Commit 2347bb57 authored by marta-sd's avatar marta-sd
Browse files

updated functions that use RdkitGridFeaturizer

parent 7b1f6500

deepchem/dock/pose_scoring.py

+2 −6
Original line number Diff line number Diff line
@@ -34,12 +34,8 @@ class GridPoseScorer(object): 
    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,

examples/pdbbind/pdbbind_datasets.py

+2 −6
Original line number Diff line number Diff line
@@ -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,

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