# HG changeset patch
# User bgruening
# Date 1570035523 14400
# Node ID f8f53668d5a29259518aac402947072bcbb8c15e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
diff -r 000000000000 -r f8f53668d5a2 sucos.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sucos.py Wed Oct 02 12:58:43 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 f8f53668d5a2 sucos.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sucos.xml Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,63 @@
+
+ - compare shape and feature overlap of docked ligand poses to a reference molecule
+
+ sucos_macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r f8f53668d5a2 sucos_cluster.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sucos_cluster.py Wed Oct 02 12:58:43 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 f8f53668d5a2 sucos_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sucos_macros.xml Wed Oct 02 12:58:43 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 f8f53668d5a2 sucos_max.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sucos_max.py Wed Oct 02 12:58:43 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 f8f53668d5a2 test-data/cluster1.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster1.sdf Wed Oct 02 12:58:43 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
+$$$$
+
+ RDKit 3D
+
+ 15 16 0 0 0 0 0 0 0 0999 V2000
+ 18.6370 11.5460 19.0470 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 19.3410 11.4910 20.6100 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 19.1300 12.5410 21.5090 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 20.1120 10.3920 20.9640 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 19.7080 12.5060 22.7780 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 20.6710 10.3800 22.2200 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 21.7320 9.9040 23.9840 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 21.1510 11.1000 24.2190 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 22.5310 9.1910 24.8790 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 21.2170 11.9110 25.4550 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 20.4620 11.2450 26.6090 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 21.0350 11.5770 27.9760 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 12 10 1 0
+ 13 12 1 0
+ 14 13 1 0
+ 15 14 1 0
+M END
+$$$$
diff -r 000000000000 -r f8f53668d5a2 test-data/cluster2.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster2.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,167 @@
+
+ RDKit 3D
+
+ 10 10 0 0 0 0 0 0 0 0999 V2000
+ 24.4730 11.1990 19.8620 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 26.1360 12.7690 19.0380 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 25.6290 12.6010 17.7470 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 4 1 1 0
+ 5 2 1 0
+ 6 3 2 0
+ 7 4 1 0
+ 8 6 1 0
+ 8 5 2 0
+ 9 7 1 0
+ 10 8 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 11 11 0 0 0 0 0 0 0 0999 V2000
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+ 24.1570 9.7480 21.5040 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 5 2 1 0
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+ 7 4 1 0
+ 8 6 1 0
+ 8 5 2 0
+ 7 9 1 1
+ 10 7 1 0
+ 11 8 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 12 12 0 0 0 0 0 0 0 0999 V2000
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+ 9 5 2 0
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+ 10 5 1 0
+ 11 10 1 0
+ 12 11 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 16 17 0 0 0 0 0 0 0 0999 V2000
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+ 22.0220 10.5180 21.1760 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 14 11 1 0
+ 14 10 1 0
+ 15 13 1 0
+ 16 15 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 18 20 0 0 0 0 0 0 0 0999 V2000
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+ 18 14 1 0
+ 18 17 1 0
+M END
+$$$$
diff -r 000000000000 -r f8f53668d5a2 test-data/cluster3.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster3.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,1024 @@
+
+ RDKit 3D
+
+ 19 20 0 0 0 0 0 0 0 0999 V2000
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+ 23.1990 10.4520 22.2010 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 19 7 2 0
+ 19 2 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 11 12 0 0 0 0 0 0 0 0999 V2000
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+ 11 6 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 11 12 0 0 0 0 0 0 0 0999 V2000
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+ 11 2 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 15 16 0 0 0 0 0 0 0 0999 V2000
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+ 15 14 2 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 14 15 0 0 0 0 0 0 0 0999 V2000
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+ 14 1 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 18 20 0 0 0 0 0 0 0 0999 V2000
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+M END
+$$$$
+
+ RDKit 3D
+
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+M END
+$$$$
+
+ RDKit 3D
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+M END
+$$$$
+
+ RDKit 3D
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+ 20 15 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 22 25 0 0 0 0 0 0 0 0999 V2000
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+ 22 21 2 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 19 21 0 0 0 0 0 0 0 0999 V2000
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+ 18 11 1 0
+ 19 17 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 16 17 0 0 0 0 0 0 0 0999 V2000
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+ 15 14 1 0
+ 16 12 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 11 12 0 0 0 0 0 0 0 0999 V2000
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+ 21.5250 10.6490 21.4640 C 0 0 2 0 0 0 0 0 0 0 0 0
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+ 8 7 1 0
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+ 11 6 1 0
+ 11 5 1 0
+M END
+$$$$
diff -r 000000000000 -r f8f53668d5a2 test-data/cluster4.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster4.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,47 @@
+
+ RDKit 3D
+
+ 20 21 0 0 0 0 0 0 0 0999 V2000
+ 21.2480 11.2160 24.5450 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 22.6540 13.4720 29.6460 S 0 0 0 0 0 0 0 0 0 0 0 0
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+ 20.7360 9.9660 23.8360 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 22.5750 10.2440 20.6540 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 25.4840 11.9720 18.9430 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 24.1890 11.6250 19.3240 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0
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+ 18 17 2 0
+ 19 18 1 0
+ 20 15 1 0
+ 20 19 2 0
+M END
+$$$$
diff -r 000000000000 -r f8f53668d5a2 test-data/cluster5.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster5.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,47 @@
+
+ RDKit 3D
+
+ 20 21 0 0 0 0 0 0 0 0999 V2000
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+ 28.6700 9.1850 21.8700 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.8180 9.9600 22.0270 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.9260 11.1970 21.3880 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 30.8240 9.5080 22.7950 F 0 0 0 0 0 0 0 0 0 0 0 0
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+ 5 14 1 1
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+ 20 11 1 0
+M END
+$$$$
diff -r 000000000000 -r f8f53668d5a2 test-data/cluster6.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster6.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,22 @@
+
+ RDKit 3D
+
+ 8 8 0 0 0 0 0 0 0 0999 V2000
+ 43.2120 1.2010 21.1900 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 42.0970 1.7030 22.0340 C 0 0 2 0 0 0 0 0 0 0 0 0
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+ 44.2130 1.9390 23.2340 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 44.4930 1.6950 21.7590 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 2 1 1 0
+ 2 3 1 6
+ 4 3 2 0
+ 5 2 1 0
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+ 7 1 1 0
+ 7 6 1 0
+ 8 3 1 0
+M END
+$$$$
diff -r 000000000000 -r f8f53668d5a2 test-data/split_1.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_1.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,389 @@
+
+ RDKit 3D
+
+ 19 20 0 0 0 0 0 0 0 0999 V2000
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+ 19 2 1 0
+M END
+$$$$
+
+ RDKit 3D
+
+ 11 12 0 0 0 0 0 0 0 0999 V2000
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+ 11 6 1 0
+M END
+$$$$
+
+ RDKit 3D
+
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+ 11 2 1 0
+M END
+$$$$
+
+ RDKit 3D
+
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+M END
+$$$$
+
+ RDKit 3D
+
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+M END
+$$$$
+
+ RDKit 3D
+
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+ 18 2 1 0
+M END
+$$$$
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diff -r 000000000000 -r f8f53668d5a2 test-data/split_2.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_2.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,385 @@
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+M END
+$$$$
diff -r 000000000000 -r f8f53668d5a2 test-data/split_3.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_3.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,399 @@
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+$$$$
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diff -r 000000000000 -r f8f53668d5a2 test-data/split_4.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/split_4.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,211 @@
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+M END
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diff -r 000000000000 -r f8f53668d5a2 test-data/sucos_cluster.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sucos_cluster.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,1384 @@
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+M END
+$$$$
+
+ RDKit 3D
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+$$$$
+
+ RDKit 3D
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+M END
+$$$$
+
+ RDKit 3D
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+M END
+$$$$
+
+ RDKit 3D
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+M END
+$$$$
+
+ RDKit 3D
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+M END
+$$$$
+
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+M END
+$$$$
+
+ RDKit 3D
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+ 17 16 1 0
+ 18 14 1 0
+ 18 17 1 0
+M END
+$$$$
diff -r 000000000000 -r f8f53668d5a2 test-data/sucos_inputs.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sucos_inputs.sdf Wed Oct 02 12:58:43 2019 -0400
@@ -0,0 +1,1420 @@
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
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+ 35.0250 -45.3160 74.0770 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.3410 -45.2900 73.1330 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.1700 -44.5940 73.4530 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.0040 -44.7840 72.7210 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.9810 -45.6590 71.6540 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.1290 -46.3590 71.3190 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.2960 -46.1720 72.0490 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.1480 -44.5380 76.0590 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.4940 -44.7080 76.2650 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 3 2 2 0 0 0 0
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+ 7 4 1 0 0 0 0
+ 9 8 2 0 0 0 0
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+ 12 7 2 0 0 0 0
+ 15 13 1 0 0 0 0
+ 15 14 1 1 0 0 0
+ 16 15 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+1
+
+>
+ VINA RESULT: -6.3 0.000 0.000
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-6.3
+
+>
+0.000
+
+>
+0.000
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 34.9980 -44.6860 75.3940 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.0270 -45.2910 74.1380 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.8490 -45.4620 73.4270 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.6180 -45.0400 73.9450 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.6210 -44.4360 75.2110 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.7890 -44.2540 75.9350 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.3460 -45.2230 73.1860 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.2400 -46.1600 72.1530 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.0470 -46.3240 71.4580 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.9380 -45.5680 71.7810 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.0210 -44.6340 72.8010 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.2120 -44.4670 73.4970 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.1760 -44.5260 76.0900 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.5270 -44.6480 76.2620 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.3680 -44.2480 75.3630 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 37.3510 -42.7680 74.9960 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.9750 -41.9580 75.8670 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.7000 -42.4690 73.8370 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 6 1 0 0 0 0
+ 1 13 1 0 0 0 0
+ 2 1 2 0 0 0 0
+ 3 4 2 0 0 0 0
+ 3 2 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 2 0 0 0 0
+ 7 12 1 0 0 0 0
+ 7 4 1 0 0 0 0
+ 8 7 2 0 0 0 0
+ 9 10 2 0 0 0 0
+ 9 8 1 0 0 0 0
+ 10 11 1 0 0 0 0
+ 11 12 2 0 0 0 0
+ 15 13 1 0 0 0 0
+ 15 14 1 1 0 0 0
+ 16 15 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+2
+
+>
+ VINA RESULT: -6.3 0.096 1.601
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-6.3
+
+>
+0.096
+
+>
+1.601
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 31.4230 -45.1380 73.6370 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.7570 -44.3390 74.7290 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.0620 -44.3190 75.1960 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.0630 -45.0910 74.5930 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.6960 -45.8850 73.4970 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.3970 -45.9160 73.0140 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.4700 -45.0750 75.0910 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.9310 -44.0690 75.9470 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.2420 -44.0690 76.4090 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.1150 -45.0730 76.0370 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.6800 -46.0790 75.1910 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.3700 -46.0810 74.7270 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.1210 -45.1500 73.1860 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.3430 -43.3440 71.8790 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.8600 -44.7730 71.8390 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 28.8640 -45.7760 71.2630 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.2180 -45.4370 70.2530 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.7530 -46.8660 71.8580 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 4 3 2 0 0 0 0
+ 5 4 1 0 0 0 0
+ 6 5 2 0 0 0 0
+ 6 1 1 0 0 0 0
+ 7 8 1 0 0 0 0
+ 8 9 2 0 0 0 0
+ 10 9 1 0 0 0 0
+ 11 10 2 0 0 0 0
+ 12 7 2 0 0 0 0
+ 12 11 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 1 0 0 0
+ 15 13 1 0 0 0 0
+ 16 15 1 0 0 0 0
+ 16 18 1 0 0 0 0
+ 17 16 2 0 0 0 0
+M END
+>
+3
+
+>
+ VINA RESULT: -5.8 3.643 7.155
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.8
+
+>
+3.643
+
+>
+7.155
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 31.4630 -45.3720 73.5650 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.4550 -46.2290 73.0910 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.7430 -46.1410 73.5970 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.0760 -45.2020 74.5810 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.0570 -44.3520 75.0360 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.7630 -44.4280 74.5440 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.4600 -45.1010 75.1280 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.4440 -46.0410 74.8060 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.7320 -45.9320 75.3180 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.0680 -44.8840 76.1520 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.1090 -43.9410 76.4850 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.8200 -44.0480 75.9750 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.1890 -45.4690 73.0500 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.3890 -44.4000 71.9580 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.8690 -44.7380 71.8720 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 30.2370 -45.6090 70.6740 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.7290 -46.7460 70.6060 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.0380 -45.1270 69.8500 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 6 1 0 0 0 0
+ 2 1 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 2 0 0 0 0
+ 4 5 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 6 5 2 0 0 0 0
+ 7 12 1 0 0 0 0
+ 8 7 2 0 0 0 0
+ 8 9 1 0 0 0 0
+ 9 10 2 0 0 0 0
+ 10 11 1 0 0 0 0
+ 12 11 2 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 1 0 0 0
+ 15 13 1 0 0 0 0
+ 16 15 1 0 0 0 0
+ 17 16 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+4
+
+>
+ VINA RESULT: -5.7 3.372 7.116
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.7
+
+>
+3.372
+
+>
+7.116
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 35.2710 -45.3020 74.6210 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.2660 -45.6340 73.7140 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.9500 -45.2910 73.9860 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.6030 -44.6140 75.1620 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.6370 -44.2950 76.0550 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.9580 -44.6280 75.7980 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.1890 -44.2430 75.4620 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.6990 -44.2280 76.7720 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.3810 -43.8750 77.0380 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.5300 -43.5220 76.0100 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.9940 -43.5300 74.7050 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.3100 -43.8830 74.4360 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.5730 -45.6520 74.3380 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.6460 -44.0130 73.0210 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.5810 -44.6500 74.4000 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 38.8790 -45.3250 74.8330 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.6810 -44.6570 75.5150 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.0560 -46.5000 74.4570 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 6 2 0 0 0 0
+ 2 3 2 0 0 0 0
+ 2 1 1 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 4 5 2 0 0 0 0
+ 6 5 1 0 0 0 0
+ 7 8 2 0 0 0 0
+ 8 9 1 0 0 0 0
+ 10 9 2 0 0 0 0
+ 11 10 1 0 0 0 0
+ 12 11 2 0 0 0 0
+ 12 7 1 0 0 0 0
+ 13 15 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 6 0 0 0
+ 15 16 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+5
+
+>
+ VINA RESULT: -5.7 2.170 3.128
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.7
+
+>
+2.170
+
+>
+3.128
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 35.8300 -45.0340 75.6080 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.7490 -44.4320 76.2500 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.4970 -44.4470 75.6530 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.2910 -45.0560 74.4090 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.3980 -45.6510 73.7880 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.6560 -45.6490 74.3700 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.9470 -45.0740 73.7610 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.9600 -44.1410 74.0980 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.7140 -44.1650 73.4820 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.4290 -45.1090 72.5160 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.3910 -46.0430 72.1670 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.6370 -46.0220 72.7810 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.0680 -45.0090 76.2120 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.3190 -42.7990 75.4190 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.0480 -44.0980 75.7260 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 38.7110 -44.7390 74.5100 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.7490 -44.0760 73.4540 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.1570 -45.8930 74.6530 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 13 1 0 0 0 0
+ 1 2 2 0 0 0 0
+ 3 2 1 0 0 0 0
+ 4 3 2 0 0 0 0
+ 5 6 2 0 0 0 0
+ 5 4 1 0 0 0 0
+ 6 1 1 0 0 0 0
+ 7 8 1 0 0 0 0
+ 7 4 1 0 0 0 0
+ 9 8 2 0 0 0 0
+ 10 9 1 0 0 0 0
+ 11 10 2 0 0 0 0
+ 11 12 1 0 0 0 0
+ 12 7 2 0 0 0 0
+ 15 14 1 6 0 0 0
+ 15 13 1 0 0 0 0
+ 16 18 1 0 0 0 0
+ 16 15 1 0 0 0 0
+ 17 16 2 0 0 0 0
+M END
+>
+6
+
+>
+ VINA RESULT: -5.6 1.269 1.698
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.6
+
+>
+1.269
+
+>
+1.698
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 35.3500 -44.6860 75.6460 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.6310 -45.1070 74.5280 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.2600 -44.9060 74.4730 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.5720 -44.2870 75.5250 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.3230 -43.8760 76.6360 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.6950 -44.0660 76.7070 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.0970 -44.0690 75.4740 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.4150 -43.9690 74.2560 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.0400 -43.7730 74.2220 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.3160 -43.6810 75.3950 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.9710 -43.7770 76.6120 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.3460 -43.9730 76.6490 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.7110 -44.8950 75.6870 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.5990 -45.5620 74.4350 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.4950 -44.5230 74.5590 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 38.0030 -43.1040 74.7960 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.1970 -42.1660 74.6420 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.2020 -42.9800 75.1140 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 13 1 0 0 0 0
+ 1 6 2 0 0 0 0
+ 2 1 1 0 0 0 0
+ 3 2 2 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 5 2 0 0 0 0
+ 5 6 1 0 0 0 0
+ 7 4 1 0 0 0 0
+ 7 12 2 0 0 0 0
+ 8 7 1 0 0 0 0
+ 9 8 2 0 0 0 0
+ 9 10 1 0 0 0 0
+ 10 11 2 0 0 0 0
+ 11 12 1 0 0 0 0
+ 15 14 1 1 0 0 0
+ 15 16 1 0 0 0 0
+ 15 13 1 0 0 0 0
+ 16 18 1 0 0 0 0
+ 17 16 2 0 0 0 0
+M END
+>
+7
+
+>
+ VINA RESULT: -5.6 1.766 2.728
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.6
+
+>
+1.766
+
+>
+2.728
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 32.1440 -44.8920 74.5920 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.7730 -44.3650 75.7190 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.1560 -44.3910 75.8130 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.9450 -44.9420 74.7950 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.2830 -45.4660 73.6750 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.9010 -45.4450 73.5620 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.4330 -44.9750 74.8910 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.1490 -46.1670 74.7400 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.5370 -46.1830 74.8260 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.2380 -45.0160 75.0540 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.5490 -43.8230 75.2060 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.1620 -43.8040 75.1210 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.7690 -44.8610 74.5140 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.8760 -43.5400 75.0100 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.1310 -43.6400 74.1560 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 29.8570 -43.6840 72.6560 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.6580 -43.0940 71.9030 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.8370 -44.2960 72.2850 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 4 3 2 0 0 0 0
+ 5 4 1 0 0 0 0
+ 6 5 2 0 0 0 0
+ 6 1 1 0 0 0 0
+ 7 12 2 0 0 0 0
+ 8 9 2 0 0 0 0
+ 8 7 1 0 0 0 0
+ 9 10 1 0 0 0 0
+ 10 11 2 0 0 0 0
+ 12 11 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 13 1 0 0 0 0
+ 15 14 1 1 0 0 0
+ 16 15 1 0 0 0 0
+ 17 16 2 0 0 0 0
+ 18 16 1 0 0 0 0
+M END
+>
+8
+
+>
+ VINA RESULT: -5.5 3.099 6.864
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.5
+
+>
+3.099
+
+>
+6.864
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 34.0370 -44.1480 76.7170 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.8450 -43.4300 76.8020 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.7400 -42.3700 77.6890 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.8120 -42.0010 78.5130 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.9960 -42.7430 78.4050 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.1210 -43.8040 77.5210 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.7050 -40.8620 79.4710 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.4630 -40.3800 79.8980 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.3780 -39.3220 80.7960 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.5230 -38.7310 81.2920 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.7630 -39.1920 80.8830 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.8520 -40.2490 79.9850 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.1250 -45.2010 75.8320 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.6370 -45.8600 73.6180 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.4770 -44.9310 74.4800 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 35.9810 -45.1500 74.3420 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.4560 -46.2100 74.7950 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.6360 -44.2400 73.7980 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 1 6 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 2 0 0 0 0
+ 4 7 1 0 0 0 0
+ 5 4 1 0 0 0 0
+ 6 5 2 0 0 0 0
+ 7 8 2 0 0 0 0
+ 7 12 1 0 0 0 0
+ 8 9 1 0 0 0 0
+ 9 10 2 0 0 0 0
+ 11 10 1 0 0 0 0
+ 12 11 2 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 6 0 0 0
+ 15 13 1 0 0 0 0
+ 16 15 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+9
+
+>
+ VINA RESULT: -5.1 4.152 6.861
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.1
+
+>
+4.152
+
+>
+6.861
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 35.8450 -42.2310 77.0780 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.0840 -42.9180 78.0230 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.5460 -42.2360 79.1040 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.7510 -40.8600 79.2720 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.5220 -40.1980 78.3060 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.0650 -40.8630 77.2170 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.1760 -40.1210 80.4330 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.8090 -40.1720 80.7280 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.2870 -39.4820 81.8170 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.1130 -38.7390 82.6370 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.4700 -38.6740 82.3630 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.9940 -39.3620 81.2750 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.3760 -42.9230 76.0120 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.2250 -44.3750 76.2200 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.7070 -44.2960 76.1830 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 36.0740 -45.0710 75.0320 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.5290 -46.2040 74.7760 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.1520 -44.5080 74.4110 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 6 2 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 5 4 2 0 0 0 0
+ 6 5 1 0 0 0 0
+ 7 8 2 0 0 0 0
+ 7 12 1 0 0 0 0
+ 8 9 1 0 0 0 0
+ 9 10 2 0 0 0 0
+ 11 10 1 0 0 0 0
+ 12 11 2 0 0 0 0
+ 13 15 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 6 0 0 0
+ 16 15 1 0 0 0 0
+ 17 16 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+10
+
+>
+ VINA RESULT: -5.1 4.978 7.604
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.1
+
+>
+4.978
+
+>
+7.604
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 30.7530 -45.6220 71.0020 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.8390 -46.5690 72.0210 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.7610 -46.4010 73.0430 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.6180 -45.2940 73.0760 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.5080 -44.3590 72.0360 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.5900 -44.5090 71.0080 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.6130 -45.1080 74.1720 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.9480 -45.4990 74.0210 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.8670 -45.3150 75.0480 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.4790 -44.7320 76.2380 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.1620 -44.3370 76.4090 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.2420 -44.5210 75.3850 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.8340 -45.8040 69.9920 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 27.8660 -46.8520 69.2150 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.4710 -46.0240 70.3380 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 27.8150 -44.6590 70.5230 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 27.6950 -43.9320 69.5180 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 27.4570 -44.3570 71.6780 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 6 2 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 5 4 2 0 0 0 0
+ 6 5 1 0 0 0 0
+ 7 12 1 0 0 0 0
+ 8 7 2 0 0 0 0
+ 8 9 1 0 0 0 0
+ 9 10 2 0 0 0 0
+ 10 11 1 0 0 0 0
+ 12 11 2 0 0 0 0
+ 13 15 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 6 0 0 0
+ 15 16 1 0 0 0 0
+ 16 18 1 0 0 0 0
+ 17 16 2 0 0 0 0
+M END
+>
+11
+
+>
+ VINA RESULT: -5.0 4.195 7.549
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.0
+
+>
+4.195
+
+>
+7.549
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 29.7540 -45.2580 71.3420 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.3150 -46.4180 71.8740 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.3850 -46.3270 72.7510 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.9230 -45.0870 73.1180 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.3370 -43.9390 72.5650 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.2650 -44.0100 71.6890 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.0750 -44.9820 74.0600 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.9270 -44.4340 75.3380 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.0070 -44.3480 76.2090 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.2510 -44.8130 75.8290 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.4210 -45.3590 74.5670 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.3430 -45.4460 73.6950 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.6930 -45.3640 70.4700 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.4780 -44.2570 68.3950 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.9620 -45.5250 69.0820 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 28.2480 -46.7920 68.6170 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.5250 -47.8590 69.1980 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 27.4460 -46.6720 67.6700 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 6 2 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 5 4 2 0 0 0 0
+ 6 5 1 0 0 0 0
+ 7 8 1 0 0 0 0
+ 8 9 2 0 0 0 0
+ 10 9 1 0 0 0 0
+ 11 10 2 0 0 0 0
+ 12 7 2 0 0 0 0
+ 12 11 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 6 0 0 0
+ 15 13 1 0 0 0 0
+ 16 15 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+12
+
+>
+ VINA RESULT: -5.0 4.679 7.828
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.0
+
+>
+4.679
+
+>
+7.828
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 36.3320 -43.5500 75.9960 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.3870 -44.0640 76.8830 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.8760 -43.2580 77.8890 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.2910 -41.9290 78.0390 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.2440 -41.4420 77.1330 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.7640 -42.2320 76.1190 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.7470 -41.0570 79.1210 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.5670 -40.1750 79.8320 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.0450 -39.3640 80.8330 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.7000 -39.4080 81.1400 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.8690 -40.2750 80.4490 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.3880 -41.0870 79.4480 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.8330 -44.3630 75.0030 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.8770 -44.0930 72.9030 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.0820 -44.0270 74.4080 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 39.1230 -45.0100 74.9350 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.9870 -44.5730 75.7210 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.0490 -46.1850 74.5260 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 6 2 0 0 0 0
+ 1 2 1 0 0 0 0
+ 2 3 2 0 0 0 0
+ 3 4 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 5 4 2 0 0 0 0
+ 6 5 1 0 0 0 0
+ 7 12 2 0 0 0 0
+ 7 8 1 0 0 0 0
+ 8 9 2 0 0 0 0
+ 9 10 1 0 0 0 0
+ 11 10 2 0 0 0 0
+ 12 11 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 6 0 0 0
+ 15 16 1 0 0 0 0
+ 15 13 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+13
+
+>
+ VINA RESULT: -5.0 4.649 6.724
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-5.0
+
+>
+4.649
+
+>
+6.724
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 34.8510 -43.5880 77.4510 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.5650 -43.1310 77.1680 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.9960 -42.1410 77.9550 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.6870 -41.5850 79.0390 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.9780 -42.0670 79.2990 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.5640 -43.0540 78.5210 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.0800 -40.5210 79.8910 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.8520 -39.7670 80.7810 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.2750 -38.7750 81.5640 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.9240 -38.5070 81.4720 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.1390 -39.2420 80.5970 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.7130 -40.2350 79.8130 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.4020 -44.5740 76.6620 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.6680 -45.6050 74.5550 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.6890 -44.2800 75.3000 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 37.0370 -43.5650 75.2560 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.0600 -44.2440 75.4730 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.0200 -42.3420 75.0200 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 6 1 0 0 0 0
+ 2 1 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 2 0 0 0 0
+ 4 5 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 6 5 2 0 0 0 0
+ 7 8 1 0 0 0 0
+ 8 9 2 0 0 0 0
+ 10 9 1 0 0 0 0
+ 11 10 2 0 0 0 0
+ 12 7 2 0 0 0 0
+ 12 11 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 6 0 0 0
+ 15 13 1 0 0 0 0
+ 16 15 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+14
+
+>
+ VINA RESULT: -4.9 4.537 6.848
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-4.9
+
+>
+4.537
+
+>
+6.848
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 32.7590 -43.8790 76.3190 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.8540 -42.9310 76.7940 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.2580 -42.0120 77.7510 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.5630 -42.0150 78.2590 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.4480 -42.9820 77.7620 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.0640 -43.9070 76.8030 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.0030 -41.0300 79.2900 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.0900 -40.4290 80.1630 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.5140 -39.5170 81.1230 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.8510 -39.1930 81.2400 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.7720 -39.7760 80.3850 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.3520 -40.6870 79.4240 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.3430 -44.7870 75.3700 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.5790 -44.5930 73.8120 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.0560 -44.3220 74.0560 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 32.9870 -45.0520 73.0940 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.1890 -44.5350 71.9770 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.4720 -46.1310 73.4860 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 1 6 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 2 0 0 0 0
+ 4 7 1 0 0 0 0
+ 5 4 1 0 0 0 0
+ 6 5 2 0 0 0 0
+ 7 12 2 0 0 0 0
+ 7 8 1 0 0 0 0
+ 8 9 2 0 0 0 0
+ 9 10 1 0 0 0 0
+ 11 10 2 0 0 0 0
+ 12 11 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 6 0 0 0
+ 15 13 1 0 0 0 0
+ 16 18 1 0 0 0 0
+ 16 15 1 0 0 0 0
+ 17 16 2 0 0 0 0
+M END
+>
+15
+
+>
+ VINA RESULT: -4.9 4.260 7.379
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-4.9
+
+>
+4.260
+
+>
+7.379
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 35.7560 -43.9150 76.0540 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.5340 -42.7890 76.3170 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.1460 -41.8970 77.3050 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.9780 -42.1010 78.0520 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.2150 -43.2420 77.7620 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.5900 -44.1460 76.7800 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.5530 -41.1450 79.1150 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.4760 -40.3190 79.7660 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.0660 -39.4280 80.7520 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.7340 -39.3350 81.1010 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.8030 -40.1430 80.4700 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.2090 -41.0350 79.4850 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.1530 -44.7900 75.0670 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.6480 -44.3010 73.3060 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.5310 -44.8500 74.7190 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 37.9810 -46.3020 74.8590 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.9270 -46.6870 74.1440 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.3550 -47.0110 75.6710 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 1 6 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 2 0 0 0 0
+ 4 7 1 0 0 0 0
+ 5 4 1 0 0 0 0
+ 6 5 2 0 0 0 0
+ 7 12 2 0 0 0 0
+ 7 8 1 0 0 0 0
+ 8 9 2 0 0 0 0
+ 9 10 1 0 0 0 0
+ 11 10 2 0 0 0 0
+ 12 11 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 6 0 0 0
+ 15 16 1 0 0 0 0
+ 15 13 1 0 0 0 0
+ 16 18 1 0 0 0 0
+ 17 16 2 0 0 0 0
+M END
+>
+16
+
+>
+ VINA RESULT: -4.8 4.248 6.765
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-4.8
+
+>
+4.248
+
+>
+6.765
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 39.5930 -41.9980 71.1320 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.5480 -42.8420 70.7600 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.9580 -43.6680 71.7050 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.3930 -43.6770 73.0370 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.4470 -42.8180 73.3790 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 40.0470 -41.9830 72.4490 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.7640 -44.5640 74.0580 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.2240 -45.8670 74.2780 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.6320 -46.6810 75.2370 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.5810 -46.2140 76.0010 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.1090 -44.9270 75.7990 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.6970 -44.1110 74.8410 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 40.1710 -41.1860 70.1810 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 42.3040 -41.7100 69.3150 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 40.8070 -41.7890 69.0600 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 40.3510 -41.0400 67.8120 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 41.0740 -40.1130 67.3950 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.2710 -41.3970 67.3010 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 6 1 0 0 0 0
+ 2 1 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 3 4 2 0 0 0 0
+ 4 5 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 6 5 2 0 0 0 0
+ 7 8 2 0 0 0 0
+ 7 12 1 0 0 0 0
+ 8 9 1 0 0 0 0
+ 9 10 2 0 0 0 0
+ 11 10 1 0 0 0 0
+ 12 11 2 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 1 0 0 0
+ 15 13 1 0 0 0 0
+ 16 15 1 0 0 0 0
+ 17 16 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+17
+
+>
+ VINA RESULT: -4.7 5.175 7.515
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-4.7
+
+>
+5.175
+
+>
+7.515
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 32.7270 -43.2690 77.0390 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.8890 -42.8910 77.7100 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.1190 -43.3650 77.2800 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.2240 -44.2240 76.1790 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.0370 -44.5870 75.5260 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.7980 -44.1210 75.9390 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.5440 -44.7390 75.7120 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.6830 -46.0300 75.1940 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.9190 -46.4950 74.7570 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.0340 -45.6840 74.8180 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.9190 -44.4010 75.3290 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.6860 -43.9340 75.7670 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.5120 -42.7920 77.4790 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.6300 -41.7900 79.4270 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.4760 -41.5570 78.1850 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 30.9100 -40.5010 77.2390 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.4240 -39.3660 77.2640 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.9550 -40.8450 76.5160 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 13 1 0 0 0 0
+ 1 2 2 0 0 0 0
+ 3 2 1 0 0 0 0
+ 4 3 2 0 0 0 0
+ 5 6 2 0 0 0 0
+ 5 4 1 0 0 0 0
+ 6 1 1 0 0 0 0
+ 7 12 1 0 0 0 0
+ 7 4 1 0 0 0 0
+ 8 7 2 0 0 0 0
+ 9 10 2 0 0 0 0
+ 9 8 1 0 0 0 0
+ 10 11 1 0 0 0 0
+ 11 12 2 0 0 0 0
+ 13 15 1 0 0 0 0
+ 15 14 1 1 0 0 0
+ 16 17 1 0 0 0 0
+ 16 15 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+18
+
+>
+ VINA RESULT: -4.5 3.887 6.713
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-4.5
+
+>
+3.887
+
+>
+6.713
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 35.3340 -44.2400 76.4330 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.2230 -43.3330 77.4860 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.9890 -42.7820 77.7940 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.8400 -43.1150 77.0650 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.9850 -44.0280 76.0110 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.2100 -44.5930 75.6900 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.5090 -42.5240 77.3900 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.2420 -41.9720 78.6470 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.0000 -41.4190 78.9350 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.0050 -41.3960 77.9790 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 29.2470 -41.9370 76.7270 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.4880 -42.4910 76.4360 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.5680 -44.7780 76.1370 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.0030 -45.7500 74.5340 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.1210 -44.5510 74.8450 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 37.8730 -43.2240 74.8910 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.2700 -42.2030 74.5030 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.0500 -43.2560 75.2990 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 1 0 0 0 0
+ 4 7 1 0 0 0 0
+ 4 3 2 0 0 0 0
+ 5 4 1 0 0 0 0
+ 6 5 2 0 0 0 0
+ 6 1 1 0 0 0 0
+ 7 8 2 0 0 0 0
+ 8 9 1 0 0 0 0
+ 10 9 2 0 0 0 0
+ 11 10 1 0 0 0 0
+ 12 11 2 0 0 0 0
+ 12 7 1 0 0 0 0
+ 13 1 1 0 0 0 0
+ 15 14 1 1 0 0 0
+ 15 16 1 0 0 0 0
+ 15 13 1 0 0 0 0
+ 16 18 1 0 0 0 0
+ 17 16 2 0 0 0 0
+M END
+>
+19
+
+>
+ VINA RESULT: -4.4 3.044 4.158
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-4.4
+
+>
+3.044
+
+>
+4.158
+
+$$$$
+=
+ OpenBabel06141912503D
+
+ 18 19 0 0 1 0 0 0 0 0999 V2000
+ 32.5500 -43.5500 76.7360 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 33.6520 -43.1880 77.5090 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.9240 -43.5810 77.1230 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 35.1310 -44.3420 75.9650 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 34.0020 -44.6910 75.2090 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 32.7230 -44.3040 75.5790 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.4970 -44.7690 75.5440 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 37.5820 -43.8860 75.5740 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.8510 -44.2990 75.1850 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 39.0680 -45.5970 74.7690 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 38.0080 -46.4890 74.7300 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 36.7380 -46.0790 75.1180 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 31.2920 -43.1540 77.1350 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.7500 -40.8560 77.1260 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 30.6100 -42.1680 76.3690 C 0 0 2 0 0 0 0 0 0 0 0 0
+ 29.1670 -42.6320 76.1960 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.9380 -43.8550 76.2740 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 28.3130 -41.7520 75.9720 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 13 1 0 0 0 0
+ 1 2 2 0 0 0 0
+ 3 2 1 0 0 0 0
+ 4 3 2 0 0 0 0
+ 5 6 2 0 0 0 0
+ 5 4 1 0 0 0 0
+ 6 1 1 0 0 0 0
+ 7 8 1 0 0 0 0
+ 7 4 1 0 0 0 0
+ 9 8 2 0 0 0 0
+ 10 9 1 0 0 0 0
+ 11 10 2 0 0 0 0
+ 11 12 1 0 0 0 0
+ 12 7 2 0 0 0 0
+ 15 14 1 1 0 0 0
+ 15 13 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 16 15 1 0 0 0 0
+ 18 16 2 0 0 0 0
+M END
+>
+20
+
+>
+ VINA RESULT: -4.4 3.679 6.880
+ Name =
+ 5 active torsions:
+ status: ('A' for Active; 'I' for Inactive)
+ 1 A between atoms: C_1 and C_8
+ 2 A between atoms: C_2 and C_13
+ 3 A between atoms: C_8 and C_9
+ 4 A between atoms: C_8 and O_18
+ 5 A between atoms: C_10 and O_18
+ x y z vdW Elec q Type
+ _______ _______ _______ _____ _____ ______ ____
+
+>
+F 4
+
+>
+-4.4
+
+>
+3.679
+
+>
+6.880
+
+$$$$
diff -r 000000000000 -r f8f53668d5a2 test-data/sucos_refmol.mol
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sucos_refmol.mol Wed Oct 02 12:58:43 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 f8f53668d5a2 utils.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.py Wed Oct 02 12:58:43 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