def test_compare_coordinates(self):
coordinates1 = model.Coordinates(11.01, 12.02, 13.03)
coordinates2 = model.Coordinates(11.01, 12.02, 13.03)
coordinates3 = model.Coordinates(15.01, 14.02, 13.03)
self.assertEqual(coordinates1, coordinates2)
self.assertNotEqual(coordinates1, coordinates3)
def test_norm(self):
coordinates1 = model.Coordinates(1.0, 0.0, 0.0)
coordinates2 = model.Coordinates(3.0, 4.0, 0.0)
coordinates3 = model.Coordinates(-1.0, 0.0, 1.0)
self.assertEqual(1.0, coordinates1.norm())
self.assertEqual(5.0, coordinates2.norm())
self.assertEqual(math.sqrt(2.0), coordinates3.norm())
def __make_example_molecule(self):
coordinatesH1 = model.Coordinates(0.0, 0.0, 0.95)
coordinatesH2 = model.Coordinates(0.89567, 0.00, -0.316663)
coordinatesO1 = model.Coordinates(0.0, 0.0, 0.0)
coordinatesO2 = model.Coordinates(4.0, 0.0, 0.0)
atomH1 = model.Atom("H", coordinatesH1)
atomH2 = model.Atom("H", coordinatesH2)
atomO1 = model.Atom("O", coordinatesO1)
atomO2 = model.Atom("O", coordinatesO2)
return model.Molecule([atomH1, atomH2, atomO1, atomO2], "MOL")
def test_compare_molecules(self):
coordinates1 = model.Coordinates()
coordinates2 = model.Coordinates(1.0, 0.0, 0.0)
coordinates3 = model.Coordinates(0.5, 1.0, 0.0)
atom1 = model.Atom("H", coordinates1)
atom2 = model.Atom("H", coordinates2)
atom3 = model.Atom("H", coordinates3)
molecule1 = model.Molecule([atom1, atom2], "MOL")
molecule2 = model.Molecule([atom2, atom1], "MOL")
molecule3 = model.Molecule([atom1, atom2, atom3], "MOL")
self.assertEqual(molecule1, molecule2)
self.assertNotEqual(molecule2, molecule3)
def test_distance(self):
coordinates1 = model.Coordinates(1.0, 0.0, 0.0)
coordinates2 = model.Coordinates(1.0, 0.0, 0.0)
distance12 = coordinates1.calculate_distance(coordinates2)
self.assertEqual(0.0, distance12)
coordinates3 = model.Coordinates(4.0, 4.0, 0.0)
distance13 = coordinates1.calculate_distance(coordinates3)
self.assertEqual(5.0, distance13)
coordinates4 = model.Coordinates(-3.0, 0.0, 4.0)
distance14 = coordinates1.calculate_distance(coordinates4)
distance43 = coordinates4.calculate_distance(coordinates3)
self.assertGreaterEqual(distance14 + distance43, distance13)
def test_xyz_tinker_reader(self):
reader = readingutils.InputReader(PACKMOL_TINKER_FILE_NAME,
tinker_format=True)
reader.parse_packmol_input()
system = reader.read_xyz_data()
f_atom = model.Atom("F",
model.Coordinates(1.714650, -1.415751, 0.421888),
-0.13, 18.9984, "Ff")
molecule = system.molecules[0][0]
atoms = molecule.atoms
self.assertIn(f_atom, atoms)
self.assertEqual(system.xyz_file_name, "fsi-tinker/fsi-res.xyz")
bonds = molecule.bonds
self.assertIn((0, 3), bonds)
self.assertIn((5, 8), bonds)
angles = molecule.angles
self.assertIn((4, 5, 6), angles)
self.assertIn((1, 0, 4), angles)
dihedrals = molecule.dihedrals
self.assertIn((3, 0, 4, 5), dihedrals)
self.assertIn((1, 0, 4, 5), dihedrals)
def test_compare_atoms(self):
coordinates = model.Coordinates(12.03, 11.01, 10.02)
atom1 = model.Atom("C", coordinates)
atom2 = model.Atom("C", coordinates)
atom3 = model.Atom("Ce", coordinates)
self.assertEqual(atom1, atom2)
self.assertNotEqual(atom1, atom3)
def test_determine_dihedrals(self):
coordinatesO1 = model.Coordinates(0.0, 0.0, 0.0)
coordinatesO2 = model.Coordinates(0.0, 0.0, 1.48)
coordinatesH1 = model.Coordinates(0.895669, 0.0, -0.316667)
coordinatesH2 = model.Coordinates(-0.895669, 0.0, 1.796667)
atomO1 = model.Atom("O", coordinatesO1)
atomO2 = model.Atom("O", coordinatesO2)
atomH1 = model.Atom("H", coordinatesH1)
atomH2 = model.Atom("H", coordinatesH2)
molecule = model.Molecule([atomO1, atomO2, atomH1, atomH2], "MOL")
molecule.determine_bonds(1.50)
molecule.determine_angles()
molecule.determine_dihedrals()
dihedrals = molecule.dihedrals
expected_dihedrals = ((2, 0, 1, 3),)
self.assertEqual(dihedrals, expected_dihedrals)
def test_xyz_default_reader(self):
reader = readingutils.InputReader(PACKMOL_FILE_NAME)
reader.parse_packmol_input()
system = reader.read_xyz_data()
li_atom = model.Atom("Li", model.Coordinates(0.0, 0.0, 0.0), 1.00,
6.997, "kLi")
molecule = model.Molecule([li_atom], "LI")
molecules = system.molecules
self.assertEqual(molecules[0][0], molecule)
self.assertEqual(system.xyz_file_name, "li-ec/li-ec-01.xyz")
def __read_xyz_data_tinker(self):
molecules = []
for (xyz_file_name, molecule_count) in self._xyz_data:
xyz_file = open(xyz_file_name, 'r')
atoms_number = int(xyz_file.readline().split()[0])
atoms = []
for xyz_line in xyz_file:
xyz_line = xyz_line.split()
if len(xyz_line) >= self.COORDINATE_LINE_COLUMNS_TINKER:
atom_symbol = xyz_line[1]
atom_coordinates = model.Coordinates(
float(xyz_line[2]), float(xyz_line[3]),
float(xyz_line[4]))
atoms.append(model.Atom(atom_symbol, atom_coordinates))
xyz_file.close()
if len(atoms) != atoms_number:
print(
'[WARNING] Difference between declared and read atoms number in file {}, declared: {}, read: {}'
.format(xyz_file_name, atoms_number, len(atoms)))
molecule = model.Molecule(atoms)
self.__read_dat_data(xyz_file_name.replace('.xyz', '.dat'),
molecule)
if molecule.atoms_number > 1:
self.__read_conn_data(xyz_file_name.replace('.xyz', '.conn'),
molecule)
molecules.append((molecule, molecule_count))
system = model.System(molecules, self._packmol_output_name)
return system
def __read_xyz_data_default(self):
molecules = []
for (xyz_file_name, molecule_count) in self._xyz_data:
xyz_file = open(xyz_file_name, 'r')
atoms_number = int(xyz_file.readline())
xyz_file.readline() # omit commentary line in XYZ file
atoms = []
for xyz_line in xyz_file:
xyz_line = xyz_line.split()
if len(xyz_line) >= self.COORDINATE_LINE_COLUMNS:
atom_symbol = xyz_line[0]
atom_coordinates = model.Coordinates(
float(xyz_line[1]), float(xyz_line[2]),
float(xyz_line[3]))
atoms.append(model.Atom(atom_symbol, atom_coordinates))
xyz_file.close()
if len(atoms) != atoms_number:
print(
'[WARNING] Difference between declared and read atoms number in file {}, declared: {}, read: {}'
.format(xyz_file_name, atoms_number, len(atoms)))
molecule = model.Molecule(atoms)
self.__read_dat_data(xyz_file_name.replace('.xyz', '.dat'),
molecule)
molecule.determine_angles()
molecule.determine_dihedrals()
molecules.append((molecule, molecule_count))
system = model.System(molecules, self._packmol_output_name)
return system
def save_to_file(self):
xyz_file = open(self._system.xyz_file_name, 'r')
occupancy = 0.00
temperature_factor = 0.00
atom_number = 1
# check if number of atoms in .xyz matches number given in system
atoms_number = int(xyz_file.readline())
if atoms_number != self._system.atoms_number:
print(
'[ERROR] Number of atoms calculated from Packmol input does not match number of atoms in .xyz file'
)
xyz_file.close()
return
# write header line in PDB
self._output_file.write(self.FIRST_LINE)
# omit commentary line in .xyz
xyz_file.readline()
for (molecule, counter) in self._system.molecules:
residue_id = 1
for i in range(0, counter):
for atom in molecule.atoms:
xyz_line = xyz_file.readline().split()
if xyz_line[0] != atom.symbol:
print(
'[ERROR] No match between atoms in line {}, symbol is {}, expected {}'
.format(xyz_line, xyz_line[0], atom.symbol))
xyz_file.close()
self._output_file.close()
return
coordinates = model.Coordinates(float(xyz_line[1]),
float(xyz_line[2]),
float(xyz_line[3]))
self._output_file.write(
self.LINE_FORMAT.format(atom_number, atom.namd_symbol,
molecule.residue_name,
residue_id, coordinates.x,
coordinates.y, coordinates.z,
occupancy, temperature_factor,
self._system.segment_id))
drude_atom = atom.drude_atom
if drude_atom is not None:
atom_number += 1
self._output_file.write(
self.LINE_FORMAT.format(
atom_number, drude_atom.namd_symbol,
molecule.residue_name, residue_id,
coordinates.x, coordinates.y, coordinates.z,
occupancy, temperature_factor,
self._system.segment_id))
atom_number += 1
residue_id += 1
self._output_file.write('END\n')
xyz_file.close()
self._output_file.close()
print('PDB file successfully written')
