Changes

import os

import unittest

import deepchem as dc

class TestContactFeaturizers(unittest.TestCase):

  """Test Contact Fingerprints and Voxelizers."""

  def setUp(self):

    # TODO test more formats for ligand

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

    self.protein_file = os.path.join(current_dir,

                                     '3ws9_protein_fixer_rdkit.pdb')

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

    self.complex_files = [(self.protein_file, self.ligand_file)]

  def test_contact_fingerprint_shape(self):

    size = 8

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

    features, failures = featurizer.featurize_complexes(

        self.complex_files)

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

  def test_contact_voxels_shape(self):

    box_width = 48 

    voxel_width = 2

    voxels_per_edge = box_width/voxel_width

    size = 8

    voxelizer = dc.feat.ContactCircularVoxelizer(box_width=box_width,

      voxel_width=voxel_width, size=size)

    features, failures = voxelizer.featurize_complexes(

        self.complex_files)

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

    for hydrogen_xyz in hydrogens:

      hydrogen_to_frag2 = frag2_atom_xyz - hydrogen_xyz

      hydrogen_to_frag1 = frag1_atom_xyz - hydrogen_xyz

      if np.abs(180 - angle_between(hydrogen_to_frag1, hydrogen_to_frag2) * 180.0 / np.pi) <= hbond_angle_cutoff:

        return True

      #if np.abs(180 - angle_between(hydrogen_to_frag1, hydrogen_to_frag2) * 180.0 / np.pi) <= hbond_angle_cutoff:

      #  return True

      return is_angle_within_cutoff(hydrgoen_to_frag2, hydrogen_to_frag1, hbond_angle_cutoff)

  return False