Commit 1f6e10d5 authored by Bharath Ramsundar's avatar Bharath Ramsundar
Browse files

changes

parent 659631da

deepchem/feat/tests/test_coulomb_matrices.py

+77 −69
Original line number Diff line number Diff line
@@ -4,8 +4,6 @@ Tests for Coulomb matrix calculation. 
import numpy as np

import unittest



from rdkit import Chem



from deepchem.feat import coulomb_matrices as cm

from deepchem.utils import conformers
@@ -14,11 +12,13 @@ class TestCoulombMatrix(unittest.TestCase): 
  """

    Tests for CoulombMatrix.

    """



  def setUp(self):

    """

        Set up tests.

        """

    smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O'

    from rdkit import Chem

    mol = Chem.MolFromSmiles(smiles)

    engine = conformers.ConformerGenerator(max_conformers=1)

    self.mol = engine.generate_conformers(mol)
@@ -30,7 +30,8 @@ class TestCoulombMatrix(unittest.TestCase): 
        """

    f = cm.CoulombMatrix(self.mol.GetNumAtoms())

    rval = f([self.mol])

        assert rval.shape == (1, self.mol.GetNumConformers(), self.mol.GetNumAtoms(), self.mol.GetNumAtoms())

    assert rval.shape == (1, self.mol.GetNumConformers(),

                          self.mol.GetNumAtoms(), self.mol.GetNumAtoms())



  def test_coulomb_matrix_padding(self):

    """
@@ -63,10 +64,11 @@ class TestCoulombMatrix(unittest.TestCase): 
    """

        Test hydrogen removal.

        """

    from rdkit import Chem

    mol = Chem.RemoveHs(self.mol)

    assert mol.GetNumAtoms() < self.mol.GetNumAtoms()

        f = cm.CoulombMatrix(max_atoms=mol.GetNumAtoms(),

                             remove_hydrogens=True, upper_tri=True)

    f = cm.CoulombMatrix(

        max_atoms=mol.GetNumAtoms(), remove_hydrogens=True, upper_tri=True)

    rval = f([self.mol])  # use the version with hydrogens

    size = np.triu_indices(mol.GetNumAtoms())[0].size

    assert rval.shape == (1, mol.GetNumConformers(), size)
@@ -75,21 +77,26 @@ class TestCoulombMatrix(unittest.TestCase): 
    """

        Test no hydrogen removal.

        """

        f = cm.CoulombMatrix(max_atoms=self.mol.GetNumAtoms(),

                             remove_hydrogens=False, upper_tri=True)

    f = cm.CoulombMatrix(

        max_atoms=self.mol.GetNumAtoms(),

        remove_hydrogens=False,

        upper_tri=True)

    rval = f([self.mol])

    size = np.triu_indices(self.mol.GetNumAtoms())[0].size

    assert rval.shape == (1, self.mol.GetNumConformers(), size)





class TestCoulombMatrixEig(unittest.TestCase):

  """

    Tests for CoulombMatrixEig.

    """



  def setUp(self):

    """

        Set up tests.

        """

    smiles = '[H]C([H])([H])[H]'

    from rdkit import Chem

    mol = Chem.MolFromSmiles(smiles)

    mol = Chem.AddHs(mol)

    engine = conformers.ConformerGenerator(max_conformers=1)
@@ -102,7 +109,8 @@ class TestCoulombMatrixEig(unittest.TestCase): 
        """

    f = cm.CoulombMatrixEig(self.mol.GetNumAtoms())

    rval = f([self.mol])

        assert rval.shape == (1, self.mol.GetNumConformers(), self.mol.GetNumAtoms())

    assert rval.shape == (1, self.mol.GetNumConformers(),

                          self.mol.GetNumAtoms())



  def test_coulomb_matrix_eig_padding(self):

    """

deepchem/feat/tests/test_fingerprints.py

+30 −31
Original line number Diff line number Diff line
@@ -2,9 +2,6 @@ 
Test topological fingerprints.

"""

import unittest



from rdkit import Chem



from deepchem.feat import fingerprints as fp
@@ -12,11 +9,13 @@ class TestCircularFingerprint(unittest.TestCase): 
  """

    Tests for CircularFingerprint.

    """



  def setUp(self):

    """

        Set up tests.

        """

    smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O'

    from rdkit import Chem

    self.mol = Chem.MolFromSmiles(smiles)

    self.engine = fp.CircularFingerprint()

deepchem/feat/tests/test_graph_features.py

+3 −1
Original line number Diff line number Diff line
@@ -12,7 +12,6 @@ import unittest 
import os

import sys

import numpy as np

import rdkit

from deepchem.feat.mol_graphs import ConvMol

from deepchem.feat.mol_graphs import MultiConvMol

from deepchem.feat.graph_features import ConvMolFeaturizer
@@ -28,6 +27,7 @@ class TestConvMolFeaturizer(unittest.TestCase): 
    # Note there is a central nitrogen of degree 4, with 4 carbons

    # of degree 1 (connected only to central nitrogen).

    raw_smiles = ['C[N+](C)(C)C']

    import rdkit

    mols = [rdkit.Chem.MolFromSmiles(s) for s in raw_smiles]

    featurizer = ConvMolFeaturizer()

    mols = featurizer.featurize(mols)
@@ -53,6 +53,7 @@ class TestConvMolFeaturizer(unittest.TestCase): 
  def test_single_carbon(self):

    """Test that single carbon atom is featurized properly."""

    raw_smiles = ['C']

    import rdkit

    mols = [rdkit.Chem.MolFromSmiles(s) for s in raw_smiles]

    featurizer = ConvMolFeaturizer()

    mol_list = featurizer.featurize(mols)
@@ -74,6 +75,7 @@ class TestConvMolFeaturizer(unittest.TestCase): 
  def test_alkane(self):

    """Test on simple alkane"""

    raw_smiles = ['CCC']

    import rdkit

    mols = [rdkit.Chem.MolFromSmiles(s) for s in raw_smiles]

    featurizer = ConvMolFeaturizer()

    mol_list = featurizer.featurize(mols)

deepchem/feat/tests/test_mol_graphs.py

+4 −5
Original line number Diff line number Diff line
@@ -12,7 +12,6 @@ import unittest 
import os

import sys

import numpy as np

import rdkit

from deepchem.feat.mol_graphs import ConvMol

from deepchem.feat.mol_graphs import MultiConvMol
@@ -66,10 +65,10 @@ class TestMolGraphs(unittest.TestCase): 
    # atom 2 has 2 neighbors

    # atom 3 has 3 neighbors.

    # Verify that atom features have been sorted by atom degree.

    assert np.array_equal(mol.get_atom_features(),

                          np.array([[56, 57, 58, 59], [40, 41, 42, 43],

                                    [44, 45, 46, 47], [48, 49, 50,

                                                       51], [52, 53, 54, 55]]))

    assert np.array_equal(

        mol.get_atom_features(),

        np.array([[56, 57, 58, 59], [40, 41, 42, 43], [44, 45, 46, 47],

                  [48, 49, 50, 51], [52, 53, 54, 55]]))



  def test_get_adjacency_list(self):

    """Tests that adj-list is canonicalized properly."""

deepchem/feat/tests/test_rdkit_grid_features.py

+3 −4
Original line number Diff line number Diff line
@@ -7,10 +7,6 @@ import unittest 


import numpy as np

np.random.seed(123)



from rdkit.Chem import MolFromSmiles

from rdkit.Chem.AllChem import Mol, ComputeGasteigerCharges



from deepchem.feat import rdkit_grid_featurizer as rgf
@@ -35,6 +31,7 @@ class TestHelperFunctions(unittest.TestCase): 


  def test_load_molecule(self):

    # adding hydrogens and charges is tested in dc.utils

    from rdkit.Chem.AllChem import Mol

    for add_hydrogens in (True, False):

      for calc_charges in (True, False):

        mol_xyz, mol_rdk = rgf.load_molecule(self.ligand_file, add_hydrogens,
@@ -173,6 +170,7 @@ class TestHelperFunctions(unittest.TestCase): 
          self.assertTrue((v2 == v_pair[1]).all())



  def test_compute_charge_dictionary(self):

    from rdkit.Chem.AllChem import ComputeGasteigerCharges

    for fname in (self.ligand_file, self.protein_file):

      _, mol = rgf.load_molecule(fname)

      ComputeGasteigerCharges(mol)
@@ -189,6 +187,7 @@ class TestPiInteractions(unittest.TestCase): 
    current_dir = os.path.dirname(os.path.realpath(__file__))



    # simple flat ring

    from rdkit.Chem import MolFromSmiles

    self.cycle4 = MolFromSmiles('C1CCC1')

    self.cycle4.Compute2DCoords()

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