# HG changeset patch # User bgruening # Date 1570035474 14400 # Node ID bb5365381c8f72108a63febf7c4427878d7df943 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645" 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 @@ -0,0 +1,202 @@ +#!/usr/bin/env python +""" +Basic SuCOS scoring. Allows a set of molecules from a SD file to be overlayed to a reference molecule, +with the resulting scores being written as properties in the output SD file. + +SuCOS is the work of Susan Leung. +GitHub: https://github.com/susanhleung/SuCOS +Publication: https://doi.org/10.26434/chemrxiv.8100203.v1 +""" + +from __future__ import print_function +import argparse, os, sys, gzip +import numpy as np +from rdkit import Chem, rdBase, RDConfig +from rdkit.Chem import AllChem, rdShapeHelpers +from rdkit.Chem.FeatMaps import FeatMaps +import utils + + +### start function definitions ######################################### + +# Setting up the features to use in FeatureMap +fdef = AllChem.BuildFeatureFactory(os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef')) + +fmParams = {} +for k in fdef.GetFeatureFamilies(): + fparams = FeatMaps.FeatMapParams() + fmParams[k] = fparams + +keep = ('Donor', 'Acceptor', 'NegIonizable', 'PosIonizable', 'ZnBinder', + 'Aromatic', 'Hydrophobe', 'LumpedHydrophobe') + +def filterFeature(f): + result = f.GetFamily() in keep + # TODO - nothing ever seems to be filtered. Is this expected? + if not result: + utils.log("Filtered out feature type", f.GetFamily()) + return result + +def getRawFeatures(mol): + + rawFeats = fdef.GetFeaturesForMol(mol) + # filter that list down to only include the ones we're interested in + filtered = list(filter(filterFeature, rawFeats)) + return filtered + +def get_FeatureMapScore(small_feats, large_feats, tani=False, score_mode=FeatMaps.FeatMapScoreMode.All): + """ + Generate the feature map score. + + :param small_feats: + :param large_feats: + :param tani: + :return: + """ + + featLists = [] + for rawFeats in [small_feats, large_feats]: + # filter that list down to only include the ones we're interested in + featLists.append(rawFeats) + fms = [FeatMaps.FeatMap(feats=x, weights=[1] * len(x), params=fmParams) for x in featLists] + # set the score mode + fms[0].scoreMode = score_mode + + try: + if tani: + c = fms[0].ScoreFeats(featLists[1]) + A = fms[0].GetNumFeatures() + B = len(featLists[1]) + if B != fms[1].GetNumFeatures(): + utils.log("Why isn't B equal to number of features...?!") + tani_score = float(c) / (A+B-c) + return tani_score + else: + fm_score = fms[0].ScoreFeats(featLists[1]) / min(fms[0].GetNumFeatures(), len(featLists[1])) + return fm_score + except ZeroDivisionError: + utils.log("ZeroDivisionError") + return 0 + + if tani: + tani_score = float(c) / (A+B-c) + return tani_score + else: + fm_score = fms[0].ScoreFeats(featLists[1]) / min(fms[0].GetNumFeatures(), len(featLists[1])) + return fm_score + + +def get_SucosScore(ref_mol, query_mol, tani=False, ref_features=None, query_features=None, score_mode=FeatMaps.FeatMapScoreMode.All): + """ + This is the key function that calculates the SuCOS scores and is expected to be called from other modules. + To improve performance you can pre-calculate the features and pass them in as optional parameters to avoid having + to recalculate them. Use the getRawFeatures function to pre-calculate the features. + + :param ref_mol: The reference molecule to compare to + :param query_mol: The molecule to align to the reference + :param tani: Whether to calculate Tanimoto distances + :param ref_features: An optional feature map for the reference molecule, avoiding the need to re-calculate it. + :param query_features: An optional feature map for the query molecule, avoiding the need to re-calculate it. + :return: A tuple of 3 values. 1 the sucos score, 2 the feature map score, + 3 the Tanimoto distance or 1 minus the protrude distance + """ + + if not ref_features: + ref_features = getRawFeatures(ref_mol) + if not query_features: + query_features = getRawFeatures(query_mol) + + fm_score = get_FeatureMapScore(ref_features, query_features, tani, score_mode) + fm_score = np.clip(fm_score, 0, 1) + + if tani: + tani_sim = 1 - float(rdShapeHelpers.ShapeTanimotoDist(ref_mol, query_mol)) + tani_sim = np.clip(tani_sim, 0, 1) + SuCOS_score = 0.5*fm_score + 0.5*tani_sim + return SuCOS_score, fm_score, tani_sim + else: + protrude_dist = rdShapeHelpers.ShapeProtrudeDist(ref_mol, query_mol, allowReordering=False) + protrude_dist = np.clip(protrude_dist, 0, 1) + protrude_val = 1.0 - protrude_dist + SuCOS_score = 0.5 * fm_score + 0.5 * protrude_val + return SuCOS_score, fm_score, protrude_val + +def process(refmol_filename, inputs_filename, outputs_filename, refmol_index=None, + refmol_format=None, tani=False, score_mode=FeatMaps.FeatMapScoreMode.All): + + ref_mol = utils.read_single_molecule(refmol_filename, index=refmol_index, format=refmol_format) + #utils.log("Reference mol has", ref_mol.GetNumHeavyAtoms(), "heavy atoms") + ref_features = getRawFeatures(ref_mol) + + input_file = utils.open_file_for_reading(inputs_filename) + suppl = Chem.ForwardSDMolSupplier(input_file) + output_file = utils.open_file_for_writing(outputs_filename) + writer = Chem.SDWriter(output_file) + + count = 0 + total = 0 + errors = 0 + for mol in suppl: + count +=1 + if mol is None: + continue + #utils.log("Mol has", str(mol.GetNumHeavyAtoms()), "heavy atoms") + try: + sucos_score, fm_score, val3 = get_SucosScore(ref_mol, mol, tani=tani, ref_features=ref_features, score_mode=score_mode) + mol.SetDoubleProp("SuCOS_Score", sucos_score) + mol.SetDoubleProp("SuCOS_FeatureMap_Score", fm_score) + if tani: + mol.SetDoubleProp("SuCOS_Tanimoto_Score", val3) + else: + mol.SetDoubleProp("SuCOS_Protrude_Score", val3) + utils.log("Scores:", sucos_score, fm_score, val3) + writer.write(mol) + total +=1 + except ValueError as e: + errors +=1 + utils.log("Molecule", count, "failed to score:", e.message) + + input_file.close() + writer.flush() + writer.close() + output_file.close() + + utils.log("Completed.", total, "processed, ", count, "succeeded, ", errors, "errors") + +def parse_score_mode(value): + if value == None or value == 'all': + return FeatMaps.FeatMapScoreMode.All + elif value == 'closest': + return FeatMaps.FeatMapScoreMode.Closest + elif value == 'best': + return FeatMaps.FeatMapScoreMode.Best + else: + raise ValueError(value + " is not a valid scoring mode option") + + +### start main execution ######################################### + +def main(): + + parser = argparse.ArgumentParser(description='SuCOS with RDKit') + parser.add_argument('-i', '--input', help='Input file in SDF format. Can be gzipped (*.gz).') + parser.add_argument('-r', '--refmol', help='Molecule to compare against in Molfile (.mol) or SDF (.sdf) format') + parser.add_argument('--refmol-format', help="Format for the reference molecule (mol or sdf). " + + "Only needed if files don't have the expected extensions") + parser.add_argument('--refmolidx', help='Reference molecule index in SD file if not the first', type=int, default=1) + parser.add_argument('-o', '--output', help='Output file in SDF format. Can be gzipped (*.gz).') + parser.add_argument('--tanimoto', action='store_true', help='Include Tanimoto distance in score') + parser.add_argument('--score_mode', choices=['all', 'closest', 'best'], + help="choose the scoring mode for the feature map, default is 'all'.") + + args = parser.parse_args() + utils.log("SuCOS Args: ", args) + + score_mode = parse_score_mode(args.score_mode) + + process(args.refmol, args.input, args.output, refmol_index=args.refmolidx, + refmol_format=args.refmol_format, tani=args.tanimoto, score_mode=score_mode) + + +if __name__ == "__main__": + main() 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 @@ -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 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 @@ -0,0 +1,19 @@ + + + + 10.26434/chemrxiv.8100203.v1 + + @article{rdkit, + author = {Greg Landrum and others}, + title = {RDKit: Open-source cheminformatics}, + url ={http://www.rdkit.org} + } + + + + + rdkit + + + + 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 @@ -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 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 @@ -0,0 +1,85 @@ + + - determine maximum SuCOS score of ligands against clustered fragment hits + + sucos_macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 @@ -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 +$$$$ + + RDKit 3D + + 15 16 0 0 0 0 0 0 0 0999 V2000 + 18.6370 11.5460 19.0470 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 19.3410 11.4910 20.6100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.1300 12.5410 21.5090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.1120 10.3920 20.9640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.7080 12.5060 22.7780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.6710 10.3800 22.2200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.4820 11.4070 23.1080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.4530 9.4460 22.7560 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7320 9.9040 23.9840 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.1510 11.1000 24.2190 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5310 9.1910 24.8790 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.2170 11.9110 25.4550 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.4620 11.2450 26.6090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.0350 11.5770 27.9760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.9480 12.9640 28.2400 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 2 1 0 + 5 3 1 0 + 6 4 2 0 + 7 6 1 0 + 7 5 2 0 + 8 6 1 0 + 9 8 2 0 + 10 9 1 0 + 10 7 1 0 + 11 9 1 0 + 12 10 1 0 + 13 12 1 0 + 14 13 1 0 + 15 14 1 0 +M END +$$$$ diff -r 000000000000 -r bb5365381c8f test-data/cluster2.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster2.sdf Wed Oct 02 12:57:54 2019 -0400 @@ -0,0 +1,167 @@ + + RDKit 3D + + 10 10 0 0 0 0 0 0 0 0999 V2000 + 24.4730 11.1990 19.8620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.5530 12.0600 20.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.9840 11.0460 18.5670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.8330 10.4330 20.9970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.1360 12.7690 19.0380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.5550 11.7420 17.5050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3160 10.6870 21.0270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.6290 12.6010 17.7470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6740 10.0940 22.2270 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.1850 13.2880 16.6940 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 1 1 0 + 4 1 1 0 + 5 2 1 0 + 6 3 2 0 + 7 4 1 0 + 8 6 1 0 + 8 5 2 0 + 9 7 1 0 + 10 8 1 0 +M END +$$$$ + + RDKit 3D + + 11 11 0 0 0 0 0 0 0 0999 V2000 + 23.8350 12.2020 19.5760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.4520 11.9220 18.2610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0420 12.8700 19.8340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9370 11.8100 20.7250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.2680 12.2940 17.1940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8750 13.2520 18.7790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8350 10.2970 20.9620 C 0 0 1 0 0 0 0 0 0 0 0 0 + 25.4680 12.9560 17.4710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1570 9.7480 21.5040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7030 9.9910 21.9220 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.2630 13.3220 16.4230 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 1 1 0 + 4 1 1 0 + 5 2 1 0 + 6 3 2 0 + 7 4 1 0 + 8 6 1 0 + 8 5 2 0 + 7 9 1 1 + 10 7 1 0 + 11 8 1 0 +M END +$$$$ + + RDKit 3D + + 12 12 0 0 0 0 0 0 0 0999 V2000 + 26.5880 11.6480 19.1670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.9260 11.0670 20.2530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8770 11.8420 17.9690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.0300 12.0720 19.2730 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.5820 10.6900 20.1310 C 0 0 0 0 0 0 0 0 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O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3630 13.3270 20.6990 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.8080 10.8590 20.6700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.5890 11.0260 18.6540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3960 9.8840 20.9090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.7810 12.1210 21.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.0220 10.5180 21.1760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.2950 9.8120 22.2580 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 1 2 0 + 4 1 1 0 + 5 2 1 0 + 6 2 1 0 + 7 3 1 0 + 8 4 2 0 + 9 4 1 0 + 10 5 1 0 + 11 6 1 0 + 12 7 2 0 + 12 8 1 0 + 13 7 1 0 + 14 11 1 0 + 14 10 1 0 + 15 13 1 0 + 16 15 1 0 +M END +$$$$ + + RDKit 3D + + 18 20 0 0 0 0 0 0 0 0999 V2000 + 28.6970 10.5240 20.4750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.9220 11.6800 20.9560 N 0 0 0 0 0 0 0 0 0 0 0 0 + 28.7880 12.6650 21.6350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.0810 12.2010 19.9710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.4190 13.2930 19.2740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.6450 13.8320 18.3200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.4810 13.2870 17.9980 N 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0290 12.1840 18.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.7860 11.6150 18.3040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3430 10.5040 18.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1080 9.9180 19.9810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.3250 10.4360 20.3200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8200 11.5870 19.6640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.1160 14.9710 17.6690 N 0 0 0 0 0 0 0 0 0 0 0 0 + 27.3480 16.1150 18.5710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.6660 17.2890 17.6050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.8670 16.9430 16.3140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3130 15.5200 16.5590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 1 0 + 4 2 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 11 10 2 0 + 12 11 1 0 + 13 12 2 0 + 13 8 1 0 + 13 4 1 0 + 14 6 1 0 + 15 14 1 0 + 16 15 1 0 + 17 16 1 0 + 18 14 1 0 + 18 17 1 0 +M END +$$$$ diff -r 000000000000 -r bb5365381c8f test-data/cluster3.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster3.sdf Wed Oct 02 12:57:54 2019 -0400 @@ -0,0 +1,1024 @@ + + RDKit 3D + + 19 20 0 0 0 0 0 0 0 0999 V2000 + 25.8690 10.6750 17.9260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.7660 11.4770 18.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1650 12.4880 17.8120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1480 13.2570 18.3640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7300 13.0010 19.6620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6190 13.8450 20.2480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3280 11.9670 20.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9000 11.7560 21.6900 O 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1990 10.4520 22.2010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3800 10.3250 23.4930 C 0 0 1 0 0 0 0 0 0 0 0 0 + 22.7510 9.1510 24.2170 O 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5930 11.5910 24.3570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2540 11.3630 25.7760 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5710 12.5910 26.5330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1760 12.4110 28.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.7810 12.0710 28.1350 O 0 0 0 0 0 0 0 0 0 0 0 0 + 20.5060 10.8660 27.4060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.8170 11.0700 25.9210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3600 11.2090 19.8480 C 0 0 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END +$$$$ + + RDKit 3D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 22.7770 9.1670 24.9740 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4280 10.0140 24.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6770 11.3690 24.2670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2930 12.2600 23.2950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6430 11.7880 22.1650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.2220 12.6270 21.1460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.5740 12.1120 20.0440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.3400 10.7540 19.9450 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.7580 9.9010 20.9470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.4090 10.3980 22.0610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7960 9.5320 23.0070 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 2 0 + 10 9 1 0 + 10 5 1 0 + 11 10 2 0 + 11 2 1 0 +M END +$$$$ + + RDKit 3D + + 15 16 0 0 0 0 0 0 0 0999 V2000 + 22.4510 9.0090 24.4670 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5180 10.3550 24.1060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9990 11.2350 24.9790 N 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1030 12.5320 24.7160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7060 13.0330 23.4860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1940 12.1570 22.5380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.0810 10.8000 22.8500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5800 9.9040 21.8960 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.5550 10.3020 20.4800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9570 10.4800 19.9210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.0930 10.2030 20.6880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.3650 10.3660 20.1600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.5090 10.8070 18.8530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3830 11.0830 18.0860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1090 10.9240 18.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 2 2 0 + 4 3 1 0 + 5 4 2 0 + 6 5 1 0 + 7 2 1 0 + 7 6 2 0 + 8 7 1 0 + 9 8 1 0 + 10 9 1 0 + 11 10 2 0 + 12 11 1 0 + 13 12 2 0 + 14 13 1 0 + 15 10 1 0 + 15 14 2 0 +M END +$$$$ + + RDKit 3D + + 14 15 0 0 0 0 0 0 0 0999 V2000 + 25.2210 12.3240 18.0720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.2950 10.9960 18.4640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3010 10.4520 19.2480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.2220 11.2280 19.6570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1370 10.6280 20.5110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4080 10.7370 21.9940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.4270 9.8630 22.7750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7420 9.8660 24.2600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1460 9.4340 24.4920 N 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1030 10.3610 23.8220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.8510 10.3500 22.3260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1570 12.5620 19.2690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1500 13.1090 18.4810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.1900 12.8500 17.2940 F 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 2 1 0 + 4 3 2 0 + 5 4 1 0 + 6 5 1 0 + 7 6 1 0 + 8 7 1 0 + 9 8 1 0 + 10 9 1 0 + 11 10 1 0 + 11 6 1 0 + 12 4 1 0 + 13 12 2 0 + 13 1 1 0 + 14 1 1 0 +M END +$$$$ + + RDKit 3D + + 18 20 0 0 0 0 0 0 0 0999 V2000 + 22.7740 9.2060 24.7160 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6730 10.1680 23.8290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6480 11.5040 24.2160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5410 12.4950 23.2640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.4360 12.1560 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9.3460 24.4820 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7870 10.6500 24.1630 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.0810 11.5110 25.1640 N 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1550 12.8130 24.8620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9370 13.3140 23.5950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6290 12.4490 22.5700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5360 11.0880 22.8330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2030 10.1450 21.8580 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.9100 10.4610 20.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1110 10.8820 19.6530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9310 11.3890 18.3770 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.0150 11.7690 17.6140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.2920 11.6680 18.1200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.5080 11.1670 19.3990 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.4040 10.7800 20.1590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.8870 11.0930 19.9590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.8330 12.0650 19.6660 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.0910 11.9730 20.2180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3740 10.9330 21.0780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.4890 9.9800 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25.2010 11.1170 19.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7570 12.0240 18.8700 F 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3200 11.2980 18.4090 F 0 0 0 0 0 0 0 0 0 0 0 0 + 3 1 1 0 + 5 1 1 0 + 7 3 1 0 + 9 8 2 0 + 10 9 1 0 + 11 8 1 0 + 12 7 1 0 + 12 8 1 6 + 12 2 1 0 + 13 12 1 0 + 13 5 1 1 + 14 13 1 0 + 14 4 1 0 + 15 6 1 0 + 15 2 2 0 + 15 4 1 0 + 16 11 2 0 + 17 10 2 0 + 17 16 1 0 + 18 11 1 0 + 19 17 1 0 +M END +$$$$ + + RDKit 3D + + 16 17 0 0 0 0 0 0 0 0999 V2000 + 20.6950 9.9560 20.8820 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2050 9.8930 22.6900 N 0 0 0 0 0 0 0 0 0 0 0 0 + 23.0060 12.0970 24.2220 S 0 0 0 0 0 0 0 0 0 0 0 0 + 21.8910 10.6980 21.5060 C 0 0 2 0 0 0 0 0 0 0 0 0 + 22.8690 9.5480 24.8150 N 0 0 0 0 0 0 0 0 0 0 0 0 + 21.4800 12.1250 21.9040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5630 12.8770 22.6580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6270 10.3910 23.7940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1060 10.7640 20.5410 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3720 10.2320 20.8590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.4690 10.3640 20.0140 C 0 0 0 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9.6990 22.5310 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5620 11.8400 24.1130 S 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 + 3 1 1 0 + 4 2 1 0 + 7 3 1 1 + 7 5 1 0 + 8 4 1 6 + 8 7 1 0 + 9 6 1 0 + 10 8 1 0 + 10 6 2 0 + 11 6 1 0 + 11 5 1 0 +M END +$$$$ diff -r 000000000000 -r bb5365381c8f test-data/cluster4.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster4.sdf Wed Oct 02 12:57:54 2019 -0400 @@ -0,0 +1,47 @@ + + RDKit 3D + + 20 21 0 0 0 0 0 0 0 0999 V2000 + 21.2480 11.2160 24.5450 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.1020 11.0880 25.9790 N 0 0 0 0 0 0 0 0 0 0 0 0 + 20.1520 11.7400 26.6430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.2750 12.3940 26.0980 O 0 0 0 0 0 0 0 0 0 0 0 0 + 20.2050 11.6230 28.1500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.1270 12.9990 28.8020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.9520 13.0380 30.0790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.6540 13.4720 29.6460 S 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7090 11.4410 24.1690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8180 11.5780 22.6520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3510 10.3050 22.0930 N 0 0 0 0 0 0 0 0 0 0 0 0 + 20.9200 10.1140 22.3280 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.7360 9.9660 23.8360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5750 10.2440 20.6540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.9890 10.6020 20.2540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0820 9.9220 20.7960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.3780 10.2710 20.4140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 26.5780 11.2950 19.4850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.4840 11.9720 18.9430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1890 11.6250 19.3240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 3 2 1 0 + 4 3 2 0 + 5 3 1 0 + 6 5 1 0 + 7 6 1 0 + 8 7 1 0 + 9 1 1 0 + 10 9 1 0 + 11 10 1 0 + 12 11 1 0 + 13 12 1 0 + 13 1 1 0 + 14 11 1 0 + 15 14 1 0 + 16 15 2 0 + 17 16 1 0 + 18 17 2 0 + 19 18 1 0 + 20 15 1 0 + 20 19 2 0 +M END +$$$$ 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 @@ -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 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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 @@ -0,0 +1,389 @@ + + RDKit 3D + + 19 20 0 0 0 0 0 0 0 0999 V2000 + 25.8690 10.6750 17.9260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.7660 11.4770 18.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1650 12.4880 17.8120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1480 13.2570 18.3640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7300 13.0010 19.6620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6190 13.8450 20.2480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3280 11.9670 20.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9000 11.7560 21.6900 O 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1990 10.4520 22.2010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3800 10.3250 23.4930 C 0 0 1 0 0 0 0 0 0 0 0 0 + 22.7510 9.1510 24.2170 O 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5930 11.5910 24.3570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2540 11.3630 25.7760 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5710 12.5910 26.5330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1760 12.4110 28.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 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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 +$$$$ + + RDKit 3D + + 20 21 0 0 0 0 0 0 0 0999 V2000 + 23.0110 10.6350 19.8150 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.2670 11.1650 19.1280 C 0 0 0 0 0 0 0 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Wed Oct 02 12:57:54 2019 -0400 @@ -0,0 +1,385 @@ + + RDKit 3D + + 11 11 0 0 0 0 0 0 0 0999 V2000 + 23.8350 12.2020 19.5760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.4520 11.9220 18.2610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.0420 12.8700 19.8340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9370 11.8100 20.7250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.2680 12.2940 17.1940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8750 13.2520 18.7790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.8350 10.2970 20.9620 C 0 0 1 0 0 0 0 0 0 0 0 0 + 25.4680 12.9560 17.4710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1570 9.7480 21.5040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.7030 9.9910 21.9220 N 0 0 0 0 0 0 0 0 0 0 0 0 + 26.2630 13.3220 16.4230 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 + 3 1 1 0 + 4 1 1 0 + 5 2 1 0 + 6 3 2 0 + 7 4 1 0 + 8 6 1 0 + 8 5 2 0 + 7 9 1 1 + 10 7 1 0 + 11 8 1 0 +M END +$$$$ + + RDKit 3D + + 12 12 0 0 0 0 0 0 0 0999 V2000 + 26.5880 11.6480 19.1670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.9260 11.0670 20.2530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 25.8770 11.8420 17.9690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 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C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.6470 11.7740 26.7230 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.4310 12.1180 27.3830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 18.6170 13.1760 26.8780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 19.0220 13.8920 25.7120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.2380 13.5470 25.0530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3110 9.9210 20.9010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.0210 11.7480 19.1870 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.4670 11.0980 20.4450 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3 2 1 0 + 5 4 2 0 + 6 5 1 0 + 6 2 1 0 + 7 3 1 0 + 7 5 1 0 + 8 2 2 0 + 9 7 1 0 + 7 10 1 6 + 11 6 1 0 + 12 11 1 0 + 13 12 2 0 + 14 13 1 0 + 15 14 2 0 + 16 15 1 0 + 16 1 1 0 + 17 16 2 0 + 17 12 1 0 + 20 18 1 0 + 20 9 1 0 + 20 19 1 0 +M END +$$$$ 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 @@ -0,0 +1,399 @@ + + 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 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0 0999 V2000 + 25.8690 10.6750 17.9260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.7660 11.4770 18.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.1650 12.4880 17.8120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1480 13.2570 18.3640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.7300 13.0010 19.6620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 21.6190 13.8450 20.2480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 23.3280 11.9670 20.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.9000 11.7560 21.6900 O 0 0 0 0 0 0 0 0 0 0 0 0 + 23.1990 10.4520 22.2010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.3800 10.3250 23.4930 C 0 0 1 0 0 0 0 0 0 0 0 0 + 22.7510 9.1510 24.2170 O 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5930 11.5910 24.3570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.2540 11.3630 25.7760 N 0 0 0 0 0 0 0 0 0 0 0 0 + 22.5710 12.5910 26.5330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 22.1760 12.4110 28.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.7810 12.0710 28.1350 O 0 0 0 0 0 0 0 0 0 0 0 0 + 20.5060 10.8660 27.4060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 20.8170 11.0700 25.9210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 24.3600 11.2090 19.8480 C 0 0 0 0 0 0 0 0 0 0 0 0 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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 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+ 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 +$$$$ diff -r 000000000000 -r bb5365381c8f test-data/sucos_inputs.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sucos_inputs.sdf Wed Oct 02 12:57:54 2019 -0400 @@ -0,0 +1,1420 @@ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 34.9890 -44.7290 75.3400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.7740 -44.3230 75.8900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.5980 -44.5060 75.1780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6020 -45.0920 73.9050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.8400 -45.4880 73.3780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.0250 -45.3160 74.0770 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3410 -45.2900 73.1330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.1700 -44.5940 73.4530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.0040 -44.7840 72.7210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.9810 -45.6590 71.6540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.1290 -46.3590 71.3190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.2960 -46.1720 72.0490 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.1480 -44.5380 76.0590 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.4940 -44.7080 76.2650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.3560 -44.2790 75.3520 C 0 0 2 0 0 0 0 0 0 0 0 0 + 37.3740 -42.7950 74.9960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.0060 -41.9850 75.8700 O 0 0 0 0 0 0 0 0 0 0 0 0 + 37.7410 -42.4950 73.8440 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 13 1 0 0 0 0 + 3 2 2 0 0 0 0 + 4 3 1 0 0 0 0 + 5 4 2 0 0 0 0 + 5 6 1 0 0 0 0 + 6 1 2 0 0 0 0 + 7 8 1 0 0 0 0 + 7 4 1 0 0 0 0 + 9 8 2 0 0 0 0 + 10 9 1 0 0 0 0 + 11 10 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 7 2 0 0 0 0 + 15 13 1 0 0 0 0 + 15 14 1 1 0 0 0 + 16 15 1 0 0 0 0 + 16 17 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +1 + +> + VINA RESULT: -6.3 0.000 0.000 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-6.3 + +> +0.000 + +> +0.000 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 34.9980 -44.6860 75.3940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.0270 -45.2910 74.1380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.8490 -45.4620 73.4270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6180 -45.0400 73.9450 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6210 -44.4360 75.2110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.7890 -44.2540 75.9350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3460 -45.2230 73.1860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.2400 -46.1600 72.1530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0470 -46.3240 71.4580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.9380 -45.5680 71.7810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.0210 -44.6340 72.8010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.2120 -44.4670 73.4970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.1760 -44.5260 76.0900 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5270 -44.6480 76.2620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.3680 -44.2480 75.3630 C 0 0 2 0 0 0 0 0 0 0 0 0 + 37.3510 -42.7680 74.9960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.9750 -41.9580 75.8670 O 0 0 0 0 0 0 0 0 0 0 0 0 + 37.7000 -42.4690 73.8370 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 1 0 0 0 0 + 1 13 1 0 0 0 0 + 2 1 2 0 0 0 0 + 3 4 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 7 12 1 0 0 0 0 + 7 4 1 0 0 0 0 + 8 7 2 0 0 0 0 + 9 10 2 0 0 0 0 + 9 8 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 + 15 13 1 0 0 0 0 + 15 14 1 1 0 0 0 + 16 15 1 0 0 0 0 + 16 17 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +2 + +> + VINA RESULT: -6.3 0.096 1.601 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-6.3 + +> +0.096 + +> +1.601 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 31.4230 -45.1380 73.6370 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7570 -44.3390 74.7290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0620 -44.3190 75.1960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0630 -45.0910 74.5930 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.6960 -45.8850 73.4970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.3970 -45.9160 73.0140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.4700 -45.0750 75.0910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.9310 -44.0690 75.9470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.2420 -44.0690 76.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.1150 -45.0730 76.0370 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.6800 -46.0790 75.1910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.3700 -46.0810 74.7270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.1210 -45.1500 73.1860 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3430 -43.3440 71.8790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.8600 -44.7730 71.8390 C 0 0 2 0 0 0 0 0 0 0 0 0 + 28.8640 -45.7760 71.2630 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.2180 -45.4370 70.2530 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.7530 -46.8660 71.8580 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 2 3 1 0 0 0 0 + 4 7 1 0 0 0 0 + 4 3 2 0 0 0 0 + 5 4 1 0 0 0 0 + 6 5 2 0 0 0 0 + 6 1 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 2 0 0 0 0 + 10 9 1 0 0 0 0 + 11 10 2 0 0 0 0 + 12 7 2 0 0 0 0 + 12 11 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 1 0 0 0 + 15 13 1 0 0 0 0 + 16 15 1 0 0 0 0 + 16 18 1 0 0 0 0 + 17 16 2 0 0 0 0 +M END +> +3 + +> + VINA RESULT: -5.8 3.643 7.155 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.8 + +> +3.643 + +> +7.155 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 31.4630 -45.3720 73.5650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.4550 -46.2290 73.0910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.7430 -46.1410 73.5970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0760 -45.2020 74.5810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0570 -44.3520 75.0360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7630 -44.4280 74.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.4600 -45.1010 75.1280 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.4440 -46.0410 74.8060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.7320 -45.9320 75.3180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.0680 -44.8840 76.1520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.1090 -43.9410 76.4850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.8200 -44.0480 75.9750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.1890 -45.4690 73.0500 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.3890 -44.4000 71.9580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.8690 -44.7380 71.8720 C 0 0 2 0 0 0 0 0 0 0 0 0 + 30.2370 -45.6090 70.6740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.7290 -46.7460 70.6060 O 0 0 0 0 0 0 0 0 0 0 0 0 + 31.0380 -45.1270 69.8500 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 1 0 0 0 0 + 2 1 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 4 7 1 0 0 0 0 + 6 5 2 0 0 0 0 + 7 12 1 0 0 0 0 + 8 7 2 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 10 11 1 0 0 0 0 + 12 11 2 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 1 0 0 0 + 15 13 1 0 0 0 0 + 16 15 1 0 0 0 0 + 17 16 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +4 + +> + VINA RESULT: -5.7 3.372 7.116 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.7 + +> +3.372 + +> +7.116 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 35.2710 -45.3020 74.6210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.2660 -45.6340 73.7140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9500 -45.2910 73.9860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6030 -44.6140 75.1620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.6370 -44.2950 76.0550 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9580 -44.6280 75.7980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.1890 -44.2430 75.4620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.6990 -44.2280 76.7720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.3810 -43.8750 77.0380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.5300 -43.5220 76.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.9940 -43.5300 74.7050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3100 -43.8830 74.4360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.5730 -45.6520 74.3380 O 0 0 0 0 0 0 0 0 0 0 0 0 + 37.6460 -44.0130 73.0210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.5810 -44.6500 74.4000 C 0 0 2 0 0 0 0 0 0 0 0 0 + 38.8790 -45.3250 74.8330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 39.6810 -44.6570 75.5150 O 0 0 0 0 0 0 0 0 0 0 0 0 + 39.0560 -46.5000 74.4570 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 2 0 0 0 0 + 2 3 2 0 0 0 0 + 2 1 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 7 1 0 0 0 0 + 4 5 2 0 0 0 0 + 6 5 1 0 0 0 0 + 7 8 2 0 0 0 0 + 8 9 1 0 0 0 0 + 10 9 2 0 0 0 0 + 11 10 1 0 0 0 0 + 12 11 2 0 0 0 0 + 12 7 1 0 0 0 0 + 13 15 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 6 0 0 0 + 15 16 1 0 0 0 0 + 16 17 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +5 + +> + VINA RESULT: -5.7 2.170 3.128 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.7 + +> +2.170 + +> +3.128 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 35.8300 -45.0340 75.6080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7490 -44.4320 76.2500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4970 -44.4470 75.6530 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2910 -45.0560 74.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3980 -45.6510 73.7880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6560 -45.6490 74.3700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9470 -45.0740 73.7610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.9600 -44.1410 74.0980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.7140 -44.1650 73.4820 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.4290 -45.1090 72.5160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3910 -46.0430 72.1670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.6370 -46.0220 72.7810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.0680 -45.0090 76.2120 O 0 0 0 0 0 0 0 0 0 0 0 0 + 37.3190 -42.7990 75.4190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.0480 -44.0980 75.7260 C 0 0 2 0 0 0 0 0 0 0 0 0 + 38.7110 -44.7390 74.5100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.7490 -44.0760 73.4540 O 0 0 0 0 0 0 0 0 0 0 0 0 + 39.1570 -45.8930 74.6530 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 13 1 0 0 0 0 + 1 2 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 2 0 0 0 0 + 5 6 2 0 0 0 0 + 5 4 1 0 0 0 0 + 6 1 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 4 1 0 0 0 0 + 9 8 2 0 0 0 0 + 10 9 1 0 0 0 0 + 11 10 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 7 2 0 0 0 0 + 15 14 1 6 0 0 0 + 15 13 1 0 0 0 0 + 16 18 1 0 0 0 0 + 16 15 1 0 0 0 0 + 17 16 2 0 0 0 0 +M END +> +6 + +> + VINA RESULT: -5.6 1.269 1.698 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.6 + +> +1.269 + +> +1.698 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 35.3500 -44.6860 75.6460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.6310 -45.1070 74.5280 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2600 -44.9060 74.4730 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.5720 -44.2870 75.5250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.3230 -43.8760 76.6360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.6950 -44.0660 76.7070 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.0970 -44.0690 75.4740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4150 -43.9690 74.2560 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.0400 -43.7730 74.2220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.3160 -43.6810 75.3950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.9710 -43.7770 76.6120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3460 -43.9730 76.6490 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.7110 -44.8950 75.6870 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5990 -45.5620 74.4350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.4950 -44.5230 74.5590 C 0 0 2 0 0 0 0 0 0 0 0 0 + 38.0030 -43.1040 74.7960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.1970 -42.1660 74.6420 O 0 0 0 0 0 0 0 0 0 0 0 0 + 39.2020 -42.9800 75.1140 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 13 1 0 0 0 0 + 1 6 2 0 0 0 0 + 2 1 1 0 0 0 0 + 3 2 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 5 6 1 0 0 0 0 + 7 4 1 0 0 0 0 + 7 12 2 0 0 0 0 + 8 7 1 0 0 0 0 + 9 8 2 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 15 14 1 1 0 0 0 + 15 16 1 0 0 0 0 + 15 13 1 0 0 0 0 + 16 18 1 0 0 0 0 + 17 16 2 0 0 0 0 +M END +> +7 + +> + VINA RESULT: -5.6 1.766 2.728 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.6 + +> +1.766 + +> +2.728 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 32.1440 -44.8920 74.5920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.7730 -44.3650 75.7190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1560 -44.3910 75.8130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9450 -44.9420 74.7950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.2830 -45.4660 73.6750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9010 -45.4450 73.5620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.4330 -44.9750 74.8910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.1490 -46.1670 74.7400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5370 -46.1830 74.8260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 39.2380 -45.0160 75.0540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5490 -43.8230 75.2060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.1620 -43.8040 75.1210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.7690 -44.8610 74.5140 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.8760 -43.5400 75.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.1310 -43.6400 74.1560 C 0 0 2 0 0 0 0 0 0 0 0 0 + 29.8570 -43.6840 72.6560 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.6580 -43.0940 71.9030 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.8370 -44.2960 72.2850 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 2 3 1 0 0 0 0 + 4 7 1 0 0 0 0 + 4 3 2 0 0 0 0 + 5 4 1 0 0 0 0 + 6 5 2 0 0 0 0 + 6 1 1 0 0 0 0 + 7 12 2 0 0 0 0 + 8 9 2 0 0 0 0 + 8 7 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 2 0 0 0 0 + 12 11 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 13 1 0 0 0 0 + 15 14 1 1 0 0 0 + 16 15 1 0 0 0 0 + 17 16 2 0 0 0 0 + 18 16 1 0 0 0 0 +M END +> +8 + +> + VINA RESULT: -5.5 3.099 6.864 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.5 + +> +3.099 + +> +6.864 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 34.0370 -44.1480 76.7170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8450 -43.4300 76.8020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.7400 -42.3700 77.6890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.8120 -42.0010 78.5130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9960 -42.7430 78.4050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1210 -43.8040 77.5210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.7050 -40.8620 79.4710 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.4630 -40.3800 79.8980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.3780 -39.3220 80.7960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.5230 -38.7310 81.2920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7630 -39.1920 80.8830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.8520 -40.2490 79.9850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1250 -45.2010 75.8320 O 0 0 0 0 0 0 0 0 0 0 0 0 + 33.6370 -45.8600 73.6180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4770 -44.9310 74.4800 C 0 0 2 0 0 0 0 0 0 0 0 0 + 35.9810 -45.1500 74.3420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.4560 -46.2100 74.7950 O 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6360 -44.2400 73.7980 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 1 6 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 7 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 5 2 0 0 0 0 + 7 8 2 0 0 0 0 + 7 12 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 11 10 1 0 0 0 0 + 12 11 2 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 6 0 0 0 + 15 13 1 0 0 0 0 + 16 15 1 0 0 0 0 + 16 17 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +9 + +> + VINA RESULT: -5.1 4.152 6.861 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.1 + +> +4.152 + +> +6.861 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 35.8450 -42.2310 77.0780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.0840 -42.9180 78.0230 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.5460 -42.2360 79.1040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7510 -40.8600 79.2720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.5220 -40.1980 78.3060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.0650 -40.8630 77.2170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1760 -40.1210 80.4330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8090 -40.1720 80.7280 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.2870 -39.4820 81.8170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1130 -38.7390 82.6370 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4700 -38.6740 82.3630 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9940 -39.3620 81.2750 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.3760 -42.9230 76.0120 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.2250 -44.3750 76.2200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.7070 -44.2960 76.1830 C 0 0 2 0 0 0 0 0 0 0 0 0 + 36.0740 -45.0710 75.0320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.5290 -46.2040 74.7760 O 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1520 -44.5080 74.4110 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 2 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 7 1 0 0 0 0 + 5 4 2 0 0 0 0 + 6 5 1 0 0 0 0 + 7 8 2 0 0 0 0 + 7 12 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 11 10 1 0 0 0 0 + 12 11 2 0 0 0 0 + 13 15 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 6 0 0 0 + 16 15 1 0 0 0 0 + 17 16 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +10 + +> + VINA RESULT: -5.1 4.978 7.604 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.1 + +> +4.978 + +> +7.604 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 30.7530 -45.6220 71.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.8390 -46.5690 72.0210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7610 -46.4010 73.0430 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.6180 -45.2940 73.0760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.5080 -44.3590 72.0360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.5900 -44.5090 71.0080 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.6130 -45.1080 74.1720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9480 -45.4990 74.0210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.8670 -45.3150 75.0480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.4790 -44.7320 76.2380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.1620 -44.3370 76.4090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2420 -44.5210 75.3850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.8340 -45.8040 69.9920 O 0 0 0 0 0 0 0 0 0 0 0 0 + 27.8660 -46.8520 69.2150 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.4710 -46.0240 70.3380 C 0 0 2 0 0 0 0 0 0 0 0 0 + 27.8150 -44.6590 70.5230 C 0 0 0 0 0 0 0 0 0 0 0 0 + 27.6950 -43.9320 69.5180 O 0 0 0 0 0 0 0 0 0 0 0 0 + 27.4570 -44.3570 71.6780 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 2 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 7 1 0 0 0 0 + 5 4 2 0 0 0 0 + 6 5 1 0 0 0 0 + 7 12 1 0 0 0 0 + 8 7 2 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 10 11 1 0 0 0 0 + 12 11 2 0 0 0 0 + 13 15 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 6 0 0 0 + 15 16 1 0 0 0 0 + 16 18 1 0 0 0 0 + 17 16 2 0 0 0 0 +M END +> +11 + +> + VINA RESULT: -5.0 4.195 7.549 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.0 + +> +4.195 + +> +7.549 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 29.7540 -45.2580 71.3420 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.3150 -46.4180 71.8740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3850 -46.3270 72.7510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9230 -45.0870 73.1180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.3370 -43.9390 72.5650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.2650 -44.0100 71.6890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0750 -44.9820 74.0600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9270 -44.4340 75.3380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0070 -44.3480 76.2090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.2510 -44.8130 75.8290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.4210 -45.3590 74.5670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.3430 -45.4460 73.6950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.6930 -45.3640 70.4700 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.4780 -44.2570 68.3950 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.9620 -45.5250 69.0820 C 0 0 2 0 0 0 0 0 0 0 0 0 + 28.2480 -46.7920 68.6170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.5250 -47.8590 69.1980 O 0 0 0 0 0 0 0 0 0 0 0 0 + 27.4460 -46.6720 67.6700 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 2 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 7 1 0 0 0 0 + 5 4 2 0 0 0 0 + 6 5 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 2 0 0 0 0 + 10 9 1 0 0 0 0 + 11 10 2 0 0 0 0 + 12 7 2 0 0 0 0 + 12 11 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 6 0 0 0 + 15 13 1 0 0 0 0 + 16 15 1 0 0 0 0 + 16 17 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +12 + +> + VINA RESULT: -5.0 4.679 7.828 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.0 + +> +4.679 + +> +7.828 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 36.3320 -43.5500 75.9960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.3870 -44.0640 76.8830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.8760 -43.2580 77.8890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.2910 -41.9290 78.0390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.2440 -41.4420 77.1330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.7640 -42.2320 76.1190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.7470 -41.0570 79.1210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.5670 -40.1750 79.8320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.0450 -39.3640 80.8330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.7000 -39.4080 81.1400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8690 -40.2750 80.4490 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.3880 -41.0870 79.4480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.8330 -44.3630 75.0030 O 0 0 0 0 0 0 0 0 0 0 0 0 + 37.8770 -44.0930 72.9030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.0820 -44.0270 74.4080 C 0 0 2 0 0 0 0 0 0 0 0 0 + 39.1230 -45.0100 74.9350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 39.9870 -44.5730 75.7210 O 0 0 0 0 0 0 0 0 0 0 0 0 + 39.0490 -46.1850 74.5260 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 2 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 7 1 0 0 0 0 + 5 4 2 0 0 0 0 + 6 5 1 0 0 0 0 + 7 12 2 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 2 0 0 0 0 + 9 10 1 0 0 0 0 + 11 10 2 0 0 0 0 + 12 11 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 6 0 0 0 + 15 16 1 0 0 0 0 + 15 13 1 0 0 0 0 + 16 17 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +13 + +> + VINA RESULT: -5.0 4.649 6.724 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-5.0 + +> +4.649 + +> +6.724 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 34.8510 -43.5880 77.4510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.5650 -43.1310 77.1680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9960 -42.1410 77.9550 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.6870 -41.5850 79.0390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9780 -42.0670 79.2990 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.5640 -43.0540 78.5210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0800 -40.5210 79.8910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.8520 -39.7670 80.7810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2750 -38.7750 81.5640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.9240 -38.5070 81.4720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.1390 -39.2420 80.5970 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.7130 -40.2350 79.8130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.4020 -44.5740 76.6620 O 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6680 -45.6050 74.5550 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.6890 -44.2800 75.3000 C 0 0 2 0 0 0 0 0 0 0 0 0 + 37.0370 -43.5650 75.2560 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.0600 -44.2440 75.4730 O 0 0 0 0 0 0 0 0 0 0 0 0 + 37.0200 -42.3420 75.0200 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 1 0 0 0 0 + 2 1 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 4 7 1 0 0 0 0 + 6 5 2 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 2 0 0 0 0 + 10 9 1 0 0 0 0 + 11 10 2 0 0 0 0 + 12 7 2 0 0 0 0 + 12 11 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 6 0 0 0 + 15 13 1 0 0 0 0 + 16 15 1 0 0 0 0 + 16 17 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +14 + +> + VINA RESULT: -4.9 4.537 6.848 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-4.9 + +> +4.537 + +> +6.848 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 32.7590 -43.8790 76.3190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.8540 -42.9310 76.7940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.2580 -42.0120 77.7510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.5630 -42.0150 78.2590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.4480 -42.9820 77.7620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0640 -43.9070 76.8030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0030 -41.0300 79.2900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.0900 -40.4290 80.1630 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.5140 -39.5170 81.1230 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.8510 -39.1930 81.2400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.7720 -39.7760 80.3850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.3520 -40.6870 79.4240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.3430 -44.7870 75.3700 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.5790 -44.5930 73.8120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.0560 -44.3220 74.0560 C 0 0 2 0 0 0 0 0 0 0 0 0 + 32.9870 -45.0520 73.0940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.1890 -44.5350 71.9770 O 0 0 0 0 0 0 0 0 0 0 0 0 + 33.4720 -46.1310 73.4860 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 1 6 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 7 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 5 2 0 0 0 0 + 7 12 2 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 2 0 0 0 0 + 9 10 1 0 0 0 0 + 11 10 2 0 0 0 0 + 12 11 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 6 0 0 0 + 15 13 1 0 0 0 0 + 16 18 1 0 0 0 0 + 16 15 1 0 0 0 0 + 17 16 2 0 0 0 0 +M END +> +15 + +> + VINA RESULT: -4.9 4.260 7.379 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-4.9 + +> +4.260 + +> +7.379 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 35.7560 -43.9150 76.0540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.5340 -42.7890 76.3170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.1460 -41.8970 77.3050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9780 -42.1010 78.0520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.2150 -43.2420 77.7620 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.5900 -44.1460 76.7800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.5530 -41.1450 79.1150 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.4760 -40.3190 79.7660 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.0660 -39.4280 80.7520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.7340 -39.3350 81.1010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8030 -40.1430 80.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.2090 -41.0350 79.4850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.1530 -44.7900 75.0670 O 0 0 0 0 0 0 0 0 0 0 0 0 + 37.6480 -44.3010 73.3060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.5310 -44.8500 74.7190 C 0 0 2 0 0 0 0 0 0 0 0 0 + 37.9810 -46.3020 74.8590 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.9270 -46.6870 74.1440 O 0 0 0 0 0 0 0 0 0 0 0 0 + 37.3550 -47.0110 75.6710 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 1 6 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 7 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 5 2 0 0 0 0 + 7 12 2 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 2 0 0 0 0 + 9 10 1 0 0 0 0 + 11 10 2 0 0 0 0 + 12 11 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 6 0 0 0 + 15 16 1 0 0 0 0 + 15 13 1 0 0 0 0 + 16 18 1 0 0 0 0 + 17 16 2 0 0 0 0 +M END +> +16 + +> + VINA RESULT: -4.8 4.248 6.765 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-4.8 + +> +4.248 + +> +6.765 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 39.5930 -41.9980 71.1320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.5480 -42.8420 70.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.9580 -43.6680 71.7050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.3930 -43.6770 73.0370 C 0 0 0 0 0 0 0 0 0 0 0 0 + 39.4470 -42.8180 73.3790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 40.0470 -41.9830 72.4490 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.7640 -44.5640 74.0580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.2240 -45.8670 74.2780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.6320 -46.6810 75.2370 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.5810 -46.2140 76.0010 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.1090 -44.9270 75.7990 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6970 -44.1110 74.8410 C 0 0 0 0 0 0 0 0 0 0 0 0 + 40.1710 -41.1860 70.1810 O 0 0 0 0 0 0 0 0 0 0 0 0 + 42.3040 -41.7100 69.3150 C 0 0 0 0 0 0 0 0 0 0 0 0 + 40.8070 -41.7890 69.0600 C 0 0 2 0 0 0 0 0 0 0 0 0 + 40.3510 -41.0400 67.8120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 41.0740 -40.1130 67.3950 O 0 0 0 0 0 0 0 0 0 0 0 0 + 39.2710 -41.3970 67.3010 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 1 0 0 0 0 + 2 1 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 4 7 1 0 0 0 0 + 6 5 2 0 0 0 0 + 7 8 2 0 0 0 0 + 7 12 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 11 10 1 0 0 0 0 + 12 11 2 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 1 0 0 0 + 15 13 1 0 0 0 0 + 16 15 1 0 0 0 0 + 17 16 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +17 + +> + VINA RESULT: -4.7 5.175 7.515 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-4.7 + +> +5.175 + +> +7.515 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 32.7270 -43.2690 77.0390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.8890 -42.8910 77.7100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1190 -43.3650 77.2800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.2240 -44.2240 76.1790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0370 -44.5870 75.5260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.7980 -44.1210 75.9390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.5440 -44.7390 75.7120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.6830 -46.0300 75.1940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.9190 -46.4950 74.7570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 39.0340 -45.6840 74.8180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.9190 -44.4010 75.3290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.6860 -43.9340 75.7670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.5120 -42.7920 77.4790 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.6300 -41.7900 79.4270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.4760 -41.5570 78.1850 C 0 0 2 0 0 0 0 0 0 0 0 0 + 30.9100 -40.5010 77.2390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.4240 -39.3660 77.2640 O 0 0 0 0 0 0 0 0 0 0 0 0 + 29.9550 -40.8450 76.5160 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 13 1 0 0 0 0 + 1 2 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 2 0 0 0 0 + 5 6 2 0 0 0 0 + 5 4 1 0 0 0 0 + 6 1 1 0 0 0 0 + 7 12 1 0 0 0 0 + 7 4 1 0 0 0 0 + 8 7 2 0 0 0 0 + 9 10 2 0 0 0 0 + 9 8 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 + 13 15 1 0 0 0 0 + 15 14 1 1 0 0 0 + 16 17 1 0 0 0 0 + 16 15 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +18 + +> + VINA RESULT: -4.5 3.887 6.713 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-4.5 + +> +3.887 + +> +6.713 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 35.3340 -44.2400 76.4330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.2230 -43.3330 77.4860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.9890 -42.7820 77.7940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.8400 -43.1150 77.0650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.9850 -44.0280 76.0110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.2100 -44.5930 75.6900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.5090 -42.5240 77.3900 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.2420 -41.9720 78.6470 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.0000 -41.4190 78.9350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.0050 -41.3960 77.9790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 29.2470 -41.9370 76.7270 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.4880 -42.4910 76.4360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.5680 -44.7780 76.1370 O 0 0 0 0 0 0 0 0 0 0 0 0 + 38.0030 -45.7500 74.5340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.1210 -44.5510 74.8450 C 0 0 2 0 0 0 0 0 0 0 0 0 + 37.8730 -43.2240 74.8910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.2700 -42.2030 74.5030 O 0 0 0 0 0 0 0 0 0 0 0 0 + 39.0500 -43.2560 75.2990 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 2 3 1 0 0 0 0 + 4 7 1 0 0 0 0 + 4 3 2 0 0 0 0 + 5 4 1 0 0 0 0 + 6 5 2 0 0 0 0 + 6 1 1 0 0 0 0 + 7 8 2 0 0 0 0 + 8 9 1 0 0 0 0 + 10 9 2 0 0 0 0 + 11 10 1 0 0 0 0 + 12 11 2 0 0 0 0 + 12 7 1 0 0 0 0 + 13 1 1 0 0 0 0 + 15 14 1 1 0 0 0 + 15 16 1 0 0 0 0 + 15 13 1 0 0 0 0 + 16 18 1 0 0 0 0 + 17 16 2 0 0 0 0 +M END +> +19 + +> + VINA RESULT: -4.4 3.044 4.158 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-4.4 + +> +3.044 + +> +4.158 + +$$$$ += + OpenBabel06141912503D + + 18 19 0 0 1 0 0 0 0 0999 V2000 + 32.5500 -43.5500 76.7360 C 0 0 0 0 0 0 0 0 0 0 0 0 + 33.6520 -43.1880 77.5090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.9240 -43.5810 77.1230 C 0 0 0 0 0 0 0 0 0 0 0 0 + 35.1310 -44.3420 75.9650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 34.0020 -44.6910 75.2090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 32.7230 -44.3040 75.5790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.4970 -44.7690 75.5440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 37.5820 -43.8860 75.5740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.8510 -44.2990 75.1850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 39.0680 -45.5970 74.7690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 38.0080 -46.4890 74.7300 C 0 0 0 0 0 0 0 0 0 0 0 0 + 36.7380 -46.0790 75.1180 C 0 0 0 0 0 0 0 0 0 0 0 0 + 31.2920 -43.1540 77.1350 O 0 0 0 0 0 0 0 0 0 0 0 0 + 30.7500 -40.8560 77.1260 C 0 0 0 0 0 0 0 0 0 0 0 0 + 30.6100 -42.1680 76.3690 C 0 0 2 0 0 0 0 0 0 0 0 0 + 29.1670 -42.6320 76.1960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 28.9380 -43.8550 76.2740 O 0 0 0 0 0 0 0 0 0 0 0 0 + 28.3130 -41.7520 75.9720 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 13 1 0 0 0 0 + 1 2 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 2 0 0 0 0 + 5 6 2 0 0 0 0 + 5 4 1 0 0 0 0 + 6 1 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 4 1 0 0 0 0 + 9 8 2 0 0 0 0 + 10 9 1 0 0 0 0 + 11 10 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 7 2 0 0 0 0 + 15 14 1 1 0 0 0 + 15 13 1 0 0 0 0 + 16 17 1 0 0 0 0 + 16 15 1 0 0 0 0 + 18 16 2 0 0 0 0 +M END +> +20 + +> + VINA RESULT: -4.4 3.679 6.880 + Name = + 5 active torsions: + status: ('A' for Active; 'I' for Inactive) + 1 A between atoms: C_1 and C_8 + 2 A between atoms: C_2 and C_13 + 3 A between atoms: C_8 and C_9 + 4 A between atoms: C_8 and O_18 + 5 A between atoms: C_10 and O_18 + x y z vdW Elec q Type + _______ _______ _______ _____ _____ ______ ____ + +> +F 4 + +> +-4.4 + +> +3.679 + +> +6.880 + +$$$$ 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 @@ -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 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 @@ -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