Mercurial > repos > bgruening > sucos_clustering

annotate sucos_max.py @ 2:58d18838e244 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
author bgruening
date Thu, 19 Mar 2020 07:25:25 -0400
parents f80cfac80c53
children bd12f4b4c3a8
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f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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diff changeset
1 #!/usr/bin/env python
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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2 """
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
3 Assess ligands against a second set of molecules using SuCOS scores.
f80cfac80c53 "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
f80cfac80c53 "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
f80cfac80c53 "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.
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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7
f80cfac80c53 "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
f80cfac80c53 "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
f80cfac80c53 "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).
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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11
f80cfac80c53 "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
f80cfac80c53 "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.
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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14
f80cfac80c53 "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,
f80cfac80c53 "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:
f80cfac80c53 "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
f80cfac80c53 "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
f80cfac80c53 "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
f80cfac80c53 "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
f80cfac80c53 "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
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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22
f80cfac80c53 "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:
f80cfac80c53 "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
f80cfac80c53 "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
f80cfac80c53 "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
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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27
f80cfac80c53 "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
f80cfac80c53 "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.
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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30
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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31
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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32 SuCOS is the work of Susan Leung.
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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33 GitHub: https://github.com/susanhleung/SuCOS
f80cfac80c53 "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
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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35 """
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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36
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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37 import sucos, utils
f80cfac80c53 "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
f80cfac80c53 "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
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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40
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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41
2
58d18838e244 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
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42 def process(inputfilename, clusterfilenames, outputfilename):
0
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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43 all_clusters = {}
f80cfac80c53 "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:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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45 cluster = []
f80cfac80c53 "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)
f80cfac80c53 "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)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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48 i = 0
f80cfac80c53 "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:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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50 i += 1
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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51 if not mol:
f80cfac80c53 "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)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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53 continue
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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54 try:
f80cfac80c53 "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)
f80cfac80c53 "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))
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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57 except:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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58 utils.log("WARNING: failed to generate features for molecule", i, "in cluster", filename)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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59
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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60 cluster_file.close()
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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61 all_clusters[filename] = cluster
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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62
f80cfac80c53 "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)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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64 suppl = Chem.ForwardSDMolSupplier(input_file)
f80cfac80c53 "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)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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66 writer = Chem.SDWriter(output_file)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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67
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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68 comparisons = 0
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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69 mol_num = 0
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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70
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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71 for mol in suppl:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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72 mol_num += 1
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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73 if not mol:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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74 utils.log("WARNING: failed to generate molecule", mol_num, "in input")
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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75 continue
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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76 try:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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77 query_features = sucos.getRawFeatures(mol)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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78 except:
f80cfac80c53 "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")
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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80 continue
2
58d18838e244 "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]
58d18838e244 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
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82 scores_cum = [0, 0, 0]
0
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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83 for clusterfilename in all_clusters:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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84 cluster = all_clusters[clusterfilename]
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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85 index = 0
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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86 for entry in cluster:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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87 hit = entry[0]
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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88 ref_features = entry[1]
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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89 index += 1
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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90 comparisons += 1
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91 sucos_score, fm_score, vol_score = sucos.get_SucosScore(hit, mol,
2
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92 tani=False, ref_features=ref_features,
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93 query_features=query_features)
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94
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95 if sucos_score > scores_max[0]:
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96 scores_max[0] = sucos_score
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97 scores_max[1] = fm_score
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98 scores_max[2] = vol_score
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99 cluster_name = clusterfilename
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100 cluster_index = index
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101
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102 scores_cum[0] += sucos_score
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103 scores_cum[1] += fm_score
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104 scores_cum[2] += vol_score
0
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105
2
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106 if scores_max[0] > 0:
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107 cluster_file_name_only = cluster_name.split(os.sep)[-1]
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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])
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110 mol.SetDoubleProp("Max_SuCOS_FeatureMap_Score", scores_max[1])
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111 mol.SetDoubleProp("Max_SuCOS_Protrude_Score", scores_max[2])
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112 mol.SetProp("Max_SuCOS_Cluster", cluster_file_name_only)
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113 mol.SetIntProp("Max_SuCOS_Index", cluster_index)
0
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114
2
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115 # utils.log("Cum SuCOS:", scores[0], "FM:", scores[1], "P:", scores[2])
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116 mol.SetDoubleProp("Cum_SuCOS_Score", scores_cum[0])
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117 mol.SetDoubleProp("Cum_SuCOS_FeatureMap_Score", scores_cum[1])
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118 mol.SetDoubleProp("Cum_SuCOS_Protrude_Score", scores_cum[2])
0
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119
2
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120 writer.write(mol)
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121
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122 input_file.close()
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123 writer.flush()
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124 writer.close()
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125 output_file.close()
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126
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127 utils.log("Completed", comparisons, "comparisons")
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128
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129
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130 ### start main execution #########################################
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131
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132 def main():
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133 parser = argparse.ArgumentParser(description='Max SuCOS scores with RDKit')
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134 parser.add_argument('-i', '--input', help='Input file to score in SDF format. Can be gzipped (*.gz).')
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135 parser.add_argument('-o', '--output', help='Output file in SDF format. Can be gzipped (*.gz).')
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136 parser.add_argument('clusters', nargs='*', help="One or more SDF files with the clustered hits")
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137
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138 args = parser.parse_args()
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139 utils.log("Max SuCOS Args: ", args)
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140
2
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141 process(args.input, args.clusters, args.output)
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142
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143
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144 if __name__ == "__main__":
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145 main()