def read_structure(f):
atoms, coordinates = [], []
line = f.readline()
while line != '\n':
line = line.split()
atoms.append(line[1])
coordinates.append(line[5:])
line = f.readline()
molecule = cc.Cartesian(atoms=atoms, coords=coordinates)
remove_digits = partial(re.sub, r'[0-9]+', '')
molecule['atom'] = molecule['atom'].apply(remove_digits)
return molecule
def set_cc_positions(self, positions):
"""
Calculates the zmat from an OpenMM modeller
Args:
positions (list): A list
"""
cc_df = self._get_cartesian_df(positions)
self.cartesian = cc.Cartesian(cc_df)
self.cartesian.set_bonds(self.cc_bonds)
self.cartesian._give_val_sorted_bond_dict(use_lookup=True)
self.zmat = self.cartesian.get_zmat(use_lookup=True)
def to_Cartesian(self):
"""
transforms the molecule into a chemcoord.Cartesian object
"""
natoms = self.xyz.shape[0]
elems = copy.deepcopy(self.elements)
for i, j in enumerate(elems):
elems[i] = j.strip().capitalize()
xyz = pandas.DataFrame(self.xyz, columns=["x","y","z"], dtype='float64')
elems = pandas.DataFrame(elems, columns=["atom"], dtype='str')
output = chemcoord.Cartesian(pandas.concat([elems, xyz], axis=1))
output.index = range(1, natoms+1)
return output
if torsion[0] is not None:
angle0 = torsion[0] * 180 / pi
if torsion[1] is not None:
angle1 = torsion[1] * 180 / pi
print((angle0, angle1))
bonds = {}
num_atoms = len(rows)
bonds[0] = {1}
bonds[num_atoms - 1] = {num_atoms - 2}
for i in range(1, num_atoms - 1):
bonds[i] = {i - 1, i + 1}
print(bonds)
df = pd.DataFrame(rows, columns=['atom', 'x', 'y', 'z'])
molecule = cc.Cartesian(df)
molecule.set_bonds(bonds)
zmat = molecule.get_zmat(use_lookup=True)
zmat_copy = molecule.get_zmat(use_lookup=True)
molecule.to_xyz(buf='xyz/1ubq_cart.xyz')
for i in range(10):
zmat.safe_loc[:, 'dihedral'] = np.random.uniform(-10*i, 10*i, num_atoms) + zmat_copy.safe_loc[:, 'dihedral']
xyz = zmat.get_cartesian()
xyz.to_xyz(buf=f'xyz/1ubq_transform_{i}.xyz')
def test_init():
with pytest.raises(ValueError):
cc.Cartesian(5)
with pytest.raises(PhysicalMeaning):
cc.Cartesian(molecule.loc[:, ['atom', 'x']])
cc_bonds[bond[0].index].add(bond[1].index)
cc_bonds[bond[1].index].add(bond[0].index)
print(len(nitro_list))
for nitro in nitro_list:
print(nitro)
with pd.option_context('display.max_rows', None):
cc_df = pd.DataFrame({
'atom': atom_names,
'x': cc_positions[0, :],
'y': cc_positions[1, :],
'z': cc_positions[2, :]
})
molecule = cc.Cartesian(cc_df)
molecule.set_bonds(cc_bonds)
molecule._give_val_sorted_bond_dict(use_lookup=True)
zmat = molecule.get_zmat(use_lookup=True)
zmat.to_zmat(buf='zmat.xyz', implicit_index=False)
molecule2 = zmat.get_cartesian()
phi_indices = []
psi_indices = []
print('getting angles')
print(zmat.shape)
for i in range(len(zmat.index)):
b_index = zmat.loc[i, 'b']
a_index = zmat.loc[i, 'a']
d_index = zmat.loc[i, 'd']