Mercurial > repos > bgruening > sucos_clustering

comparison sucos.py @ 2:58d18838e244 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6f1ee2812cca091561a2b2e464498dae2f913b8d"
author bgruening
date Thu, 19 Mar 2020 07:25:25 -0400
parents f80cfac80c53
children b8725fec8c7b
comparison
equal deleted inserted replaced
1:334ad24525db 2:58d18838e244
107 query_features = getRawFeatures(query_mol) 107 query_features = getRawFeatures(query_mol)
108 108
109 fm_score = get_FeatureMapScore(ref_features, query_features, tani, score_mode) 109 fm_score = get_FeatureMapScore(ref_features, query_features, tani, score_mode)
110 fm_score = np.clip(fm_score, 0, 1) 110 fm_score = np.clip(fm_score, 0, 1)
111 111
112 if tani: 112 try :
113 tani_sim = 1 - float(rdShapeHelpers.ShapeTanimotoDist(ref_mol, query_mol)) 113 if tani:
114 tani_sim = np.clip(tani_sim, 0, 1) 114 tani_sim = 1 - float(rdShapeHelpers.ShapeTanimotoDist(ref_mol, query_mol))
115 SuCOS_score = 0.5*fm_score + 0.5*tani_sim 115 tani_sim = np.clip(tani_sim, 0, 1)
116 return SuCOS_score, fm_score, tani_sim 116 SuCOS_score = 0.5*fm_score + 0.5*tani_sim
117 else: 117 return SuCOS_score, fm_score, tani_sim
118 protrude_dist = rdShapeHelpers.ShapeProtrudeDist(ref_mol, query_mol, allowReordering=False) 118 else:
119 protrude_dist = np.clip(protrude_dist, 0, 1) 119 protrude_dist = rdShapeHelpers.ShapeProtrudeDist(ref_mol, query_mol, allowReordering=False)
120 protrude_val = 1.0 - protrude_dist 120 protrude_dist = np.clip(protrude_dist, 0, 1)
121 SuCOS_score = 0.5 * fm_score + 0.5 * protrude_val 121 protrude_val = 1.0 - protrude_dist
122 return SuCOS_score, fm_score, protrude_val 122 SuCOS_score = 0.5 * fm_score + 0.5 * protrude_val
123 return SuCOS_score, fm_score, protrude_val
124 except:
125 utils.log("Failed to calculate SuCOS scores. Returning 0,0,0")
126 return 0, 0, 0
123 127
124 def process(refmol_filename, inputs_filename, outputs_filename, refmol_index=None, 128 def process(refmol_filename, inputs_filename, outputs_filename, refmol_index=None,
125 refmol_format=None, tani=False, score_mode=FeatMaps.FeatMapScoreMode.All): 129 refmol_format=None, tani=False, score_mode=FeatMaps.FeatMapScoreMode.All):
126 130
127 ref_mol = utils.read_single_molecule(refmol_filename, index=refmol_index, format=refmol_format) 131 ref_mol = utils.read_single_molecule(refmol_filename, index=refmol_index, format=refmol_format)