def test_merge_molecules_xyz(self):
current_dir = os.path.dirname(os.path.realpath(__file__))
ligand_file = os.path.join(current_dir, "../../dock/tests/1jld_ligand.sdf")
xyz, mol = rdkit_util.load_molecule(
ligand_file, calc_charges=False, add_hydrogens=False)
merged = rdkit_util.merge_molecules_xyz(xyz, xyz)
for i in range(len(xyz)):
first_atom_equal = np.all(xyz[i] == merged[i])
second_atom_equal = np.all(xyz[i] == merged[i + len(xyz)])
assert_true(first_atom_equal)
assert_true(second_atom_equal)
def test_merge_molecules_xyz(self):
current_dir = os.path.dirname(os.path.realpath(__file__))
ligand_file = os.path.join(current_dir,
"../../dock/tests/1jld_ligand.sdf")
xyz, mol = rdkit_util.load_molecule(ligand_file,
calc_charges=False,
add_hydrogens=False)
merged = rdkit_util.merge_molecules_xyz([xyz, xyz])
for i in range(len(xyz)):
first_atom_equal = np.all(xyz[i] == merged[i])
second_atom_equal = np.all(xyz[i] == merged[i + len(xyz)])
assert first_atom_equal
assert second_atom_equal
def _featurize_complex(self, mol_pdb_file, protein_pdb_file):
"""
Compute neighbor list for complex.
Parameters
----------
mol_pdb: list
Should be a list of lines of the PDB file.
complex_pdb: list
Should be a list of lines of the PDB file.
"""
mol_coords, ob_mol = rdkit_util.load_molecule(mol_pdb_file)
protein_coords, protein_mol = rdkit_util.load_molecule(protein_pdb_file)
system_coords = rdkit_util.merge_molecules_xyz(mol_coords, protein_coords)
system_neighbor_list = compute_neighbor_list(
system_coords, self.neighbor_cutoff, self.max_num_neighbors, None)
return (system_coords, system_neighbor_list)
def _featurize_complex(self, mol_pdb_file, protein_pdb_file):
"""
Compute neighbor list for complex.
Parameters
----------
mol_pdb_file: Str
Filename for ligand pdb file.
protein_pdb_file: Str
Filename for protein pdb file.
"""
mol_coords, ob_mol = rdkit_util.load_molecule(mol_pdb_file)
protein_coords, protein_mol = rdkit_util.load_molecule(protein_pdb_file)
system_coords = rdkit_util.merge_molecules_xyz([mol_coords, protein_coords])
system_neighbor_list = compute_neighbor_list(
system_coords, self.neighbor_cutoff, self.max_num_neighbors, None)
return (system_coords, system_neighbor_list)
def _featurize_complex(self, mol_pdb_file, protein_pdb_file):
"""
Compute neighbor list for complex.
Parameters
----------
mol_pdb: list
Should be a list of lines of the PDB file.
complex_pdb: list
Should be a list of lines of the PDB file.
"""
mol_coords, ob_mol = rdkit_util.load_molecule(mol_pdb_file)
protein_coords, protein_mol = rdkit_util.load_molecule(protein_pdb_file)
system_coords = rdkit_util.merge_molecules_xyz(mol_coords, protein_coords)
system_neighbor_list = compute_neighbor_list(
system_coords, self.neighbor_cutoff, self.max_num_neighbors, None)
return (system_coords, system_neighbor_list)