Changes (c6f169a3) · Commits · 钟慕尧 / deepchem

deepchem/utils/fragment_util.py

+22 −0

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@
		import itertools
		import numpy as np
		from deepchem.utils.geometry_utils import compute_pairwise_distances
		from deepchem.utils.rdkit_util import compute_charges


		def get_partial_charge(atom):
		@@ -11,6 +12,18 @@ def get_partial_charge(atom):
		----------
		atom: rdkit atom or `AtomShim` object
		Either an rdkit atom or `AtomShim`

		Note
		----
		This function requires RDKit to be installed.

		Examples
		--------
		>>> from rdkit import Chem
		>>> mol = Chem.MolFromSmiles("CC")
		>>> atom = mol.GetAtoms()[0]
		>>> get_partial_charge(atom)
		0
		"""
		from rdkit import Chem
		if isinstance(atom, Chem.Atom):
		@@ -35,6 +48,15 @@ class MolecularFragment(object):

		Ideally, we'd be able to do this in RDKit direct, but manipulating
		molecular fragments doesn't seem to be supported functionality.

		Examples
		--------
		>>> import numpy as np
		>>> from rdkit import Chem
		>>> mol = Chem.MolFromSmiles("C")
		>>> coords = np.array([[0.0, 0.0, 0.0]])
		>>> atom = mol.GetAtoms()[0]
		>>> fragment = MolecularFragment([atom], coords)
		"""

		def __init__(self, atoms, coords):

deepchem/utils/test/test_fragment_util.py

+28 −1

Original line number	Diff line number	Diff line
		import os
		import unittest
		import numpy as np
		from deepchem.utils import rdkit_util
		from deepchem.utils.fragment_util import get_contact_atom_indices
		from deepchem.utils.fragment_util import merge_molecular_fragments
		from deepchem.utils.fragment_util import get_partial_charge
		from deepchem.utils.fragment_util import strip_hydrogens
		from deepchem.utils.fragment_util import MolecularFragment
		from deepchem.utils.fragment_util import AtomShim


		class TestFragmentUtil(unittest.TestCase):
		@@ -27,9 +31,32 @@ class TestFragmentUtil(unittest.TestCase):
		assert len(mol_rdk.GetAtoms()) == len(fragment.GetAtoms())
		assert (fragment.GetCoords() == mol_xyz).all()

		def test_strip_hydrogens(self):
		mol_xyz, mol_rdk = rdkit_util.load_molecule(self.ligand_file)
		fragment = MolecularFragment(mol_rdk.GetAtoms(), mol_xyz)

		# Test on RDKit
		frag = strip_hydrogens(mol_xyz, mol_rdk)

		def test_merge_molecular_fragments(self):
		mol_xyz, mol_rdk = rdkit_util.load_molecule(self.ligand_file)
		fragment1 = MolecularFragment(mol_rdk.GetAtoms(), mol_xyz)
		fragment2 = MolecularFragment(mol_rdk.GetAtoms(), mol_xyz)
		joint = merge_molecular_fragments([fragment1, fragment2])
		assert len(mol_rdk.GetAtoms()) * 2 == len(joint.GetAtoms())

		def test_get_partial_charge(self):
		from rdkit import Chem
		mol = Chem.MolFromSmiles("CC")
		atom = mol.GetAtoms()[0]
		partial_charge = get_partial_charge(atom)
		assert partial_charge == 0

		def test_atom_shim(self):
		atomic_num = 5
		partial_charge = 1
		atom_coords = np.array([0., 1., 2.])
		shim = AtomShim(atomic_num, partial_charge, atom_coords)
		assert shim.GetAtomicNum() == atomic_num
		assert shim.GetPartialCharge() == partial_charge
		assert (shim.GetCoords() == atom_coords).all()

docs/utils.rst

+12 −1

Original line number	Diff line number	Diff line
		@@ -93,9 +93,20 @@ Molecular Fragment Utilities

		It's often convenient to manipulate subsets of a molecule. The :code:`MolecularFragment` class aids in such manipulations.

		.. autoclass:: deepchem.utils.MolecularFragment
		.. autoclass:: deepchem.utils.fragment_util.MolecularFragment
		:members:

		.. autoclass:: deepchem.utils.fragment_util.AtomShim
		:members:

		.. autofunction:: deepchem.utils.fragment_util.strip_hydrogens

		.. autofunction:: deepchem.utils.fragment_util.merge_molecular_fragments

		.. autofunction:: deepchem.utils.fragment_util.get_contact_atom_indices

		.. autofunction:: deepchem.utils.fragment_util.reduce_molecular_complex_to_contacts

		Coordinate Box Utilities
		------------------------

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