def string_array_to_molecule(parser_fun, file_name, mol=None):
"""
Convert a Numpy string array like:
[['C', '-1.487460', '-0.028670', '-0.000060'],
['O', '0.376340', '0.028670', '-0.000060'],
['H', '-1.818910', '-1.067060', '-0.000060'],
['H', '-1.866470', '0.473700', '0.889930'],
['H', '-1.866470', '0.473700', '-0.890040'],
['H', '0.756720', '-0.950010', '-0.000060']]
To a plams ``Molecule``.
"""
string_array_to_float = np.vectorize(float)
mols = parse_file(parser_fun, file_name).asList()
last_mol = np.array(mols[-1])
elems = last_mol[:, 0]
coords = string_array_to_float(last_mol[:, 1:])
if mol:
if len(coords) == len(mol):
plams_mol = mol
for i in range(len(plams_mol)):
plams_mol.atoms[i].coords = tuple(
[float(c) for c in coords[i]])
else:
raise RuntimeError("Output molecule does not match input molecule")
else:
plams_mol = Molecule()
for e, c in zip(elems, coords):
plams_mol.add_atom(Atom(symbol=e, coords=tuple(c)))
return plams_mol
def tuplesXYZ_to_plams(xs):
""" Transform a list of namedTuples to a Plams molecule """
plams_mol = Molecule()
for at in xs:
symb = at.symbol
cs = at.xyz
plams_mol.add_atom(Atom(symbol=symb, coords=tuple(cs)))
return plams_mol
def parse_molecule_traj(file_traj):
"""
Read Molecules from the job_name.traj file.
"""
mols = manyXYZ(file_traj)
# Last geometry corresponds to the optimized structure
opt_mol = mols[-1]
plams_mol = Molecule()
for at in opt_mol:
symb = at.symbol
cs = at.xyz
plams_mol.add_atom(Atom(symbol=symb, coords=tuple(cs)))
return plams_mol
def adf_fragmentsjob(settings, mol, *frozen_frags):
mol_tot = Molecule()
frag_settings = Settings()
for i, frag in enumerate(frozen_frags):
frag_id = "frag" + str(i + 1)
for m in frag.mol_list:
for a in m:
a.fragment = frag_id
mol_tot += m
path = frag.result.kf.path + " type=FDE"
frag_settings.specific.adf.fragments[frag_id] = path
frag_settings.specific.adf.fde.PW91k = ""
mol_tot += mol
return adf(settings.overlay(frag_settings), mol_tot, job_name="fde")
def from_rdmol(rdkit_mol):
"""
Translate an RDKit molecule into a PLAMS molecule type
"""
plams_mol = Molecule()
total_charge = 0
Chem.Kekulize(rdkit_mol)
conf = rdkit_mol.GetConformer()
for atom in rdkit_mol.GetAtoms():
pos = conf.GetAtomPosition(atom.GetIdx())
ch = atom.GetFormalCharge()
plams_mol.add_atom(
Atom(atom.GetAtomicNum(), coords=(pos.x, pos.y, pos.z), charge=ch))
total_charge += ch
for bond in rdkit_mol.GetBonds():
at1 = plams_mol.atoms[bond.GetBeginAtomIdx()]
at2 = plams_mol.atoms[bond.GetEndAtomIdx()]
plams_mol.add_bond(Bond(at1, at2, bond.GetBondTypeAsDouble()))
plams_mol.charge = total_charge
for propname in rdkit_mol.GetPropNames():
plams_mol.properties[propname] = rdkit_mol.GetProp(propname)
return plams_mol