Commit 1ae9bc95 authored by marta-sd's avatar marta-sd
Browse files

do not use aromatic interactions is pose scoring and examples 

(they require sanitized molecules to work correctly)
parent 8ffc36fe

deepchem/dock/pose_scoring.py

+5 −3
Original line number Diff line number Diff line
@@ -34,11 +34,13 @@ class GridPoseScorer(object): 
    if feat == "grid":

      self.featurizer = RdkitGridFeaturizer(

          voxel_width=16.0,

          feature_types=["ecfp", "splif", "hbond", "pi_stack", "cation_pi",

          "salt_bridge"],

          # TODO: add pi_stack and cation_pi to feature_types (it's not trivial

          # because they require sanitized molecules)

          # feature_types=["ecfp", "splif", "hbond", "pi_stack", "cation_pi",

          # "salt_bridge"],

          feature_types=["ecfp", "splif", "hbond", "salt_bridge"],

          ecfp_power=9,

          splif_power=9,

          parallel=True,

          flatten=True)

    else:

      raise ValueError("feat not defined.")

examples/pdbbind/pdbbind_datasets.py

+5 −3
Original line number Diff line number Diff line
@@ -71,11 +71,13 @@ def featurize_pdbbind(data_dir=None, feat="grid", subset="core"): 
  if feat == "grid":

    featurizer = dc.feat.RdkitGridFeaturizer(

        voxel_width=16.0,

        feature_types=["ecfp", "splif", "hbond", "pi_stack", "cation_pi",

        "salt_bridge"],

        # TODO: add pi_stack and cation_pi to feature_types (it's not trivial

        # because they require sanitized molecules)

        # feature_types=["ecfp", "splif", "hbond", "pi_stack", "cation_pi",

        # "salt_bridge"],

        feature_types=["ecfp", "splif", "hbond", "salt_bridge"],

        ecfp_power=9,

        splif_power=9,

        parallel=True,

        flatten=True)

  elif feat == "coord":

    neighbor_cutoff = 4

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