Mercurial > repos > bgruening > sucos_max_score

annotate sucos.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 2f110aef9b53
children
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bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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1 #!/usr/bin/env python
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2 """
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3 Basic SuCOS scoring. Allows a set of molecules from a SD file to be overlayed to a reference molecule,
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4 with the resulting scores being written as properties in the output SD file.
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6 SuCOS is the work of Susan Leung.
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7 GitHub: https://github.com/susanhleung/SuCOS
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8 Publication: https://doi.org/10.26434/chemrxiv.8100203.v1
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9 """
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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11 from __future__ import print_function
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13 import argparse
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14 import os
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16 import numpy as np
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17 import utils
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18 from rdkit import Chem, RDConfig
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19 from rdkit.Chem import AllChem, rdShapeHelpers
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20 from rdkit.Chem.FeatMaps import FeatMaps
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21
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22 # start function definitions #########################################
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24 # Setting up the features to use in FeatureMap
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25 fdef = AllChem.BuildFeatureFactory(
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26 os.path.join(RDConfig.RDDataDir, "BaseFeatures.fdef")
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27 )
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29 fmParams = {}
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30 for k in fdef.GetFeatureFamilies():
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31 fparams = FeatMaps.FeatMapParams()
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32 fmParams[k] = fparams
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33
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34 keep = (
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35 "Donor",
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36 "Acceptor",
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37 "NegIonizable",
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38 "PosIonizable",
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39 "ZnBinder",
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40 "Aromatic",
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41 "Hydrophobe",
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42 "LumpedHydrophobe",
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43 )
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44
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46 def filterFeature(f):
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47 result = f.GetFamily() in keep
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48 # TODO - nothing ever seems to be filtered. Is this expected?
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49 if not result:
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50 utils.log("Filtered out feature type", f.GetFamily())
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51 return result
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52
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54 def getRawFeatures(mol):
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56 rawFeats = fdef.GetFeaturesForMol(mol)
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57 # filter that list down to only include the ones we're interested in
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58 filtered = list(filter(filterFeature, rawFeats))
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59 return filtered
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62 def get_FeatureMapScore(
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63 small_feats, large_feats, tani=False, score_mode=FeatMaps.FeatMapScoreMode.All
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64 ):
0
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65 """
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66 Generate the feature map score.
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67
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68 :param small_feats:
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69 :param large_feats:
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70 :param tani:
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71 :return:
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72 """
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74 featLists = []
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75 for rawFeats in [small_feats, large_feats]:
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76 # filter that list down to only include the ones we're interested in
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77 featLists.append(rawFeats)
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78 fms = [
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79 FeatMaps.FeatMap(feats=x, weights=[1] * len(x), params=fmParams)
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80 for x in featLists
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81 ]
0
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82 # set the score mode
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83 fms[0].scoreMode = score_mode
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84
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85 try:
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86 if tani:
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87 c = fms[0].ScoreFeats(featLists[1])
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88 A = fms[0].GetNumFeatures()
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89 B = len(featLists[1])
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90 if B != fms[1].GetNumFeatures():
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91 utils.log("Why isn't B equal to number of features...?!")
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92 tani_score = float(c) / (A + B - c)
0
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bgruening
parents:
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93 return tani_score
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bgruening
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diff changeset
94 else:
7
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bgruening
parents: 2
diff changeset
95 fm_score = fms[0].ScoreFeats(featLists[1]) / min(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
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96 fms[0].GetNumFeatures(), len(featLists[1])
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
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diff changeset
97 )
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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98 return fm_score
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
99 except ZeroDivisionError:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
100 utils.log("ZeroDivisionError")
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
101 return 0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
102
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
103 if tani:
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
104 tani_score = float(c) / (A + B - c)
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
105 return tani_score
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
106 else:
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
107 fm_score = fms[0].ScoreFeats(featLists[1]) / min(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
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108 fms[0].GetNumFeatures(), len(featLists[1])
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
109 )
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
110 return fm_score
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
111
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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112
7
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bgruening
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113 def get_SucosScore(
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114 ref_mol,
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115 query_mol,
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116 tani=False,
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117 ref_features=None,
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118 query_features=None,
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bgruening
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119 score_mode=FeatMaps.FeatMapScoreMode.All,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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diff changeset
120 ):
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
121 """
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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122 This is the key function that calculates the SuCOS scores and is expected to be called from other modules.
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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123 To improve performance you can pre-calculate the features and pass them in as optional parameters to avoid having
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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diff changeset
124 to recalculate them. Use the getRawFeatures function to pre-calculate the features.
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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125
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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126 :param ref_mol: The reference molecule to compare to
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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127 :param query_mol: The molecule to align to the reference
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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128 :param tani: Whether to calculate Tanimoto distances
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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129 :param ref_features: An optional feature map for the reference molecule, avoiding the need to re-calculate it.
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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130 :param query_features: An optional feature map for the query molecule, avoiding the need to re-calculate it.
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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131 :return: A tuple of 3 values. 1 the sucos score, 2 the feature map score,
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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132 3 the Tanimoto distance or 1 minus the protrude distance
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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133 """
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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134
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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135 if not ref_features:
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bgruening
parents:
diff changeset
136 ref_features = getRawFeatures(ref_mol)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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137 if not query_features:
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bgruening
parents:
diff changeset
138 query_features = getRawFeatures(query_mol)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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139
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
140 fm_score = get_FeatureMapScore(ref_features, query_features, tani, score_mode)
7
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diff changeset
141 fm_score = np.float(np.clip(fm_score, 0, 1))
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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142
7
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bgruening
parents: 2
diff changeset
143 try:
2
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bgruening
parents: 0
diff changeset
144 if tani:
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
145 tani_sim = 1 - float(rdShapeHelpers.ShapeTanimotoDist(ref_mol, query_mol))
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
146 tani_sim = np.clip(tani_sim, 0, 1)
7
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bgruening
parents: 2
diff changeset
147 SuCOS_score = 0.5 * fm_score + 0.5 * tani_sim
2
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
148 return SuCOS_score, fm_score, tani_sim
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
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parents: 0
diff changeset
149 else:
7
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parents: 2
diff changeset
150 protrude_dist = rdShapeHelpers.ShapeProtrudeDist(
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diff changeset
151 ref_mol, query_mol, allowReordering=False
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parents: 2
diff changeset
152 )
2
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
153 protrude_dist = np.clip(protrude_dist, 0, 1)
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
154 protrude_val = 1.0 - protrude_dist
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
155 SuCOS_score = 0.5 * fm_score + 0.5 * protrude_val
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
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156 return SuCOS_score, fm_score, protrude_val
7
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parents: 2
diff changeset
157 except Exception:
2
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
158 utils.log("Failed to calculate SuCOS scores. Returning 0,0,0")
2f110aef9b53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
bgruening
parents: 0
diff changeset
159 return 0, 0, 0
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
diff changeset
160
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
diff changeset
161
7
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bgruening
parents: 2
diff changeset
162 def process(
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diff changeset
163 refmol_filename,
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diff changeset
164 inputs_filename,
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diff changeset
165 outputs_filename,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
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diff changeset
166 refmol_index=None,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
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diff changeset
167 refmol_format=None,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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diff changeset
168 tani=False,
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diff changeset
169 score_mode=FeatMaps.FeatMapScoreMode.All,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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parents: 2
diff changeset
170 ):
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
171
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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parents: 2
diff changeset
172 ref_mol = utils.read_single_molecule(
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diff changeset
173 refmol_filename, index=refmol_index, format=refmol_format
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parents: 2
diff changeset
174 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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parents: 2
diff changeset
175 # utils.log("Reference mol has", ref_mol.GetNumHeavyAtoms(), "heavy atoms")
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
176 ref_features = getRawFeatures(ref_mol)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
diff changeset
177
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
diff changeset
178 input_file = utils.open_file_for_reading(inputs_filename)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
diff changeset
179 suppl = Chem.ForwardSDMolSupplier(input_file)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
diff changeset
180 output_file = utils.open_file_for_writing(outputs_filename)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
diff changeset
181 writer = Chem.SDWriter(output_file)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
182
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
183 count = 0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
184 total = 0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
185 errors = 0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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186 for mol in suppl:
7
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bgruening
parents: 2
diff changeset
187 count += 1
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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188 if mol is None:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
189 continue
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
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diff changeset
190 # utils.log("Mol has", str(mol.GetNumHeavyAtoms()), "heavy atoms")
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
191 try:
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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diff changeset
192 sucos_score, fm_score, val3 = get_SucosScore(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
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diff changeset
193 ref_mol,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
194 mol,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
195 tani=tani,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
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diff changeset
196 ref_features=ref_features,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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diff changeset
197 score_mode=score_mode,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
198 )
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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199 mol.SetDoubleProp("SuCOS_Score", sucos_score)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
200 mol.SetDoubleProp("SuCOS_FeatureMap_Score", fm_score)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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201 if tani:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
202 mol.SetDoubleProp("SuCOS_Tanimoto_Score", val3)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
203 else:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
204 mol.SetDoubleProp("SuCOS_Protrude_Score", val3)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
205 utils.log("Scores:", sucos_score, fm_score, val3)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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206 writer.write(mol)
7
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bgruening
parents: 2
diff changeset
207 total += 1
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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208 except ValueError as e:
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
209 errors += 1
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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210 utils.log("Molecule", count, "failed to score:", e.message)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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211
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
212 input_file.close()
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
213 writer.flush()
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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214 writer.close()
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
215 output_file.close()
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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216
7
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bgruening
parents: 2
diff changeset
217 utils.log(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
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diff changeset
218 "Completed.", total, "processed, ", count, "succeeded, ", errors, "errors"
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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parents: 2
diff changeset
219 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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diff changeset
220
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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221
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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222 def parse_score_mode(value):
7
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parents: 2
diff changeset
223 if value is None or value == "all":
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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224 return FeatMaps.FeatMapScoreMode.All
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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diff changeset
225 elif value == "closest":
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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226 return FeatMaps.FeatMapScoreMode.Closest
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
227 elif value == "best":
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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228 return FeatMaps.FeatMapScoreMode.Best
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
229 else:
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
230 raise ValueError(value + " is not a valid scoring mode option")
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
diff changeset
231
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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232
7
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bgruening
parents: 2
diff changeset
233 # start main execution #########################################
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parents: 2
diff changeset
234
0
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parents:
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235
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
236 def main():
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
diff changeset
237
7
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
238 parser = argparse.ArgumentParser(description="SuCOS with RDKit")
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
239 parser.add_argument(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
240 "-i", "--input", help="Input 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: 2
diff changeset
241 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
242 parser.add_argument(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
243 "-r",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
244 "--refmol",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
245 help="Molecule to compare against in Molfile (.mol) or SDF (.sdf) format",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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parents: 2
diff changeset
246 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
247 parser.add_argument(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
248 "--refmol-format",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
249 help="Format for the reference molecule (mol or sdf). "
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
250 + "Only needed if files don't have the expected extensions",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
251 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
252 parser.add_argument(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
253 "--refmolidx",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
254 help="Reference molecule index in SD file if not the first",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
255 type=int,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
256 default=1,
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
257 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
258 parser.add_argument(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
259 "-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"
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parents: 2
diff changeset
260 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
261 parser.add_argument(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
262 "--tanimoto", action="store_true", help="Include Tanimoto distance in score"
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
263 )
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
264 parser.add_argument(
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
265 "--score_mode",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
266 choices=["all", "closest", "best"],
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
267 help="choose the scoring mode for the feature map, default is 'all'.",
9b48456a96fe "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
bgruening
parents: 2
diff changeset
268 )
0
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
269
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
270 args = parser.parse_args()
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
271 utils.log("SuCOS Args: ", args)
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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272
bb5365381c8f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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273 score_mode = parse_score_mode(args.score_mode)
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274
7
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275 process(
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276 args.refmol,
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277 args.input,
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278 args.output,
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279 refmol_index=args.refmolidx,
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280 refmol_format=args.refmol_format,
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281 tani=args.tanimoto,
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282 score_mode=score_mode,
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283 )
0
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284
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285
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286 if __name__ == "__main__":
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287 main()