Add RFscore v4 (12x1A bin + 11 Vina terms)

oddt · Dec 14, 2017 · c52e03f · c52e03f
1 parent 7ce63af
commit c52e03f
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diff --git a/oddt/scoring/functions/RFScore.py b/oddt/scoring/functions/RFScore.py
@@ -61,6 +61,27 @@ def __init__(self, protein=None, n_jobs=-1, version=1, spr=0, **kwargs):
                            'vina_num_rotors']
             vina = oddt_vina_descriptor(protein, vina_scores=vina_scores)
             descriptors = ensemble_descriptor((vina, cc))
+        elif version == 4:
+            cutoff = 12
+            mtry = 12
+            cc = close_contacts(protein,
+                                cutoff=cutoff,
+                                protein_types=protein_atomic_nums,
+                                ligand_types=ligand_atomic_nums)
+            vina_scores = ['vina_gauss1',
+                           'vina_gauss2',
+                           'vina_repulsion',
+                           'vina_hydrophobic',
+                           'vina_hydrogen',
+                           'vina_intra_gauss1',
+                           'vina_intra_gauss2',
+                           'vina_intra_repulsion',
+                           'vina_intra_hydrophobic',
+                           'vina_intra_hydrogen',
+                           'vina_num_rotors']
+            vina = oddt_vina_descriptor(protein, vina_scores=vina_scores)
+            descriptors = ensemble_descriptor((vina, cc))
+
         model = randomforest(n_estimators=500,
                              oob_score=True,
                              n_jobs=n_jobs,