Merge pull request #1840 from deepchem/nnscore

Remove nnscore_utils
deepchem · May 3, 2020 · 3a5addb · 3a5addb
2 parents 6b02b45 + d66e03f
commit 3a5addb
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Showing 3 changed files with 10 additions and 552 deletions.
diff --git a/deepchem/dock/pose_generation.py b/deepchem/dock/pose_generation.py
@@ -12,7 +12,7 @@
 import os
 import tempfile
 from subprocess import call
-from deepchem.feat import hydrogenate_and_compute_partial_charges
+from deepchem.utils.rdkit_util import add_hydrogens_to_mol
 from deepchem.dock.binding_pocket import RFConvexHullPocketFinder
 from deepchem.utils import rdkit_util
 
@@ -91,14 +91,9 @@ def generate_poses(self,
 
     # Prepare receptor
     receptor_name = os.path.basename(protein_file).split(".")[0]
-    protein_hyd = os.path.join(out_dir, "%s.pdb" % receptor_name)
+    protein_hyd = os.path.join(out_dir, "%s_hyd.pdb" % receptor_name)
     protein_pdbqt = os.path.join(out_dir, "%s.pdbqt" % receptor_name)
-    hydrogenate_and_compute_partial_charges(
-        protein_file,
-        "pdb",
-        hyd_output=protein_hyd,
-        pdbqt_output=protein_pdbqt,
-        protein=True)
+
     # Get protein centroid and range
     # TODO(rbharath): Need to add some way to identify binding pocket, or this is
     # going to be extremely slow!
@@ -107,7 +102,10 @@ def generate_poses(self,
     else:
       if not self.detect_pockets:
         receptor_mol = rdkit_util.load_molecule(
-            protein_hyd, calc_charges=False, add_hydrogens=False)
+            protein_file, calc_charges=True, add_hydrogens=True)
+        rdkit_util.write_molecule(receptor_mol[1], protein_hyd, is_protein=True)
+        rdkit_util.write_molecule(
+            receptor_mol[1], protein_pdbqt, is_protein=True)
         protein_centroid = mol_xyz_util.get_molecule_centroid(receptor_mol[0])
         protein_range = mol_xyz_util.get_molecule_range(receptor_mol[0])
         box_dims = protein_range + 5.0
@@ -129,16 +127,12 @@ def generate_poses(self,
 
     # Prepare receptor
     ligand_name = os.path.basename(ligand_file).split(".")[0]
-    ligand_hyd = os.path.join(out_dir, "%s.pdb" % ligand_name)
     ligand_pdbqt = os.path.join(out_dir, "%s.pdbqt" % ligand_name)
 
     # TODO(rbharath): Generalize this so can support mol2 files as well.
-    hydrogenate_and_compute_partial_charges(
-        ligand_file,
-        "sdf",
-        hyd_output=ligand_hyd,
-        pdbqt_output=ligand_pdbqt,
-        protein=False)
+    ligand_mol = rdkit_util.load_molecule(
+        ligand_file, calc_charges=True, add_hydrogens=True)
+    rdkit_util.write_molecule(ligand_mol[1], ligand_pdbqt)
     # Write Vina conf file
     conf_file = os.path.join(out_dir, "conf.txt")
     write_conf(

diff --git a/deepchem/feat/__init__.py b/deepchem/feat/__init__.py
@@ -16,7 +16,6 @@
 from deepchem.feat.coulomb_matrices import CoulombMatrixEig
 from deepchem.feat.coulomb_matrices import BPSymmetryFunctionInput
 from deepchem.feat.rdkit_grid_featurizer import RdkitGridFeaturizer
-from deepchem.feat.nnscore_utils import hydrogenate_and_compute_partial_charges
 from deepchem.feat.binding_pocket_features import BindingPocketFeaturizer
 from deepchem.feat.one_hot import OneHotFeaturizer
 from deepchem.feat.raw_featurizer import RawFeaturizer