do not use aromatic interactions is pose scoring and examples

(they require sanitized molecules to work correctly)
kyscg · Nov 2, 2017 · 1ae9bc9 · 1ae9bc9
1 parent 8ffc36f
commit 1ae9bc9
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Showing 2 changed files with 10 additions and 6 deletions.
diff --git a/deepchem/dock/pose_scoring.py b/deepchem/dock/pose_scoring.py
@@ -34,11 +34,13 @@ def __init__(self, model, feat="grid"):
     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.")

diff --git a/examples/pdbbind/pdbbind_datasets.py b/examples/pdbbind/pdbbind_datasets.py
@@ -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