updated functions that use RdkitGridFeaturizer

joe-nano · Nov 2, 2017 · 2347bb5 · 2347bb5
1 parent 7b1f650
commit 2347bb5
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Showing 2 changed files with 4 additions and 12 deletions.
diff --git a/deepchem/dock/pose_scoring.py b/deepchem/dock/pose_scoring.py
@@ -34,12 +34,8 @@ def __init__(self, model, feat="grid"):
     if feat == "grid":
       self.featurizer = RdkitGridFeaturizer(
           voxel_width=16.0,
-          feature_types="voxel_combined",
-          # TODO(rbharath, enf): Figure out why pi_stack is slow and cation_pi
-          # causes segfaults.
-          #voxel_feature_types=["ecfp", "splif", "hbond", "pi_stack", "cation_pi",
-          #"salt_bridge"], ecfp_power=9, splif_power=9,
-          voxel_feature_types=["ecfp", "splif", "hbond", "salt_bridge"],
+          feature_types=["ecfp", "splif", "hbond", "pi_stack", "cation_pi",
+          "salt_bridge"],
           ecfp_power=9,
           splif_power=9,
           parallel=True,

diff --git a/examples/pdbbind/pdbbind_datasets.py b/examples/pdbbind/pdbbind_datasets.py
@@ -71,12 +71,8 @@ def featurize_pdbbind(data_dir=None, feat="grid", subset="core"):
   if feat == "grid":
     featurizer = dc.feat.RdkitGridFeaturizer(
         voxel_width=16.0,
-        feature_types="voxel_combined",
-        # TODO(rbharath, enf, leswing): Figure out why pi_stack and cation_pi
-        # reduce validation performance
-        # voxel_feature_types=["ecfp", "splif", "hbond", "pi_stack", "cation_pi",
-        # "salt_bridge"], ecfp_power=9, splif_power=9,
-        voxel_feature_types=["ecfp", "splif", "hbond", "salt_bridge"],
+        feature_types=["ecfp", "splif", "hbond", "pi_stack", "cation_pi",
+        "salt_bridge"],
         ecfp_power=9,
         splif_power=9,
         parallel=True,