Mercurial > repos > bgruening > sucos_max_score

annotate sucos_max.py @ 5:887706e7c3d4 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 12:11:29 +0000
parents 276243f0de02
children f67eb93bba2a
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0
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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2 """
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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3 Assess ligands against a second set of molecules using SuCOS scores.
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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4 This is a quite specialised function that is designed to take a set of potential follow up
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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5 compounds and compare them to a set of clustered fragment hits to help identify which follow up
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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6 ligands best map to the binding space of the hits.
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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7
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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8 The clustering of the fragment hits is expected to be performed with the sucos_cluster.py module
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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9 and will generate a set of SD files, one for each cluster of hits (presumably corresponding to a
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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10 binding pocket in the protein target).
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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11
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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12 Each molecule in the input ligands is then compared (using SuCOS) to each hit in the clusters. There
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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13 are different modes which determine how the ligand is assessed.
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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14
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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15 In mode 'max' the hit with the best SuCOS score is identified. The output is a SD file with each of the ligands,
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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16 with these additional fields for each molecule:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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17 Max_SuCOS_Score - the best score
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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18 Max_SuCOS_FeatureMap_Score - the feature map score for the hit that has the best SuCOS score
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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19 Max_SuCOS_Protrude_Score - the protrude volume for the hit that has the best SuCOS score
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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20 Max_SuCOS_Cluster - the name of the cluster SD file that contains the best hit
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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21 Max_SuCOS_Index - the index of the best hit in the SD file
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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22
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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23 In mode 'cum' the sum of all the scores is calculated and reported as the following properties for each molecule:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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24 Cum_SuCOS_Score property: the sum of the SuCOS scores
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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25 Cum_SuCOS_FeatureMap_Score: the sum of the feature map scores
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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26 Cum_SuCOS_Protrude_Score: the sum of the protrude volume scores
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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27
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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28 If a molecule has no alignment to any of the clustered hits (all alignment scores of zero) then it is not
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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29 included in the results.
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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30
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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31
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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32 SuCOS is the work of Susan Leung.
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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33 GitHub: https://github.com/susanhleung/SuCOS
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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34 Publication: https://doi.org/10.26434/chemrxiv.8100203.v1
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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35 """
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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36
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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37 import sucos, utils
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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38 import argparse, gzip, os
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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39 from rdkit import Chem
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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40
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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41
4
276243f0de02 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
bgruening
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42 def process(inputfilename, clusterfilenames, outputfilename, filter_value, filter_field):
0
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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43 all_clusters = {}
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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44 for filename in clusterfilenames:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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45 cluster = []
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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46 cluster_file = utils.open_file_for_reading(filename)
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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47 suppl = Chem.ForwardSDMolSupplier(cluster_file)
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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48 i = 0
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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49 for mol in suppl:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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50 i += 1
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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51 if not mol:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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52 utils.log("WARNING: failed to generate molecule", i, "in cluster", filename)
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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53 continue
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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54 try:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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55 features = sucos.getRawFeatures(mol)
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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56 cluster.append((mol, features))
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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57 except:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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58 utils.log("WARNING: failed to generate features for molecule", i, "in cluster", filename)
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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59
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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60 cluster_file.close()
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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61 all_clusters[filename] = cluster
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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62
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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63 input_file = utils.open_file_for_reading(inputfilename)
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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64 suppl = Chem.ForwardSDMolSupplier(input_file)
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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65 output_file = utils.open_file_for_writing(outputfilename)
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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66 writer = Chem.SDWriter(output_file)
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67
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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68 comparisons = 0
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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69 mol_num = 0
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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70
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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71 for mol in suppl:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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72 mol_num += 1
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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73 if not mol:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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74 utils.log("WARNING: failed to generate molecule", mol_num, "in input")
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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75 continue
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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76 try:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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77 query_features = sucos.getRawFeatures(mol)
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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78 except:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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79 utils.log("WARNING: failed to generate features for molecule", mol_num, "in input")
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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80 continue
1
3550e4d214bd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
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81 scores_max = [0, 0, 0]
3550e4d214bd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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82 scores_cum = [0, 0, 0]
3
cb3a498925be "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 2a74332a201fa9bb53f8e7dc3cc497f653d12929"
bgruening
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83 cluster_name = None
0
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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84 for clusterfilename in all_clusters:
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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85 cluster = all_clusters[clusterfilename]
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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86 index = 0
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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87 for entry in cluster:
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88 hit = entry[0]
b44d22769ef4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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89 ref_features = entry[1]
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90 index += 1
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91 comparisons += 1
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92 sucos_score, fm_score, vol_score = sucos.get_SucosScore(hit, mol,
1
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93 tani=False, ref_features=ref_features,
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94 query_features=query_features)
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95
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96 if sucos_score > scores_max[0]:
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97 scores_max[0] = sucos_score
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98 scores_max[1] = fm_score
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99 scores_max[2] = vol_score
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100 cluster_name = clusterfilename
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101 cluster_index = index
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102
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103 scores_cum[0] += sucos_score
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104 scores_cum[1] += fm_score
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105 scores_cum[2] += vol_score
0
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106
2
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107
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108 # utils.log("Max SuCOS:", scores[0], "FM:", scores[1], "P:", scores[2],"File:", cluster_file_name_only, "Index:", cluster_index)
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109 mol.SetDoubleProp("Max_SuCOS_Score", scores_max[0] if scores_max[0] > 0 else 0)
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110 mol.SetDoubleProp("Max_SuCOS_FeatureMap_Score", scores_max[1] if scores_max[1] > 0 else 0)
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111 mol.SetDoubleProp("Max_SuCOS_Protrude_Score", scores_max[2] if scores_max[2] > 0 else 0)
3
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112
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113 if cluster_name:
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114 cluster_file_name_only = cluster_name.split(os.sep)[-1]
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115 mol.SetProp("Max_SuCOS_Cluster", cluster_file_name_only)
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116 mol.SetIntProp("Max_SuCOS_Index", cluster_index)
2
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117
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118 # utils.log("Cum SuCOS:", scores[0], "FM:", scores[1], "P:", scores[2])
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119 mol.SetDoubleProp("Cum_SuCOS_Score", scores_cum[0] if scores_cum[0] > 0 else 0)
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120 mol.SetDoubleProp("Cum_SuCOS_FeatureMap_Score", scores_cum[1] if scores_cum[1] > 0 else 0)
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121 mol.SetDoubleProp("Cum_SuCOS_Protrude_Score", scores_cum[2] if scores_cum[2] > 0 else 0)
0
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122
4
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123 if filter_value and filter_field:
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124 if mol.HasProp(filter_field):
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125 val = mol.GetDoubleProp(filter_field)
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126 if val > filter_value:
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127 writer.write(mol)
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128 else:
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129 writer.write(mol)
0
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130
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131 input_file.close()
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132 writer.flush()
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133 writer.close()
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134 output_file.close()
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135
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136 utils.log("Completed", comparisons, "comparisons")
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137
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138
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139 ### start main execution #########################################
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140
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141 def main():
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142 parser = argparse.ArgumentParser(description='Max SuCOS scores with RDKit')
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143 parser.add_argument('-i', '--input', help='Input file to score in SDF format. Can be gzipped (*.gz).')
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144 parser.add_argument('-o', '--output', help='Output file in SDF format. Can be gzipped (*.gz).')
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145 parser.add_argument('clusters', nargs='*', help="One or more SDF files with the clustered hits")
4
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146 parser.add_argument('--filter-value', type=float, help='Filter out values with scores less than this.')
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147 parser.add_argument('--filter-field', help='Field to use to filter values.')
0
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148
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149 args = parser.parse_args()
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150 utils.log("Max SuCOS Args: ", args)
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151
4
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152 process(args.input, args.clusters, args.output, args.filter_value, args.filter_field)
0
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153
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154
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155 if __name__ == "__main__":
1
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156 main()