Commit 03b787d3 authored by Bharath Ramsundar's avatar Bharath Ramsundar Committed by Bharath Ramsundar
Browse files

Working towards fixing contact tests

parent ef84623c

datasets/.gitignore

0 → 100644
+9 −0
Original line number Diff line number Diff line 
PPB.csv

SAMPL.csv

bace.csv

bace_c-featurized/

clintox-featurized/

clintox.csv.gz

core_grid.json

ppb-featurized/

sampl-featurized/

deepchem/feat/complex_featurizers/__init__.py

+8 −0
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@@ -6,3 +6,11 @@ from deepchem.feat.complex_featurizers.rdkit_grid_featurizer import RdkitGridFea 
from deepchem.feat.complex_featurizers.complex_atomic_coordinates import NeighborListAtomicCoordinates

from deepchem.feat.complex_featurizers.complex_atomic_coordinates import NeighborListComplexAtomicCoordinates

from deepchem.feat.complex_featurizers.complex_atomic_coordinates import ComplexNeighborListFragmentAtomicCoordinates

from deepchem.feat.complex_featurizers.contact_fingerprints import ContactCircularFingerprint

from deepchem.feat.complex_featurizers.contact_fingerprints import ContactCircularVoxelizer

from deepchem.feat.complex_featurizers.grid_featurizers import ChargeVoxelizer

from deepchem.feat.complex_featurizers.grid_featurizers import SaltBridgeVoxelizer

from deepchem.feat.complex_featurizers.grid_featurizers import CationPiVoxelizer

from deepchem.feat.complex_featurizers.grid_featurizers import PiStackVoxelizer

from deepchem.feat.complex_featurizers.grid_featurizers import HydrogenBondVoxelizer

from deepchem.feat.complex_featurizers.grid_featurizers import HydrogenBondCounter

deepchem/feat/complex_featurizers/contact_fingerprints.py

+4 −4
Original line number Diff line number Diff line
@@ -6,13 +6,13 @@ import logging 
import itertools

from deepchem.utils.hash_utils import hash_ecfp

from deepchem.feat import ComplexFeaturizer

from deepchem.utils import rdkit_util

from deepchem.utils import rdkit_utils

from deepchem.utils.hash_utils import vectorize

from deepchem.utils.voxel_utils import voxelize

from deepchem.utils.voxel_utils import convert_atom_to_voxel

from deepchem.utils.rdkit_util import compute_all_ecfp

from deepchem.utils.rdkit_util import compute_contact_centroid

from deepchem.utils.rdkit_util import MoleculeLoadException

from deepchem.utils.rdkit_utils import compute_all_ecfp

from deepchem.utils.rdkit_utils import compute_contact_centroid

from deepchem.utils.rdkit_utils import MoleculeLoadException

from deepchem.utils.geometry_utils import compute_pairwise_distances

from deepchem.utils.geometry_utils import subtract_centroid

deepchem/feat/complex_featurizers/grid_featurizers.py

+5 −5
Original line number Diff line number Diff line
@@ -4,7 +4,7 @@ Compute various spatial fingerprints for macromolecular complexes. 
import itertools

import logging

import numpy as np

from deepchem.utils import rdkit_util

from deepchem.utils import rdkit_utils

from deepchem.feat import ComplexFeaturizer

from deepchem.utils.hash_utils import hash_ecfp_pair

from deepchem.utils.voxel_utils import voxelize
@@ -14,12 +14,12 @@ from deepchem.utils.noncovalent_utils import compute_salt_bridges 
from deepchem.utils.noncovalent_utils import compute_binding_pocket_cation_pi

from deepchem.utils.noncovalent_utils import compute_pi_stack

from deepchem.utils.noncovalent_utils import compute_hydrogen_bonds

from deepchem.utils.rdkit_util import MoleculeLoadException

from deepchem.utils.rdkit_util import compute_contact_centroid

from deepchem.utils.rdkit_utils import MoleculeLoadException

from deepchem.utils.rdkit_utils import compute_contact_centroid

from deepchem.utils.geometry_utils import compute_pairwise_distances

from deepchem.utils.geometry_utils import subtract_centroid

from deepchem.utils.fragment_util import get_partial_charge

from deepchem.utils.fragment_util import reduce_molecular_complex_to_contacts

from deepchem.utils.fragment_utils import get_partial_charge

from deepchem.utils.fragment_utils import reduce_molecular_complex_to_contacts



logger = logging.getLogger(__name__)

deepchem/feat/tests/test_contact_fingerprints.py

+6 −3
Original line number Diff line number Diff line
@@ -17,7 +17,8 @@ class TestContactFeaturizers(unittest.TestCase): 
  def test_contact_fingerprint_shape(self):

    size = 8

    featurizer = dc.feat.ContactCircularFingerprint(size=size)

    features, failures = featurizer.featurize_complexes(self.complex_files)

    features, failures = featurizer.featurize([self.ligand_file],

                                              [self.protein_file])

    assert features.shape == (1, 2 * size)



  def test_contact_voxels_shape(self):
@@ -27,7 +28,8 @@ class TestContactFeaturizers(unittest.TestCase): 
    size = 8

    voxelizer = dc.feat.ContactCircularVoxelizer(

        box_width=box_width, voxel_width=voxel_width, size=size)

    features, failures = voxelizer.featurize_complexes(self.complex_files)

    features, failures = voxelizer.featurize([self.ligand_file],

                                             [self.protein_file])

    assert features.shape == (1, voxels_per_edge, voxels_per_edge,

                              voxels_per_edge, size)
@@ -38,5 +40,6 @@ class TestContactFeaturizers(unittest.TestCase): 
    size = 8

    voxelizer = dc.feat.ContactCircularVoxelizer(

        box_width=box_width, voxel_width=voxel_width, size=size, flatten=True)

    features, failures = voxelizer.featurize_complexes(self.complex_files)

    features, failures = voxelizer.featurize([self.ligand_file],

                                             [self.protein_file])

    assert features.shape == (1, int(size * voxels_per_edge**3))

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