Mercurial > repos > bgruening > sucos_clustering

annotate sucos.py @ 1:334ad24525db draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6fa2a0294d615c9f267b766337dca0b2d3637219"
author bgruening
date Fri, 11 Oct 2019 18:26:08 -0400
parents f80cfac80c53
children 58d18838e244
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f80cfac80c53 "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 """
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11 from __future__ import print_function
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12 import argparse, os, sys, gzip
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13 import numpy as np
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14 from rdkit import Chem, rdBase, RDConfig
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15 from rdkit.Chem import AllChem, rdShapeHelpers
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16 from rdkit.Chem.FeatMaps import FeatMaps
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17 import utils
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20 ### start function definitions #########################################
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22 # Setting up the features to use in FeatureMap
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23 fdef = AllChem.BuildFeatureFactory(os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef'))
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25 fmParams = {}
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26 for k in fdef.GetFeatureFamilies():
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27 fparams = FeatMaps.FeatMapParams()
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28 fmParams[k] = fparams
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29
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30 keep = ('Donor', 'Acceptor', 'NegIonizable', 'PosIonizable', 'ZnBinder',
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31 'Aromatic', 'Hydrophobe', 'LumpedHydrophobe')
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33 def filterFeature(f):
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34 result = f.GetFamily() in keep
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35 # TODO - nothing ever seems to be filtered. Is this expected?
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36 if not result:
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37 utils.log("Filtered out feature type", f.GetFamily())
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38 return result
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39
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40 def getRawFeatures(mol):
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41
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42 rawFeats = fdef.GetFeaturesForMol(mol)
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43 # filter that list down to only include the ones we're interested in
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44 filtered = list(filter(filterFeature, rawFeats))
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45 return filtered
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47 def get_FeatureMapScore(small_feats, large_feats, tani=False, score_mode=FeatMaps.FeatMapScoreMode.All):
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48 """
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49 Generate the feature map score.
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50
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51 :param small_feats:
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52 :param large_feats:
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53 :param tani:
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54 :return:
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55 """
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56
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57 featLists = []
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58 for rawFeats in [small_feats, large_feats]:
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59 # filter that list down to only include the ones we're interested in
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60 featLists.append(rawFeats)
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61 fms = [FeatMaps.FeatMap(feats=x, weights=[1] * len(x), params=fmParams) for x in featLists]
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62 # set the score mode
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63 fms[0].scoreMode = score_mode
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64
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65 try:
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66 if tani:
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67 c = fms[0].ScoreFeats(featLists[1])
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68 A = fms[0].GetNumFeatures()
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69 B = len(featLists[1])
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70 if B != fms[1].GetNumFeatures():
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71 utils.log("Why isn't B equal to number of features...?!")
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72 tani_score = float(c) / (A+B-c)
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73 return tani_score
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74 else:
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75 fm_score = fms[0].ScoreFeats(featLists[1]) / min(fms[0].GetNumFeatures(), len(featLists[1]))
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76 return fm_score
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77 except ZeroDivisionError:
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78 utils.log("ZeroDivisionError")
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79 return 0
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80
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81 if tani:
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82 tani_score = float(c) / (A+B-c)
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83 return tani_score
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84 else:
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85 fm_score = fms[0].ScoreFeats(featLists[1]) / min(fms[0].GetNumFeatures(), len(featLists[1]))
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86 return fm_score
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87
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88
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89 def get_SucosScore(ref_mol, query_mol, tani=False, ref_features=None, query_features=None, score_mode=FeatMaps.FeatMapScoreMode.All):
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90 """
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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91 This is the key function that calculates the SuCOS scores and is expected to be called from other modules.
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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92 To improve performance you can pre-calculate the features and pass them in as optional parameters to avoid having
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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93 to recalculate them. Use the getRawFeatures function to pre-calculate the features.
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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94
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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95 :param ref_mol: The reference molecule to compare to
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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96 :param query_mol: The molecule to align to the reference
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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97 :param tani: Whether to calculate Tanimoto distances
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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98 :param ref_features: An optional feature map for the reference molecule, avoiding the need to re-calculate it.
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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99 :param query_features: An optional feature map for the query molecule, avoiding the need to re-calculate it.
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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100 :return: A tuple of 3 values. 1 the sucos score, 2 the feature map score,
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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101 3 the Tanimoto distance or 1 minus the protrude distance
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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102 """
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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103
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104 if not ref_features:
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105 ref_features = getRawFeatures(ref_mol)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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106 if not query_features:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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107 query_features = getRawFeatures(query_mol)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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108
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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109 fm_score = get_FeatureMapScore(ref_features, query_features, tani, score_mode)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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110 fm_score = np.clip(fm_score, 0, 1)
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111
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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112 if tani:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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113 tani_sim = 1 - float(rdShapeHelpers.ShapeTanimotoDist(ref_mol, query_mol))
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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114 tani_sim = np.clip(tani_sim, 0, 1)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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115 SuCOS_score = 0.5*fm_score + 0.5*tani_sim
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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116 return SuCOS_score, fm_score, tani_sim
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117 else:
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118 protrude_dist = rdShapeHelpers.ShapeProtrudeDist(ref_mol, query_mol, allowReordering=False)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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119 protrude_dist = np.clip(protrude_dist, 0, 1)
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120 protrude_val = 1.0 - protrude_dist
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121 SuCOS_score = 0.5 * fm_score + 0.5 * protrude_val
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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122 return SuCOS_score, fm_score, protrude_val
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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123
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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124 def process(refmol_filename, inputs_filename, outputs_filename, refmol_index=None,
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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125 refmol_format=None, tani=False, score_mode=FeatMaps.FeatMapScoreMode.All):
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126
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127 ref_mol = utils.read_single_molecule(refmol_filename, index=refmol_index, format=refmol_format)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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128 #utils.log("Reference mol has", ref_mol.GetNumHeavyAtoms(), "heavy atoms")
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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129 ref_features = getRawFeatures(ref_mol)
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130
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131 input_file = utils.open_file_for_reading(inputs_filename)
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132 suppl = Chem.ForwardSDMolSupplier(input_file)
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133 output_file = utils.open_file_for_writing(outputs_filename)
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134 writer = Chem.SDWriter(output_file)
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135
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136 count = 0
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137 total = 0
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138 errors = 0
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139 for mol in suppl:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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140 count +=1
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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141 if mol is None:
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diff changeset
142 continue
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143 #utils.log("Mol has", str(mol.GetNumHeavyAtoms()), "heavy atoms")
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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144 try:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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145 sucos_score, fm_score, val3 = get_SucosScore(ref_mol, mol, tani=tani, ref_features=ref_features, score_mode=score_mode)
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146 mol.SetDoubleProp("SuCOS_Score", sucos_score)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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147 mol.SetDoubleProp("SuCOS_FeatureMap_Score", fm_score)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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148 if tani:
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149 mol.SetDoubleProp("SuCOS_Tanimoto_Score", val3)
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150 else:
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151 mol.SetDoubleProp("SuCOS_Protrude_Score", val3)
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152 utils.log("Scores:", sucos_score, fm_score, val3)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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153 writer.write(mol)
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diff changeset
154 total +=1
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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parents:
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155 except ValueError as e:
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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156 errors +=1
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157 utils.log("Molecule", count, "failed to score:", e.message)
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158
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159 input_file.close()
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160 writer.flush()
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161 writer.close()
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162 output_file.close()
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163
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164 utils.log("Completed.", total, "processed, ", count, "succeeded, ", errors, "errors")
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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165
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166 def parse_score_mode(value):
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167 if value == None or value == 'all':
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168 return FeatMaps.FeatMapScoreMode.All
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parents:
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169 elif value == 'closest':
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170 return FeatMaps.FeatMapScoreMode.Closest
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171 elif value == 'best':
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172 return FeatMaps.FeatMapScoreMode.Best
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173 else:
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parents:
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174 raise ValueError(value + " is not a valid scoring mode option")
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175
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176
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177 ### start main execution #########################################
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178
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179 def main():
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180
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181 parser = argparse.ArgumentParser(description='SuCOS with RDKit')
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182 parser.add_argument('-i', '--input', help='Input file in SDF format. Can be gzipped (*.gz).')
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183 parser.add_argument('-r', '--refmol', help='Molecule to compare against in Molfile (.mol) or SDF (.sdf) format')
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184 parser.add_argument('--refmol-format', help="Format for the reference molecule (mol or sdf). " +
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185 "Only needed if files don't have the expected extensions")
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186 parser.add_argument('--refmolidx', help='Reference molecule index in SD file if not the first', type=int, default=1)
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187 parser.add_argument('-o', '--output', help='Output file in SDF format. Can be gzipped (*.gz).')
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188 parser.add_argument('--tanimoto', action='store_true', help='Include Tanimoto distance in score')
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189 parser.add_argument('--score_mode', choices=['all', 'closest', 'best'],
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190 help="choose the scoring mode for the feature map, default is 'all'.")
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191
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192 args = parser.parse_args()
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193 utils.log("SuCOS Args: ", args)
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194
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195 score_mode = parse_score_mode(args.score_mode)
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196
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197 process(args.refmol, args.input, args.output, refmol_index=args.refmolidx,
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198 refmol_format=args.refmol_format, tani=args.tanimoto, score_mode=score_mode)
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199
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200
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201 if __name__ == "__main__":
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202 main()