Mercurial > repos > bgruening > sucos_max_score

annotate sucos_max.py @ 7:9b48456a96fe draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
author bgruening
date Wed, 14 Apr 2021 09:30:28 +0000
parents d4c67ced6abc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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1 #!/usr/bin/env python
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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2 """
bb5365381c8f "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.
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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4 This is a quite specialised function that is designed to take a set of potential follow up
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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5 compounds and compare them to a set of clustered fragment hits to help identify which follow up
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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6 ligands best map to the binding space of the hits.
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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7
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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8 The clustering of the fragment hits is expected to be performed with the sucos_cluster.py module
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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9 and will generate a set of SD files, one for each cluster of hits (presumably corresponding to a
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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10 binding pocket in the protein target).
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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11
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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12 Each molecule in the input ligands is then compared (using SuCOS) to each hit in the clusters. There
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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13 are different modes which determine how the ligand is assessed.
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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14
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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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,
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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16 with these additional fields for each molecule:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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17 Max_SuCOS_Score - the best score
bb5365381c8f "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
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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19 Max_SuCOS_Protrude_Score - the protrude volume for the hit that has the best SuCOS score
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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20 Max_SuCOS_Cluster - the name of the cluster SD file that contains the best hit
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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21 Max_SuCOS_Index - the index of the best hit in the SD file
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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:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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24 Cum_SuCOS_Score property: the sum of the SuCOS scores
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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25 Cum_SuCOS_FeatureMap_Score: the sum of the feature map scores
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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26 Cum_SuCOS_Protrude_Score: the sum of the protrude volume scores
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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27
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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
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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29 included in the results.
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30
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31
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32 SuCOS is the work of Susan Leung.
bb5365381c8f "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
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34 Publication: https://doi.org/10.26434/chemrxiv.8100203.v1
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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35 """
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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36
7
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37 import argparse
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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38 import os
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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39
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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40 import sucos
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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41 import utils
0
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42 from rdkit import Chem
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43
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44
7
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45 def process(
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46 inputfilename, clusterfilenames, outputfilename, filter_value, filter_field
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47 ):
0
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48 all_clusters = {}
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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49 for filename in clusterfilenames:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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50 cluster = []
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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51 cluster_file = utils.open_file_for_reading(filename)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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52 suppl = Chem.ForwardSDMolSupplier(cluster_file)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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53 i = 0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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54 for mol in suppl:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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55 i += 1
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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56 if not mol:
7
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57 utils.log(
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58 "WARNING: failed to generate molecule", i, "in cluster", filename
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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59 )
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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60 continue
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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61 try:
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62 features = sucos.getRawFeatures(mol)
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63 cluster.append((mol, features))
7
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64 except Exception:
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65 utils.log(
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66 "WARNING: failed to generate features for molecule",
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67 i,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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68 "in cluster",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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69 filename,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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70 )
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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71
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72 cluster_file.close()
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73 all_clusters[filename] = cluster
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74
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75 input_file = utils.open_file_for_reading(inputfilename)
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76 suppl = Chem.ForwardSDMolSupplier(input_file)
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77 output_file = utils.open_file_for_writing(outputfilename)
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78 writer = Chem.SDWriter(output_file)
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79
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80 comparisons = 0
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81 mol_num = 0
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82
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83 for mol in suppl:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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84 mol_num += 1
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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85 if not mol:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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86 utils.log("WARNING: failed to generate molecule", mol_num, "in input")
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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87 continue
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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88 try:
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89 query_features = sucos.getRawFeatures(mol)
7
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90 except Exception:
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
91 utils.log(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
92 "WARNING: failed to generate features for molecule", mol_num, "in input"
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
93 )
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
94 continue
2
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
95 scores_max = [0, 0, 0]
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
96 scores_cum = [0, 0, 0]
4
85fad59f8168 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 2a74332a201fa9bb53f8e7dc3cc497f653d12929"
bgruening
parents: 3
diff changeset
97 cluster_name = None
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
98 for clusterfilename in all_clusters:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
99 cluster = all_clusters[clusterfilename]
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
100 index = 0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
101 for entry in cluster:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
102 hit = entry[0]
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
103 ref_features = entry[1]
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
104 index += 1
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
105 comparisons += 1
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
106 sucos_score, fm_score, vol_score = sucos.get_SucosScore(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
107 hit,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
108 mol,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
109 tani=False,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
110 ref_features=ref_features,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
111 query_features=query_features,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
112 )
2
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
113
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
114 if sucos_score > scores_max[0]:
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
115 scores_max[0] = sucos_score
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
116 scores_max[1] = fm_score
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
117 scores_max[2] = vol_score
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
118 cluster_name = clusterfilename
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
119 cluster_index = index
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
120
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
121 scores_cum[0] += sucos_score
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
122 scores_cum[1] += fm_score
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
123 scores_cum[2] += vol_score
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
124
3
bf99565cec1f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 8542cbcae3ebed4cb9a6c20b1fabd418a6efb7e8"
bgruening
parents: 2
diff changeset
125 # utils.log("Max SuCOS:", scores[0], "FM:", scores[1], "P:", scores[2],"File:", cluster_file_name_only, "Index:", cluster_index)
bf99565cec1f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 8542cbcae3ebed4cb9a6c20b1fabd418a6efb7e8"
bgruening
parents: 2
diff changeset
126 mol.SetDoubleProp("Max_SuCOS_Score", scores_max[0] if scores_max[0] > 0 else 0)
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
127 mol.SetDoubleProp(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
128 "Max_SuCOS_FeatureMap_Score", scores_max[1] if scores_max[1] > 0 else 0
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
129 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
130 mol.SetDoubleProp(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
131 "Max_SuCOS_Protrude_Score", scores_max[2] if scores_max[2] > 0 else 0
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
132 )
4
85fad59f8168 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 2a74332a201fa9bb53f8e7dc3cc497f653d12929"
bgruening
parents: 3
diff changeset
133
85fad59f8168 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 2a74332a201fa9bb53f8e7dc3cc497f653d12929"
bgruening
parents: 3
diff changeset
134 if cluster_name:
85fad59f8168 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 2a74332a201fa9bb53f8e7dc3cc497f653d12929"
bgruening
parents: 3
diff changeset
135 cluster_file_name_only = cluster_name.split(os.sep)[-1]
85fad59f8168 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 2a74332a201fa9bb53f8e7dc3cc497f653d12929"
bgruening
parents: 3
diff changeset
136 mol.SetProp("Max_SuCOS_Cluster", cluster_file_name_only)
85fad59f8168 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 2a74332a201fa9bb53f8e7dc3cc497f653d12929"
bgruening
parents: 3
diff changeset
137 mol.SetIntProp("Max_SuCOS_Index", cluster_index)
3
bf99565cec1f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 8542cbcae3ebed4cb9a6c20b1fabd418a6efb7e8"
bgruening
parents: 2
diff changeset
138
bf99565cec1f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 8542cbcae3ebed4cb9a6c20b1fabd418a6efb7e8"
bgruening
parents: 2
diff changeset
139 # utils.log("Cum SuCOS:", scores[0], "FM:", scores[1], "P:", scores[2])
bf99565cec1f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 8542cbcae3ebed4cb9a6c20b1fabd418a6efb7e8"
bgruening
parents: 2
diff changeset
140 mol.SetDoubleProp("Cum_SuCOS_Score", scores_cum[0] if scores_cum[0] > 0 else 0)
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
141 mol.SetDoubleProp(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
142 "Cum_SuCOS_FeatureMap_Score", scores_cum[1] if scores_cum[1] > 0 else 0
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
143 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
144 mol.SetDoubleProp(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
145 "Cum_SuCOS_Protrude_Score", scores_cum[2] if scores_cum[2] > 0 else 0
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
146 )
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
147
5
d4c67ced6abc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
bgruening
parents: 4
diff changeset
148 if filter_value and filter_field:
d4c67ced6abc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
bgruening
parents: 4
diff changeset
149 if mol.HasProp(filter_field):
d4c67ced6abc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
bgruening
parents: 4
diff changeset
150 val = mol.GetDoubleProp(filter_field)
d4c67ced6abc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
bgruening
parents: 4
diff changeset
151 if val > filter_value:
d4c67ced6abc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
bgruening
parents: 4
diff changeset
152 writer.write(mol)
d4c67ced6abc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
bgruening
parents: 4
diff changeset
153 else:
d4c67ced6abc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
bgruening
parents: 4
diff changeset
154 writer.write(mol)
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
155
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
156 input_file.close()
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
157 writer.flush()
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
158 writer.close()
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
159 output_file.close()
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
160
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
161 utils.log("Completed", comparisons, "comparisons")
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
diff changeset
162
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
163
7
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bgruening
parents: 5
diff changeset
164 # start main execution #########################################
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
165
0
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bgruening
parents:
diff changeset
166
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
167 def main():
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
168 parser = argparse.ArgumentParser(description="Max SuCOS scores with RDKit")
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
169 parser.add_argument(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
170 "-i",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
171 "--input",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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parents: 5
diff changeset
172 help="Input file to score in SDF format. Can be gzipped (*.gz).",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
173 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
174 parser.add_argument(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
175 "-o", "--output", help="Output file in SDF format. Can be gzipped (*.gz)."
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
176 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
177 parser.add_argument(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
diff changeset
178 "clusters", nargs="*", help="One or more SDF files with the clustered hits"
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 5
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179 )
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180 parser.add_argument(
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181 "--filter-value",
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182 type=float,
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183 help="Filter out values with scores less than this.",
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184 )
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185 parser.add_argument("--filter-field", help="Field to use to filter values.")
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186
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187 args = parser.parse_args()
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188 utils.log("Max SuCOS Args: ", args)
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189
7
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190 process(
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191 args.input, args.clusters, args.output, args.filter_value, args.filter_field
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192 )
0
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193
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194
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195 if __name__ == "__main__":
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196 main()