12.1840 18.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7860 11.6150 18.3040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3430 10.5040 18.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1080 9.9180 19.9810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.3250 10.4360 20.3200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8200 11.5870 19.6640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.1160 14.9710 17.6690 N 0 0 0 0 0 0 0 0 0 0 0 0 + 27.3480 16.1150 18.5710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.6660 17.2890 17.6050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.8670 16.9430 16.3140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3130 15.5200 16.5590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 1 0 + 4 2 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 11 10 2 0 + 12 11 1 0 + 13 12 2 0 + 13 8 1 0 + 13 4 1 0 + 14 6 1 0 + 15 14 1 0 + 16 15 1 0 + 17 16 1 0 + 18 14 1 0 + 18 17 1 0 +M END +$$$$ |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/cluster3.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster3.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| b'@@ -0,0 +1,1024 @@\n+\n+ RDKit 3D\n+\n+ 19 20 0 0 0 0 0 0 0 0999 V2000\n+ 25.8690 10.6750 17.9260 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.7660 11.4770 18.5500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1650 12.4880 17.8120 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1480 13.2570 18.3640 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.7300 13.0010 19.6620 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6190 13.8450 20.2480 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.3280 11.9670 20.4090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.9000 11.7560 21.6900 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1990 10.4520 22.2010 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3800 10.3250 23.4930 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 22.7510 9.1510 24.2170 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5930 11.5910 24.3570 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.2540 11.3630 25.7760 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5710 12.5910 26.5330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.1760 12.4110 28.0100 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.7810 12.0710 28.1350 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.5060 10.8660 27.4060 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.8170 11.0700 25.9210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.3600 11.2090 19.8480 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 2 0\n+ 4 3 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 7 5 1 0\n+ 8 7 1 0\n+ 9 8 1 0\n+ 10 9 1 0\n+ 10 11 1 1\n+ 12 10 1 0\n+ 13 12 1 0\n+ 14 13 1 0\n+ 15 14 1 0\n+ 16 15 1 0\n+ 17 16 1 0\n+ 18 17 1 0\n+ 18 13 1 0\n+ 19 7 2 0\n+ 19 2 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 12 0 0 0 0 0 0 0 0999 V2000\n+ 22.8090 9.2070 24.2800 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4710 10.1080 23.3190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8900 9.6340 22.1960 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.5680 10.5170 21.2440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7580 11.8790 21.3690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3130 12.3920 22.5320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5210 13.7530 22.7260 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0810 14.2110 23.9020 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.4470 13.3190 24.8860 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.2450 11.9700 24.7110 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6750 11.4850 23.5440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 2 0\n+ 4 3 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 7 6 2 0\n+ 8 7 1 0\n+ 9 8 2 0\n+ 10 9 1 0\n+ 11 2 1 0\n+ 11 10 2 0\n+ 11 6 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 12 0 0 0 0 0 0 0 0999 V2000\n+ 22.7770 9.1670 24.9740 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4280 10.0140 24.0880 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6770 11.3690 24.2670 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.2930 12.2600 23.2950 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6430 11.7880 22.1650 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.2220 12.6270 21.1460 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.5740 12.1120 20.0440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.3400 10.7540 19.9450 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.7580 9.9010 20.9470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.4090 10.3980 22.0610 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7960 9.5320 23.0070 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 2 0\n+ 4 3 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 7 6 2 0\n+ 8 7 1 0\n+ 9 8 2 0\n+ 10 9 1 0\n+ 10 5 1 0\n+ 11 10 2 0\n+ 11 2 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 15 16 0 0 0 0 0 0 0 0999 V2000\n+ 22.4510 9.0090 24.4670 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5180 10.3550 24.1060 C 0 0 0 0 0 0 0 0 0 0'..b'9.3450 9.6270 21.1760 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4790 11.8080 24.2920 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.5140 11.7630 22.5130 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.7100 9.2150 24.7670 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.5550 9.7530 20.5440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.8590 10.7120 20.6250 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1020 10.1890 21.0270 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.2620 10.3730 20.2980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.8630 11.5080 19.3970 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.5800 10.5280 21.4490 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 20.9500 11.9060 21.9290 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 21.9600 12.7150 22.7910 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3230 10.0930 23.7780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.0040 11.6730 18.6170 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.2010 11.1170 19.0930 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7570 12.0240 18.8700 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.3200 11.2980 18.4090 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3 1 1 0\n+ 5 1 1 0\n+ 7 3 1 0\n+ 9 8 2 0\n+ 10 9 1 0\n+ 11 8 1 0\n+ 12 7 1 0\n+ 12 8 1 6\n+ 12 2 1 0\n+ 13 12 1 0\n+ 13 5 1 1\n+ 14 13 1 0\n+ 14 4 1 0\n+ 15 6 1 0\n+ 15 2 2 0\n+ 15 4 1 0\n+ 16 11 2 0\n+ 17 10 2 0\n+ 17 16 1 0\n+ 18 11 1 0\n+ 19 17 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 16 17 0 0 0 0 0 0 0 0999 V2000\n+ 20.6950 9.9560 20.8820 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.2050 9.8930 22.6900 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0060 12.0970 24.2220 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8910 10.6980 21.5060 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 22.8690 9.5480 24.8150 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.4800 12.1250 21.9040 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5630 12.8770 22.6580 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6270 10.3910 23.7940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1060 10.7640 20.5410 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.3720 10.2320 20.8590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.4690 10.3640 20.0140 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.3420 11.0350 18.7800 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1030 11.5640 18.3850 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0130 11.4340 19.2760 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8840 12.0230 18.8800 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.4280 11.2380 18.0020 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4 1 1 6\n+ 4 2 1 0\n+ 6 4 1 0\n+ 7 6 1 0\n+ 7 3 1 0\n+ 8 5 1 0\n+ 8 2 2 0\n+ 8 3 1 0\n+ 9 4 1 0\n+ 10 9 2 0\n+ 11 10 1 0\n+ 12 11 2 0\n+ 13 12 1 0\n+ 14 9 1 0\n+ 14 13 2 0\n+ 15 14 1 0\n+ 16 12 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 12 0 0 0 0 0 0 0 0999 V2000\n+ 23.8920 10.9750 19.7100 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1430 9.6540 19.8400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.7820 11.7530 20.9950 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6770 9.8870 20.1680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.1750 12.7870 22.6090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3660 10.1400 23.6660 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3180 11.9530 21.3510 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 21.5250 10.6490 21.4640 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 22.7380 9.3100 24.6900 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.9210 9.6990 22.5310 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5620 11.8400 24.1130 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 1 1 0\n+ 4 2 1 0\n+ 7 3 1 1\n+ 7 5 1 0\n+ 8 4 1 6\n+ 8 7 1 0\n+ 9 6 1 0\n+ 10 8 1 0\n+ 10 6 2 0\n+ 11 6 1 0\n+ 11 5 1 0\n+M END\n+$$$$\n' |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/cluster4.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster4.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| @@ -0,0 +1,47 @@ + + RDKit 3D + + 20 21 0 0 0 0 0 0 0 0999 V2000 + 21.2480 11.2160 24.5450 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.1020 11.0880 25.9790 N 0 0 0 0 0 0 0 0 0 0 0 0 + 20.1520 11.7400 26.6430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.2750 12.3940 26.0980 O 0 0 0 0 0 0 0 0 0 0 0 0 + 20.2050 11.6230 28.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.1270 12.9990 28.8020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.9520 13.0380 30.0790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6540 13.4720 29.6460 S 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7090 11.4410 24.1690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8180 11.5780 22.6520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3510 10.3050 22.0930 N 0 0 0 0 0 0 0 0 0 0 0 0 + 20.9200 10.1140 22.3280 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.7360 9.9660 23.8360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5750 10.2440 20.6540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.9890 10.6020 20.2540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0820 9.9220 20.7960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3780 10.2710 20.4140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.5780 11.2950 19.4850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.4840 11.9720 18.9430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1890 11.6250 19.3240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 3 2 1 0 + 4 3 2 0 + 5 3 1 0 + 6 5 1 0 + 7 6 1 0 + 8 7 1 0 + 9 1 1 0 + 10 9 1 0 + 11 10 1 0 + 12 11 1 0 + 13 12 1 0 + 13 1 1 0 + 14 11 1 0 + 15 14 1 0 + 16 15 2 0 + 17 16 1 0 + 18 17 2 0 + 19 18 1 0 + 20 15 1 0 + 20 19 2 0 +M END +$$$$ |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/cluster5.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster5.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| @@ -0,0 +1,47 @@ + + RDKit 3D + + 20 21 0 0 0 0 0 0 0 0999 V2000 + 23.0110 10.6350 19.8150 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.2670 11.1650 19.1280 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.2960 11.1360 20.1630 N 0 0 0 0 0 0 0 0 0 0 0 0 + 24.9890 12.0920 21.2290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7420 11.5350 21.9210 C 0 0 2 0 0 0 0 0 0 0 0 0 + 22.6410 11.4290 20.9740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.6000 11.4040 19.5610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.7300 10.8900 20.4300 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.6290 9.6500 21.0680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.6700 9.1850 21.8700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.8180 9.9600 22.0270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.9260 11.1970 21.3880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.8800 11.6630 20.5900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3760 12.3720 23.1130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.0930 12.1770 24.2210 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4610 13.1780 23.0440 O 0 0 0 0 0 0 0 0 0 0 0 0 + 23.8850 12.9460 25.4360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.7100 14.2290 25.4520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3830 13.8570 26.0370 S 0 0 0 0 0 0 0 0 0 0 0 0 + 30.8240 9.5080 22.7950 F 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 1 0 + 4 3 1 0 + 5 4 1 0 + 6 1 1 0 + 6 5 1 0 + 7 3 1 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 11 10 2 0 + 12 11 1 0 + 13 8 1 0 + 13 12 2 0 + 5 14 1 1 + 15 14 1 0 + 16 14 2 0 + 17 15 1 0 + 18 17 1 0 + 19 18 1 0 + 20 11 1 0 +M END +$$$$ |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/cluster6.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster6.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| @@ -0,0 +1,22 @@ + + RDKit 3D + + 8 8 0 0 0 0 0 0 0 0999 V2000 + 43.2120 1.2010 21.1900 N 0 0 0 0 0 0 0 0 0 0 0 0 + 42.0970 1.7030 22.0340 C 0 0 2 0 0 0 0 0 0 0 0 0 + 41.2120 2.6840 21.2450 C 0 0 0 0 0 0 0 0 0 0 0 0 + 41.4260 2.9540 20.0390 O 0 0 0 0 0 0 0 0 0 0 0 0 + 42.6930 2.1910 23.3430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 44.2130 1.9390 23.2340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 44.4930 1.6950 21.7590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 40.1570 3.2440 21.9570 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 2 3 1 6 + 4 3 2 0 + 5 2 1 0 + 6 5 1 0 + 7 1 1 0 + 7 6 1 0 + 8 3 1 0 +M END +$$$$ |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/split_1.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_1.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| b'@@ -0,0 +1,389 @@\n+\n+ RDKit 3D\n+\n+ 19 20 0 0 0 0 0 0 0 0999 V2000\n+ 25.8690 10.6750 17.9260 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.7660 11.4770 18.5500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1650 12.4880 17.8120 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1480 13.2570 18.3640 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.7300 13.0010 19.6620 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6190 13.8450 20.2480 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.3280 11.9670 20.4090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.9000 11.7560 21.6900 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1990 10.4520 22.2010 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3800 10.3250 23.4930 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 22.7510 9.1510 24.2170 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5930 11.5910 24.3570 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.2540 11.3630 25.7760 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5710 12.5910 26.5330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.1760 12.4110 28.0100 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.7810 12.0710 28.1350 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.5060 10.8660 27.4060 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.8170 11.0700 25.9210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.3600 11.2090 19.8480 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 2 0\n+ 4 3 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 7 5 1 0\n+ 8 7 1 0\n+ 9 8 1 0\n+ 10 9 1 0\n+ 10 11 1 1\n+ 12 10 1 0\n+ 13 12 1 0\n+ 14 13 1 0\n+ 15 14 1 0\n+ 16 15 1 0\n+ 17 16 1 0\n+ 18 17 1 0\n+ 18 13 1 0\n+ 19 7 2 0\n+ 19 2 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 12 0 0 0 0 0 0 0 0999 V2000\n+ 22.8090 9.2070 24.2800 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4710 10.1080 23.3190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8900 9.6340 22.1960 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.5680 10.5170 21.2440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7580 11.8790 21.3690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3130 12.3920 22.5320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5210 13.7530 22.7260 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0810 14.2110 23.9020 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.4470 13.3190 24.8860 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.2450 11.9700 24.7110 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6750 11.4850 23.5440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 2 0\n+ 4 3 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 7 6 2 0\n+ 8 7 1 0\n+ 9 8 2 0\n+ 10 9 1 0\n+ 11 2 1 0\n+ 11 10 2 0\n+ 11 6 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 12 0 0 0 0 0 0 0 0999 V2000\n+ 22.7770 9.1670 24.9740 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4280 10.0140 24.0880 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6770 11.3690 24.2670 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.2930 12.2600 23.2950 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6430 11.7880 22.1650 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.2220 12.6270 21.1460 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.5740 12.1120 20.0440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.3400 10.7540 19.9450 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.7580 9.9010 20.9470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.4090 10.3980 22.0610 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7960 9.5320 23.0070 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 2 0\n+ 4 3 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 7 6 2 0\n+ 8 7 1 0\n+ 9 8 2 0\n+ 10 9 1 0\n+ 10 5 1 0\n+ 11 10 2 0\n+ 11 2 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 15 16 0 0 0 0 0 0 0 0999 V2000\n+ 22.4510 9.0090 24.4670 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5180 10.3550 24.1060 C 0 0 0 0 0 0 0 0 0 0 '..b' 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6540 13.4720 29.6460 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.7090 11.4410 24.1690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.8180 11.5780 22.6520 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3510 10.3050 22.0930 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.9200 10.1140 22.3280 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.7360 9.9660 23.8360 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5750 10.2440 20.6540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.9890 10.6020 20.2540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.0820 9.9220 20.7960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.3780 10.2710 20.4140 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.5780 11.2950 19.4850 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.4840 11.9720 18.9430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1890 11.6250 19.3240 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 3 2 1 0\n+ 4 3 2 0\n+ 5 3 1 0\n+ 6 5 1 0\n+ 7 6 1 0\n+ 8 7 1 0\n+ 9 1 1 0\n+ 10 9 1 0\n+ 11 10 1 0\n+ 12 11 1 0\n+ 13 12 1 0\n+ 13 1 1 0\n+ 14 11 1 0\n+ 15 14 1 0\n+ 16 15 2 0\n+ 17 16 1 0\n+ 18 17 2 0\n+ 19 18 1 0\n+ 20 15 1 0\n+ 20 19 2 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 20 21 0 0 0 0 0 0 0 0999 V2000\n+ 23.0110 10.6350 19.8150 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.2670 11.1650 19.1280 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.2960 11.1360 20.1630 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.9890 12.0920 21.2290 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.7420 11.5350 21.9210 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 22.6410 11.4290 20.9740 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.6000 11.4040 19.5610 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.7300 10.8900 20.4300 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.6290 9.6500 21.0680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.6700 9.1850 21.8700 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.8180 9.9600 22.0270 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.9260 11.1970 21.3880 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.8800 11.6630 20.5900 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.3760 12.3720 23.1130 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.0930 12.1770 24.2210 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4610 13.1780 23.0440 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.8850 12.9460 25.4360 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.7100 14.2290 25.4520 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.3830 13.8570 26.0370 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.8240 9.5080 22.7950 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 1 0\n+ 4 3 1 0\n+ 5 4 1 0\n+ 6 1 1 0\n+ 6 5 1 0\n+ 7 3 1 0\n+ 8 7 1 0\n+ 9 8 2 0\n+ 10 9 1 0\n+ 11 10 2 0\n+ 12 11 1 0\n+ 13 8 1 0\n+ 13 12 2 0\n+ 5 14 1 1\n+ 15 14 1 0\n+ 16 14 2 0\n+ 17 15 1 0\n+ 18 17 1 0\n+ 19 18 1 0\n+ 20 11 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 10 10 0 0 0 0 0 0 0 0999 V2000\n+ 24.4730 11.1990 19.8620 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.5530 12.0600 20.0930 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.9840 11.0460 18.5670 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.8330 10.4330 20.9970 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.1360 12.7690 19.0380 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.5550 11.7420 17.5050 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3160 10.6870 21.0270 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.6290 12.6010 17.7470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6740 10.0940 22.2270 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.1850 13.2880 16.6940 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 2 0\n+ 3 1 1 0\n+ 4 1 1 0\n+ 5 2 1 0\n+ 6 3 2 0\n+ 7 4 1 0\n+ 8 6 1 0\n+ 8 5 2 0\n+ 9 7 1 0\n+ 10 8 1 0\n+M END\n+$$$$\n' |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/split_2.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_2.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| b'@@ -0,0 +1,385 @@\n+\n+ RDKit 3D\n+\n+ 11 11 0 0 0 0 0 0 0 0999 V2000\n+ 23.8350 12.2020 19.5760 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.4520 11.9220 18.2610 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.0420 12.8700 19.8340 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.9370 11.8100 20.7250 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.2680 12.2940 17.1940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.8750 13.2520 18.7790 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.8350 10.2970 20.9620 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 25.4680 12.9560 17.4710 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1570 9.7480 21.5040 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7030 9.9910 21.9220 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.2630 13.3220 16.4230 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 2 0\n+ 3 1 1 0\n+ 4 1 1 0\n+ 5 2 1 0\n+ 6 3 2 0\n+ 7 4 1 0\n+ 8 6 1 0\n+ 8 5 2 0\n+ 7 9 1 1\n+ 10 7 1 0\n+ 11 8 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 12 12 0 0 0 0 0 0 0 0999 V2000\n+ 26.5880 11.6480 19.1670 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.9260 11.0670 20.2530 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.8770 11.8420 17.9690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.0300 12.0720 19.2730 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.5820 10.6900 20.1310 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.5420 11.4720 17.8340 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.4990 12.4120 16.8870 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.9860 10.8940 19.5000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.8950 10.8910 18.9250 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.8700 10.0590 21.2980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.8110 11.0000 21.8820 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6380 10.2010 22.3970 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 2 0\n+ 3 1 1 0\n+ 4 1 1 0\n+ 5 2 1 0\n+ 6 3 2 0\n+ 7 3 1 0\n+ 8 4 1 0\n+ 9 5 2 0\n+ 9 6 1 0\n+ 10 5 1 0\n+ 11 10 1 0\n+ 12 11 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 16 17 0 0 0 0 0 0 0 0999 V2000\n+ 26.3090 11.5670 19.1200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.7750 11.8580 19.3620 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.5460 10.8930 20.0800 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.6820 11.9660 17.9260 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.9150 13.1100 20.2510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.4910 10.6030 19.9180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1900 10.6200 19.8540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.3290 11.7060 17.6830 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.3920 12.6330 16.9610 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.3630 13.3270 20.6990 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.8080 10.8590 20.6700 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.5890 11.0260 18.6540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.3960 9.8840 20.9090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.7810 12.1210 21.5440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.0220 10.5180 21.1760 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.2950 9.8120 22.2580 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 1 2 0\n+ 4 1 1 0\n+ 5 2 1 0\n+ 6 2 1 0\n+ 7 3 1 0\n+ 8 4 2 0\n+ 9 4 1 0\n+ 10 5 1 0\n+ 11 6 1 0\n+ 12 7 2 0\n+ 12 8 1 0\n+ 13 7 1 0\n+ 14 11 1 0\n+ 14 10 1 0\n+ 15 13 1 0\n+ 16 15 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 11 0 0 0 0 0 0 0 0999 V2000\n+ 22.7740 12.1470 21.7380 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.7850 10.8240 21.5130 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6560 12.6100 23.1270 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6870 9.8820 22.6510 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5650 11.6780 24.1480 N 0 0 0 0 0 '..b'070 20.2350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.7250 12.3660 20.5390 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.9740 13.5980 19.8680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0570 14.0730 18.8890 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8900 13.3170 18.5790 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6410 12.0820 19.2490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3 2 2 0\n+ 4 3 1 0\n+ 5 4 1 0\n+ 6 4 2 0\n+ 7 6 1 0\n+ 8 7 2 0\n+ 8 2 1 0\n+ 9 6 1 0\n+ 10 9 1 0\n+ 11 10 1 0\n+ 12 11 2 0\n+ 13 12 1 0\n+ 14 13 2 0\n+ 15 1 1 0\n+ 15 14 1 0\n+ 16 15 2 0\n+ 16 11 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 17 18 0 0 0 0 0 0 0 0999 V2000\n+ 25.3290 10.4220 19.4450 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8630 10.2850 24.5540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7910 10.8780 25.7630 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.3810 12.4340 23.7140 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.2730 11.7550 24.2280 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.9910 10.7760 23.6530 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.7520 11.8870 25.6690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.7100 9.3050 24.2610 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.5480 11.5280 26.5490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.3220 13.3140 25.8640 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.8570 10.3260 22.2690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8180 11.0860 21.3800 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.5520 12.4460 21.0380 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4570 13.1680 20.2040 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.6300 12.5320 19.7130 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.9010 11.1800 20.0500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.9980 10.4540 20.8840 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3 2 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 6 2 1 0\n+ 7 3 1 0\n+ 7 5 1 0\n+ 8 2 2 0\n+ 7 9 1 0\n+ 10 7 1 0\n+ 11 6 1 0\n+ 12 11 1 0\n+ 13 12 2 0\n+ 14 13 1 0\n+ 15 14 2 0\n+ 16 1 1 0\n+ 16 15 1 0\n+ 17 16 2 0\n+ 17 12 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 20 21 0 0 0 0 0 0 0 0999 V2000\n+ 18.0360 15.1780 25.0870 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.1580 9.9560 23.5460 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7380 9.4450 22.3670 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.3070 12.9370 22.1820 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.5180 11.7630 22.4850 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.0160 11.2920 23.6430 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.2400 10.5640 21.5800 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 22.6590 9.2240 24.5370 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.0010 10.7000 20.2550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.7110 10.4760 21.4070 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3150 12.0980 24.8270 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.0470 12.4840 25.5530 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.6470 11.7740 26.7230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.4310 12.1180 27.3830 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 18.6170 13.1760 26.8780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.0220 13.8920 25.7120 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.2380 13.5470 25.0530 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.3110 9.9210 20.9010 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.0210 11.7480 19.1870 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.4670 11.0980 20.4450 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3 2 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 6 2 1 0\n+ 7 3 1 0\n+ 7 5 1 0\n+ 8 2 2 0\n+ 9 7 1 0\n+ 7 10 1 6\n+ 11 6 1 0\n+ 12 11 1 0\n+ 13 12 2 0\n+ 14 13 1 0\n+ 15 14 2 0\n+ 16 15 1 0\n+ 16 1 1 0\n+ 17 16 2 0\n+ 17 12 1 0\n+ 20 18 1 0\n+ 20 9 1 0\n+ 20 19 1 0\n+M END\n+$$$$\n' |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/split_3.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_3.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| b'@@ -0,0 +1,399 @@\n+\n+ RDKit 3D\n+\n+ 15 16 0 0 0 0 0 0 0 0999 V2000\n+ 18.6370 11.5460 19.0470 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.3410 11.4910 20.6100 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.1300 12.5410 21.5090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.1120 10.3920 20.9640 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.7080 12.5060 22.7780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.6710 10.3800 22.2200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.4820 11.4070 23.1080 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.4530 9.4460 22.7560 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7320 9.9040 23.9840 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.1510 11.1000 24.2190 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5310 9.1910 24.8790 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.2170 11.9110 25.4550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.4620 11.2450 26.6090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.0350 11.5770 27.9760 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.9480 12.9640 28.2400 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 2 0\n+ 4 2 1 0\n+ 5 3 1 0\n+ 6 4 2 0\n+ 7 6 1 0\n+ 7 5 2 0\n+ 8 6 1 0\n+ 9 8 2 0\n+ 10 9 1 0\n+ 10 7 1 0\n+ 11 9 1 0\n+ 12 10 1 0\n+ 13 12 1 0\n+ 14 13 1 0\n+ 15 14 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 16 18 0 0 0 0 0 0 0 0999 V2000\n+ 20.6710 12.3670 19.5500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.3560 11.0080 19.5110 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.7970 10.1550 20.5260 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.5490 10.6510 21.5910 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8550 12.0130 21.6470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.4090 12.8650 20.6370 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.2040 13.2140 18.5400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 18.9460 13.0790 18.0310 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.8500 14.9600 16.8550 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.8860 14.2450 18.0080 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 18.5460 13.9340 17.0770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.9520 9.8170 22.5630 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6670 10.2610 23.6190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0100 11.6160 23.7210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5970 12.5050 22.7210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0640 9.3990 24.5550 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 2 0\n+ 3 2 1 0\n+ 4 3 2 0\n+ 5 4 1 0\n+ 6 1 1 0\n+ 6 5 2 0\n+ 7 1 1 0\n+ 8 7 1 0\n+ 10 9 1 0\n+ 10 7 2 0\n+ 11 9 1 0\n+ 11 8 2 0\n+ 12 4 1 0\n+ 13 12 2 0\n+ 14 13 1 0\n+ 15 5 1 0\n+ 15 14 2 0\n+ 16 13 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 14 16 0 0 0 0 0 0 0 0999 V2000\n+ 22.5850 11.1260 22.4670 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 22.4650 13.2910 21.5170 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.5180 12.9300 23.6420 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1760 11.1930 21.1020 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.7650 9.4680 24.1810 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.1720 12.5670 22.6700 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.3450 10.2690 22.4850 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.5010 10.6150 23.5600 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0740 12.4520 20.5910 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.7590 10.2030 20.3680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.3310 9.5780 23.8310 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.5150 12.7690 19.3280 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.2170 10.4950 19.0970 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1050 11.7710 18.5900 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4 1 1 0\n+ 6 3 2 0\n+ 6 2 1 0\n+ 6 1 1 0\n+ 1 7 1 6\n+ 8 '..b' 17 0 0 0 0 0 0 0 0999 V2000\n+ 21.3640 10.5720 21.8100 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 22.5260 10.7940 20.8840 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7650 9.7570 22.9510 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.8520 11.9280 22.2760 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.2790 9.8280 21.0370 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.8090 10.3570 21.2290 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3130 11.4350 19.6600 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4050 10.1940 23.9570 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.0020 12.7140 22.8990 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.8880 10.5560 20.3660 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.3940 11.6280 18.7960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6430 11.8420 24.2920 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.9320 9.2680 24.7800 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.6750 11.1950 19.1430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.7040 11.4130 18.2580 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.1050 11.3380 18.6380 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 1 1 0\n+ 4 1 1 0\n+ 1 5 1 6\n+ 6 2 2 0\n+ 7 2 1 0\n+ 8 3 2 0\n+ 9 4 1 0\n+ 10 6 1 0\n+ 11 7 2 0\n+ 12 8 1 0\n+ 12 9 1 0\n+ 13 8 1 0\n+ 14 10 2 0\n+ 14 11 1 0\n+ 15 14 1 0\n+ 16 15 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 20 22 0 0 0 0 0 0 0 0999 V2000\n+ 21.9670 12.1590 22.5710 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.0870 9.7810 22.3570 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7990 13.3470 22.3700 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7250 10.9910 21.5730 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4050 11.6040 23.7520 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4510 10.1860 23.5940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.8260 9.3810 24.5860 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.7290 12.3950 24.9450 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.2460 10.8230 21.1770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.8630 9.8830 20.2250 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 18.5290 9.7390 19.8610 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 17.5600 10.5330 20.4430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 17.9210 11.4590 21.3960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 19.2540 11.6030 21.7650 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6070 11.2230 20.3330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4200 12.3320 19.5090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.2410 12.5470 18.4040 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.2630 11.6640 18.1130 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.4610 10.5600 18.9190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.6360 10.3370 20.0200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3 1 2 0\n+ 4 2 1 0\n+ 4 1 1 0\n+ 5 1 1 0\n+ 6 2 1 0\n+ 6 5 1 0\n+ 7 6 2 0\n+ 8 5 1 0\n+ 4 9 1 0\n+ 10 9 2 0\n+ 11 10 1 0\n+ 12 11 2 0\n+ 13 12 1 0\n+ 14 9 1 0\n+ 14 13 2 0\n+ 15 4 1 0\n+ 16 15 2 0\n+ 17 16 1 0\n+ 18 17 2 0\n+ 19 18 1 0\n+ 20 19 2 0\n+ 20 15 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 8 8 0 0 0 0 0 0 0 0999 V2000\n+ 43.2120 1.2010 21.1900 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 42.0970 1.7030 22.0340 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 41.2120 2.6840 21.2450 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 41.4260 2.9540 20.0390 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 42.6930 2.1910 23.3430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 44.2130 1.9390 23.2340 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 44.4930 1.6950 21.7590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 40.1570 3.2440 21.9570 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 2 3 1 6\n+ 4 3 2 0\n+ 5 2 1 0\n+ 6 5 1 0\n+ 7 1 1 0\n+ 7 6 1 0\n+ 8 3 1 0\n+M END\n+$$$$\n' |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/split_4.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_4.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| @@ -0,0 +1,211 @@ + + RDKit 3D + + 22 25 0 0 0 0 0 0 0 0999 V2000 + 23.9890 11.5960 18.4360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.3210 11.4640 18.7840 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.6630 11.0960 20.0820 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.6490 10.8840 21.0220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3190 11.0270 20.6770 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9880 11.3810 19.3750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2440 10.8070 21.7330 C 0 0 2 0 0 0 0 0 0 0 0 0 + 20.8520 10.8680 21.1250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.8540 10.6460 22.2900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.0450 11.6270 23.3000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 20.9870 12.6610 22.9460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3270 11.9770 22.7910 C 0 0 1 0 0 0 0 0 0 0 0 0 + 22.7770 11.3400 23.9760 O 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7260 10.0020 23.7830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4730 9.6360 22.5540 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9310 9.1250 24.7980 N 0 0 0 0 0 0 0 0 0 0 0 0 + 27.0780 10.9870 20.5190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.5170 9.9760 21.3750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.7840 9.9640 21.7630 N 0 0 0 0 0 0 0 0 0 0 0 0 + 29.6370 10.8810 21.3400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.2680 11.8600 20.5370 N 0 0 0 0 0 0 0 0 0 0 0 0 + 28.0170 11.9450 20.1110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 2 1 0 + 4 3 2 0 + 5 4 1 0 + 6 5 2 0 + 6 1 1 0 + 7 5 1 6 + 8 7 1 0 + 9 8 1 0 + 10 9 1 0 + 11 10 1 0 + 12 11 1 1 + 12 7 1 0 + 13 12 1 0 + 14 13 1 0 + 15 7 1 0 + 15 14 2 0 + 16 14 1 0 + 17 3 1 0 + 18 17 2 0 + 19 18 1 0 + 20 19 2 0 + 21 20 1 0 + 22 17 1 0 + 22 21 2 0 +M END +$$$$ + + RDKit 3D + + 19 21 0 0 0 0 0 0 0 0999 V2000 + 18.6790 10.8940 21.5160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.8760 9.6220 22.6190 N 0 0 0 0 0 0 0 0 0 0 0 0 + 19.3450 9.6270 21.1760 O 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4790 11.8080 24.2920 S 0 0 0 0 0 0 0 0 0 0 0 0 + 19.5140 11.7630 22.5130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7100 9.2150 24.7670 N 0 0 0 0 0 0 0 0 0 0 0 0 + 20.5550 9.7530 20.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8590 10.7120 20.6250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1020 10.1890 21.0270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.2620 10.3730 20.2980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8630 11.5080 19.3970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5800 10.5280 21.4490 C 0 0 2 0 0 0 0 0 0 0 0 0 + 20.9500 11.9060 21.9290 C 0 0 2 0 0 0 0 0 0 0 0 0 + 21.9600 12.7150 22.7910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3230 10.0930 23.7780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.0040 11.6730 18.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.2010 11.1170 19.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7570 12.0240 18.8700 F 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3200 11.2980 18.4090 F 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 1 0 + 5 1 1 0 + 7 3 1 0 + 9 8 2 0 + 10 9 1 0 + 11 8 1 0 + 12 7 1 0 + 12 8 1 6 + 12 2 1 0 + 13 12 1 0 + 13 5 1 1 + 14 13 1 0 + 14 4 1 0 + 15 6 1 0 + 15 2 2 0 + 15 4 1 0 + 16 11 2 0 + 17 10 2 0 + 17 16 1 0 + 18 11 1 0 + 19 17 1 0 +M END +$$$$ + + RDKit 3D + + 16 17 0 0 0 0 0 0 0 0999 V2000 + 20.6950 9.9560 20.8820 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2050 9.8930 22.6900 N 0 0 0 0 0 0 0 0 0 0 0 0 + 23.0060 12.0970 24.2220 S 0 0 0 0 0 0 0 0 0 0 0 0 + 21.8910 10.6980 21.5060 C 0 0 2 0 0 0 0 0 0 0 0 0 + 22.8690 9.5480 24.8150 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.4800 12.1250 21.9040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5630 12.8770 22.6580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6270 10.3910 23.7940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1060 10.7640 20.5410 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3720 10.2320 20.8590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.4690 10.3640 20.0140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.3420 11.0350 18.7800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1030 11.5640 18.3850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.0130 11.4340 19.2760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.8840 12.0230 18.8800 F 0 0 0 0 0 0 0 0 0 0 0 0 + 26.4280 11.2380 18.0020 F 0 0 0 0 0 0 0 0 0 0 0 0 + 4 1 1 6 + 4 2 1 0 + 6 4 1 0 + 7 6 1 0 + 7 3 1 0 + 8 5 1 0 + 8 2 2 0 + 8 3 1 0 + 9 4 1 0 + 10 9 2 0 + 11 10 1 0 + 12 11 2 0 + 13 12 1 0 + 14 9 1 0 + 14 13 2 0 + 15 14 1 0 + 16 12 1 0 +M END +$$$$ + + RDKit 3D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 23.8920 10.9750 19.7100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1430 9.6540 19.8400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7820 11.7530 20.9950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6770 9.8870 20.1680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1750 12.7870 22.6090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3660 10.1400 23.6660 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3180 11.9530 21.3510 C 0 0 2 0 0 0 0 0 0 0 0 0 + 21.5250 10.6490 21.4640 C 0 0 2 0 0 0 0 0 0 0 0 0 + 22.7380 9.3100 24.6900 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.9210 9.6990 22.5310 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5620 11.8400 24.1130 S 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 1 1 0 + 4 2 1 0 + 7 3 1 1 + 7 5 1 0 + 8 4 1 6 + 8 7 1 0 + 9 6 1 0 + 10 8 1 0 + 10 6 2 0 + 11 6 1 0 + 11 5 1 0 +M END +$$$$ + + RDKit 3D + + 18 20 0 0 0 0 0 0 0 0999 V2000 + 28.6970 10.5240 20.4750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.9220 11.6800 20.9560 N 0 0 0 0 0 0 0 0 0 0 0 0 + 28.7880 12.6650 21.6350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.0810 12.2010 19.9710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.4190 13.2930 19.2740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.6450 13.8320 18.3200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.4810 13.2870 17.9980 N 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0290 12.1840 18.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7860 11.6150 18.3040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3430 10.5040 18.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1080 9.9180 19.9810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.3250 10.4360 20.3200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8200 11.5870 19.6640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.1160 14.9710 17.6690 N 0 0 0 0 0 0 0 0 0 0 0 0 + 27.3480 16.1150 18.5710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.6660 17.2890 17.6050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.8670 16.9430 16.3140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3130 15.5200 16.5590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 1 0 + 4 2 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 11 10 2 0 + 12 11 1 0 + 13 12 2 0 + 13 8 1 0 + 13 4 1 0 + 14 6 1 0 + 15 14 1 0 + 16 15 1 0 + 17 16 1 0 + 18 14 1 0 + 18 17 1 0 +M END +$$$$ |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/sucos_cluster.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sucos_cluster.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| b'@@ -0,0 +1,1384 @@\n+\n+ RDKit 3D\n+\n+ 19 20 0 0 0 0 0 0 0 0999 V2000\n+ 25.8690 10.6750 17.9260 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.7660 11.4770 18.5500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1650 12.4880 17.8120 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1480 13.2570 18.3640 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.7300 13.0010 19.6620 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6190 13.8450 20.2480 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.3280 11.9670 20.4090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.9000 11.7560 21.6900 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1990 10.4520 22.2010 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3800 10.3250 23.4930 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 22.7510 9.1510 24.2170 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5930 11.5910 24.3570 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.2540 11.3630 25.7760 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5710 12.5910 26.5330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.1760 12.4110 28.0100 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.7810 12.0710 28.1350 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.5060 10.8660 27.4060 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.8170 11.0700 25.9210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.3600 11.2090 19.8480 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 2 0\n+ 4 3 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 7 5 1 0\n+ 8 7 1 0\n+ 9 8 1 0\n+ 10 9 1 0\n+ 10 11 1 1\n+ 12 10 1 0\n+ 13 12 1 0\n+ 14 13 1 0\n+ 15 14 1 0\n+ 16 15 1 0\n+ 17 16 1 0\n+ 18 17 1 0\n+ 18 13 1 0\n+ 19 7 2 0\n+ 19 2 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 12 0 0 0 0 0 0 0 0999 V2000\n+ 22.8090 9.2070 24.2800 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4710 10.1080 23.3190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8900 9.6340 22.1960 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.5680 10.5170 21.2440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7580 11.8790 21.3690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3130 12.3920 22.5320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5210 13.7530 22.7260 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0810 14.2110 23.9020 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.4470 13.3190 24.8860 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.2450 11.9700 24.7110 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6750 11.4850 23.5440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 2 0\n+ 4 3 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 7 6 2 0\n+ 8 7 1 0\n+ 9 8 2 0\n+ 10 9 1 0\n+ 11 2 1 0\n+ 11 10 2 0\n+ 11 6 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 12 0 0 0 0 0 0 0 0999 V2000\n+ 22.7770 9.1670 24.9740 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.4280 10.0140 24.0880 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6770 11.3690 24.2670 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.2930 12.2600 23.2950 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6430 11.7880 22.1650 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.2220 12.6270 21.1460 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.5740 12.1120 20.0440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.3400 10.7540 19.9450 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 20.7580 9.9010 20.9470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.4090 10.3980 22.0610 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.7960 9.5320 23.0070 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 2 0\n+ 4 3 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 7 6 2 0\n+ 8 7 1 0\n+ 9 8 2 0\n+ 10 9 1 0\n+ 10 5 1 0\n+ 11 10 2 0\n+ 11 2 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 15 16 0 0 0 0 0 0 0 0999 V2000\n+ 22.4510 9.0090 24.4670 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5180 10.3550 24.1060 C 0 0 0 0 0 0 0 0 0 0'..b' 0 0 0\n+ 22.2050 9.8930 22.6900 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0060 12.0970 24.2220 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8910 10.6980 21.5060 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 22.8690 9.5480 24.8150 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.4800 12.1250 21.9040 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5630 12.8770 22.6580 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.6270 10.3910 23.7940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1060 10.7640 20.5410 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.3720 10.2320 20.8590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.4690 10.3640 20.0140 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.3420 11.0350 18.7800 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1030 11.5640 18.3850 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.0130 11.4340 19.2760 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.8840 12.0230 18.8800 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.4280 11.2380 18.0020 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4 1 1 6\n+ 4 2 1 0\n+ 6 4 1 0\n+ 7 6 1 0\n+ 7 3 1 0\n+ 8 5 1 0\n+ 8 2 2 0\n+ 8 3 1 0\n+ 9 4 1 0\n+ 10 9 2 0\n+ 11 10 1 0\n+ 12 11 2 0\n+ 13 12 1 0\n+ 14 9 1 0\n+ 14 13 2 0\n+ 15 14 1 0\n+ 16 12 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 11 12 0 0 0 0 0 0 0 0999 V2000\n+ 23.8920 10.9750 19.7100 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.1430 9.6540 19.8400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.7820 11.7530 20.9950 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.6770 9.8870 20.1680 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.1750 12.7870 22.6090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3660 10.1400 23.6660 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.3180 11.9530 21.3510 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 21.5250 10.6490 21.4640 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 22.7380 9.3100 24.6900 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 21.9210 9.6990 22.5310 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 22.5620 11.8400 24.1130 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 1 1 0\n+ 4 2 1 0\n+ 7 3 1 1\n+ 7 5 1 0\n+ 8 4 1 6\n+ 8 7 1 0\n+ 9 6 1 0\n+ 10 8 1 0\n+ 10 6 2 0\n+ 11 6 1 0\n+ 11 5 1 0\n+M END\n+$$$$\n+\n+ RDKit 3D\n+\n+ 18 20 0 0 0 0 0 0 0 0999 V2000\n+ 28.6970 10.5240 20.4750 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.9220 11.6800 20.9560 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.7880 12.6650 21.6350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.0810 12.2010 19.9710 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.4190 13.2930 19.2740 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.6450 13.8320 18.3200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.4810 13.2870 17.9980 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.0290 12.1840 18.6310 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.7860 11.6150 18.3040 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 23.3430 10.5040 18.9720 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 24.1080 9.9180 19.9810 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.3250 10.4360 20.3200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 25.8200 11.5870 19.6640 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.1160 14.9710 17.6690 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.3480 16.1150 18.5710 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 27.6660 17.2890 17.6050 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.8670 16.9430 16.3140 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 26.3130 15.5200 16.5590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 0\n+ 3 2 1 0\n+ 4 2 1 0\n+ 5 4 2 0\n+ 6 5 1 0\n+ 7 6 2 0\n+ 8 7 1 0\n+ 9 8 2 0\n+ 10 9 1 0\n+ 11 10 2 0\n+ 12 11 1 0\n+ 13 12 2 0\n+ 13 8 1 0\n+ 13 4 1 0\n+ 14 6 1 0\n+ 15 14 1 0\n+ 16 15 1 0\n+ 17 16 1 0\n+ 18 14 1 0\n+ 18 17 1 0\n+M END\n+$$$$\n' |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/sucos_inputs.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sucos_inputs.sdf Wed Oct 02 12:57:54 2019 -0400 |
| b |
| b"@@ -0,0 +1,1420 @@\n+=\n+ OpenBabel06141912503D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 34.9890 -44.7290 75.3400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.7740 -44.3230 75.8900 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.5980 -44.5060 75.1780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.6020 -45.0920 73.9050 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.8400 -45.4880 73.3780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0250 -45.3160 74.0770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.3410 -45.2900 73.1330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.1700 -44.5940 73.4530 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.0040 -44.7840 72.7210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.9810 -45.6590 71.6540 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.1290 -46.3590 71.3190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.2960 -46.1720 72.0490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.1480 -44.5380 76.0590 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.4940 -44.7080 76.2650 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.3560 -44.2790 75.3520 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 37.3740 -42.7950 74.9960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.0060 -41.9850 75.8700 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.7410 -42.4950 73.8440 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0\n+ 1 13 1 0 0 0 0\n+ 3 2 2 0 0 0 0\n+ 4 3 1 0 0 0 0\n+ 5 4 2 0 0 0 0\n+ 5 6 1 0 0 0 0\n+ 6 1 2 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 7 4 1 0 0 0 0\n+ 9 8 2 0 0 0 0\n+ 10 9 1 0 0 0 0\n+ 11 10 2 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 12 7 2 0 0 0 0\n+ 15 13 1 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 16 15 1 0 0 0 0\n+ 16 17 1 0 0 0 0\n+ 18 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+1\n+\n+> <REMARK>\n+ VINA RESULT: -6.3 0.000 0.000\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-6.3\n+\n+> <RMSD_LB>\n+0.000\n+\n+> <RMSD_UB>\n+0.000\n+\n+$$$$\n+=\n+ OpenBabel06141912503D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 34.9980 -44.6860 75.3940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.0270 -45.2910 74.1380 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.8490 -45.4620 73.4270 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.6180 -45.0400 73.9450 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.6210 -44.4360 75.2110 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.7890 -44.2540 75.9350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.3460 -45.2230 73.1860 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.2400 -46.1600 72.1530 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.0470 -46.3240 71.4580 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.9380 -45.5680 71.7810 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 29.0210 -44.6340 72.8010 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.2120 -44.4670 73.4970 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.1760 -44.5260 76.0900 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.5270 -44.6480 76.2620 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.3680 -44.2480 75.3630 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 37.3510 -42.7680 74.9960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.9750 -41.9580 75.8670 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.7000 -42.4690 73.8370 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 6 1 0 0 0 0\n+ 1 13 1 0 0 0 0\n+ 2 1 2 0 0 0 0\n+ 3 4 2 0 0 0 0\n+ 3 2 1 0 0 0 0\n+ 4 5 1 0 0 0 0\n+ 5 6 2 0 0 0 0\n+ 7 12 1 0 0 0 0\n+ 7 4 1 0 0 0 0\n+ 8 7 2 0 "..b"0 0 0 0 0 0 0 0 0\n+ 30.4880 -42.4910 76.4360 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.5680 -44.7780 76.1370 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.0030 -45.7500 74.5340 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.1210 -44.5510 74.8450 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 37.8730 -43.2240 74.8910 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.2700 -42.2030 74.5030 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 39.0500 -43.2560 75.2990 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0 0 0 0\n+ 2 3 1 0 0 0 0\n+ 4 7 1 0 0 0 0\n+ 4 3 2 0 0 0 0\n+ 5 4 1 0 0 0 0\n+ 6 5 2 0 0 0 0\n+ 6 1 1 0 0 0 0\n+ 7 8 2 0 0 0 0\n+ 8 9 1 0 0 0 0\n+ 10 9 2 0 0 0 0\n+ 11 10 1 0 0 0 0\n+ 12 11 2 0 0 0 0\n+ 12 7 1 0 0 0 0\n+ 13 1 1 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 15 16 1 0 0 0 0\n+ 15 13 1 0 0 0 0\n+ 16 18 1 0 0 0 0\n+ 17 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+19\n+\n+> <REMARK>\n+ VINA RESULT: -4.4 3.044 4.158\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-4.4\n+\n+> <RMSD_LB>\n+3.044\n+\n+> <RMSD_UB>\n+4.158\n+\n+$$$$\n+=\n+ OpenBabel06141912503D\n+\n+ 18 19 0 0 1 0 0 0 0 0999 V2000\n+ 32.5500 -43.5500 76.7360 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 33.6520 -43.1880 77.5090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.9240 -43.5810 77.1230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 35.1310 -44.3420 75.9650 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 34.0020 -44.6910 75.2090 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 32.7230 -44.3040 75.5790 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.4970 -44.7690 75.5440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 37.5820 -43.8860 75.5740 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.8510 -44.2990 75.1850 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 39.0680 -45.5970 74.7690 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 38.0080 -46.4890 74.7300 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 36.7380 -46.0790 75.1180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 31.2920 -43.1540 77.1350 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.7500 -40.8560 77.1260 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 30.6100 -42.1680 76.3690 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 29.1670 -42.6320 76.1960 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.9380 -43.8550 76.2740 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 28.3130 -41.7520 75.9720 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 13 1 0 0 0 0\n+ 1 2 2 0 0 0 0\n+ 3 2 1 0 0 0 0\n+ 4 3 2 0 0 0 0\n+ 5 6 2 0 0 0 0\n+ 5 4 1 0 0 0 0\n+ 6 1 1 0 0 0 0\n+ 7 8 1 0 0 0 0\n+ 7 4 1 0 0 0 0\n+ 9 8 2 0 0 0 0\n+ 10 9 1 0 0 0 0\n+ 11 10 2 0 0 0 0\n+ 11 12 1 0 0 0 0\n+ 12 7 2 0 0 0 0\n+ 15 14 1 1 0 0 0\n+ 15 13 1 0 0 0 0\n+ 16 17 1 0 0 0 0\n+ 16 15 1 0 0 0 0\n+ 18 16 2 0 0 0 0\n+M END\n+> <MODEL>\n+20\n+\n+> <REMARK>\n+ VINA RESULT: -4.4 3.679 6.880\n+ Name = \n+ 5 active torsions:\n+ status: ('A' for Active; 'I' for Inactive)\n+ 1 A between atoms: C_1 and C_8\n+ 2 A between atoms: C_2 and C_13\n+ 3 A between atoms: C_8 and C_9\n+ 4 A between atoms: C_8 and O_18\n+ 5 A between atoms: C_10 and O_18\n+ x y z vdW Elec q Type\n+ _______ _______ _______ _____ _____ ______ ____\n+\n+> <TORSDO>\n+F 4\n+\n+> <SCORE>\n+-4.4\n+\n+> <RMSD_LB>\n+3.679\n+\n+> <RMSD_UB>\n+6.880\n+\n+$$$$\n" |
| b |
| diff -r 000000000000 -r bb5365381c8f test-data/sucos_refmol.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sucos_refmol.mol Wed Oct 02 12:57:54 2019 -0400 |
| b |
| @@ -0,0 +1,43 @@ + + OpenBabel06051719483D + + 18 19 0 0 0 0 2 V2000 + 29.0700 -43.2240 73.7660 C 0 0 0 0 0 + 36.2650 -44.8070 74.9140 C 0 0 0 0 0 + 37.1260 -44.6280 73.8270 C 0 0 0 0 0 + 38.5050 -44.6030 73.9960 C 0 0 0 0 0 + 39.0530 -44.7650 75.2580 C 0 0 0 0 0 + 38.2200 -44.9420 76.3450 C 0 0 0 0 0 + 36.8400 -44.9680 76.1790 C 0 0 0 0 0 + 30.0630 -44.1750 73.1160 C 0 0 0 0 0 + 29.4310 -45.1480 72.1250 C 0 0 0 0 0 + 32.0050 -44.9160 74.3360 C 0 0 0 0 0 + 32.8370 -45.6680 73.5100 C 0 0 0 0 0 + 34.2080 -45.6230 73.7110 C 0 0 0 0 0 + 34.7860 -44.8390 74.7200 C 0 0 0 0 0 + 33.9230 -44.0930 75.5330 C 0 0 0 0 0 + 32.5490 -44.1280 75.3490 C 0 0 0 0 0 + 30.2050 -45.7640 71.3670 O 0 0 0 0 0 + 28.1910 -45.2760 72.1490 O 0 0 0 0 0 + 30.6380 -44.9430 74.1670 O 0 0 0 0 0 + 1 8 1 0 0 0 + 2 3 2 0 0 0 + 2 7 1 0 0 0 + 2 13 1 0 0 0 + 3 4 1 0 0 0 + 4 5 2 0 0 0 + 5 6 1 0 0 0 + 6 7 2 0 0 0 + 8 9 1 0 0 0 + 8 18 1 0 0 0 + 9 16 2 0 0 0 + 9 17 1 0 0 0 + 10 11 2 0 0 0 + 10 15 1 0 0 0 + 10 18 1 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 + 13 14 1 0 0 0 + 14 15 2 0 0 0 +M CHG 1 17 -1 +M END |
| b |
| diff -r 000000000000 -r bb5365381c8f utils.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils.py Wed Oct 02 12:57:54 2019 -0400 |
| b |
| @@ -0,0 +1,49 @@ +#!/usr/bin/env python +""" +Utility functions for SuCOS and other RDKit modules +""" + +from __future__ import print_function +import sys, gzip +from rdkit import Chem + +def log(*args, **kwargs): + """Log output to STDERR + """ + print(*args, file=sys.stderr, **kwargs) + +def open_file_for_reading(filename): + """Open the file gunzipping it if it ends with .gz.""" + if filename.lower().endswith('.gz'): + return gzip.open(filename, 'rb') + else: + return open(filename, 'rb') + +def open_file_for_writing(filename): + if filename.lower().endswith('.gz'): + return gzip.open(filename, 'at') + else: + return open(filename, 'w+') + +def read_single_molecule(filename, index=1, format=None): + """Read a single molecule as a RDKit Mol object. This can come from a file in molfile or SDF format. + If SDF then you can also specify an index of the molecule that is read (default is the first) + """ + mol = None + if format == 'mol' or filename.lower().endswith('.mol') or filename.lower().endswith('.mol.gz'): + file = open_file_for_reading(filename) + mol = Chem.MolFromMolBlock(file.read()) + file.close() + elif format == 'sdf' or filename.lower().endswith('.sdf') or filename.lower().endswith('.sdf.gz'): + file = open_file_for_reading(filename) + supplier = Chem.ForwardSDMolSupplier(file) + for i in range(0,index): + if supplier.atEnd(): + break + mol = next(supplier) + file.close() + + if not mol: + raise ValueError("Unable to read molecule") + + return mol \ No newline at end of file |