diff sucos_max.py @ 0:f80cfac80c53 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sucos_max.py	Wed Oct 02 12:58:19 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()
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