Commit 260581b8 authored by Bharath Ramsundar's avatar Bharath Ramsundar
Browse files

Starting to add tests for grid featurizers

parent dce38628

deepchem/feat/complex_featurizers/contact_fingerprints.py

+7 −7
Original line number Diff line number Diff line
@@ -95,7 +95,7 @@ class ContactCircularFingerprint(ComplexFeaturizer): 
    self.radius = radius

    self.size = size



  def _featurize(self, mol_pdb: str, complex_pdb: str):

  def _featurize(self, mol_pdb: str, protein_pdb: str):

    """

    Compute featurization for a molecular complex
@@ -103,11 +103,11 @@ class ContactCircularFingerprint(ComplexFeaturizer): 
    ----------

    mol_pdb: str

      Filename for ligand molecule

    complex_pdb: str

    protein_pdb: str

      Filename for protein molecule

    """

    try:

      fragments = load_complex((mol_pdb, complex_pdb), add_hydrogens=False)

      fragments = load_complex((mol_pdb, protein_pdb), add_hydrogens=False)



    except MoleculeLoadException:

      logger.warning("This molecule cannot be loaded by Rdkit. Returning None")
@@ -183,7 +183,7 @@ class ContactCircularVoxelizer(ComplexFeaturizer): 
    self.voxels_per_edge = int(self.box_width / self.voxel_width)

    self.flatten = flatten



  def _featurize(self, mol_pdb: str, complex_pdb: str):

  def _featurize(self, mol_pdb: str, protein_pdb: str):

    """

    Compute featurization for a molecular complex
@@ -191,10 +191,10 @@ class ContactCircularVoxelizer(ComplexFeaturizer): 
    ----------

    mol_pdb: str

      Filename for ligand molecule

    complex_pdb: str

    protein_pdb: str

      Filename for protein molecule

    """

    molecular_complex = (mol_pdb, complex_pdb)

    molecular_complex = (mol_pdb, protein_pdb)

    try:

      fragments = load_complex(molecular_complex, add_hydrogens=False)

deepchem/feat/complex_featurizers/grid_featurizers.py

+30 −20
Original line number Diff line number Diff line
@@ -81,17 +81,20 @@ class ChargeVoxelizer(ComplexFeaturizer): 
    self.voxel_width = voxel_width

    self.reduce_to_contacts = reduce_to_contacts



  def _featurize_complex(self, molecular_complex):

  def _featurize(self, mol_pdb: str, protein_pdb: str):

    """

    Compute featurization for a single mol/protein complex



    Parameters

    ----------

    molecular_complex: Object

      Some representation of a molecular complex.

    mol_pdb: str

      Filename for ligand molecule

    protein_pdb: str

      Filename for protein molecule

    """

    molecular_complex = (mol_pdb, protein_pdb)

    try:

      fragments = rdkit_util.load_complex(

      fragments = rdkit_utils.load_complex(

          molecular_complex, add_hydrogens=False)



    except MoleculeLoadException:
@@ -114,10 +117,10 @@ class ChargeVoxelizer(ComplexFeaturizer): 
          sum([

              voxelize(

                  convert_atom_to_voxel,

                  self.box_width,

                  self.voxel_width,

                  None,

                  xyz,

                  hash_function=hash_ecfp_pair,

                  coordinates=xyz,

                  box_width=self.box_width,

                  voxel_width=self.voxel_width,

                  feature_dict=compute_charge_dictionary(mol),

                  nb_channel=1,

                  dtype="np.float16") for xyz, mol in zip(xyzs, rdks)
@@ -168,7 +171,7 @@ class SaltBridgeVoxelizer(ComplexFeaturizer): 
    self.voxel_width = voxel_width

    self.reduce_to_contacts = reduce_to_contacts



  def _featurize_complex(self, molecular_complex):

  def _featurize(self, mol_pdb: str, protein_pdb: str):

    """

    Compute featurization for a single mol/protein complex
@@ -177,8 +180,9 @@ class SaltBridgeVoxelizer(ComplexFeaturizer): 
    molecular_complex: Object

      Some representation of a molecular complex.

    """

    molecular_complex = (mol_pdb, protein_pdb)

    try:

      fragments = rdkit_util.load_complex(

      fragments = rdkit_utils.load_complex(

          molecular_complex, add_hydrogens=False)



    except MoleculeLoadException:
@@ -256,17 +260,20 @@ class CationPiVoxelizer(ComplexFeaturizer): 
    self.box_width = box_width

    self.voxel_width = voxel_width



  def _featurize_complex(self, molecular_complex):

  def _featurize(self, mol_pdb: str, protein_pdb: str):

    """

    Compute featurization for a single mol/protein complex



    Parameters

    ----------

    molecular_complex: Object

      Some representation of a molecular complex.

    mol_pdb: str

      Filename for ligand molecule

    protein_pdb: str

      Filename for protein molecule

    """

    molecular_complex = (mol_pdb, protein_pdb)

    try:

      fragments = rdkit_util.load_complex(

      fragments = rdkit_utils.load_complex(

          molecular_complex, add_hydrogens=False)



    except MoleculeLoadException:
@@ -348,17 +355,20 @@ class PiStackVoxelizer(ComplexFeaturizer): 
    self.box_width = box_width

    self.voxel_width = voxel_width



  def _featurize_complex(self, molecular_complex):

  def _featurize(self, mol_pdb: str, protein_pdb: str):

    """

    Compute featurization for a single mol/protein complex



    Parameters

    ----------

    molecular_complex: Object

      Some representation of a molecular complex.

    mol_pdb: str

      Filename for ligand molecule

    protein_pdb: str

      Filename for protein molecule

    """

    molecular_complex = (mol_pdb, protein_pdb)

    try:

      fragments = rdkit_util.load_complex(

      fragments = rdkit_utils.load_complex(

          molecular_complex, add_hydrogens=False)



    except MoleculeLoadException:
@@ -479,7 +489,7 @@ class HydrogenBondCounter(ComplexFeaturizer): 
      Some representation of a molecular complex.

    """

    try:

      fragments = rdkit_util.load_complex(

      fragments = rdkit_utils.load_complex(

          molecular_complex, add_hydrogens=False)



    except MoleculeLoadException:
@@ -585,7 +595,7 @@ class HydrogenBondVoxelizer(ComplexFeaturizer): 
      Some representation of a molecular complex.

    """

    try:

      fragments = rdkit_util.load_complex(

      fragments = rdkit_utils.load_complex(

          molecular_complex, add_hydrogens=False)



    except MoleculeLoadException:

deepchem/feat/tests/test_grid_featurizers.py

0 → 100644
+37 −0
Original line number Diff line number Diff line 
import os

import unittest

import deepchem as dc





def test_charge_voxelizer():

  current_dir = os.path.dirname(os.path.realpath(__file__))

  protein_file = os.path.join(current_dir, 'data',

                              '3ws9_protein_fixer_rdkit.pdb')

  ligand_file = os.path.join(current_dir, 'data', '3ws9_ligand.sdf')



  cutoff = 4.5

  box_width = 16

  voxel_width = 1.0

  voxelizer = dc.feat.ChargeVoxelizer(

      cutoff=cutoff, box_width=box_width, voxel_width=voxel_width)

  features, failures = voxelizer.featurize([ligand_file], [protein_file])





def test_salt_bridge_voxelizer():

  pass





def test_cation_pi_voxelizer():

  pass





def test_pi_stack_voxelizer():

  pass





def test_hydrogen_bond_counter():

  pass





def test_hydrogen_bond_voxelizer():

  pass

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