def without_dummy_atoms(geo):
""" Return a copy of the molecular geometry without dummy atoms.
"""
symbs = symbols(geo)
non_dummy_idxs = [
idx for idx, symb in enumerate(symbs) if ptab.to_number(symb)
]
return from_subset(geo, non_dummy_idxs)
def formula(geo):
""" Generate a stoichiometric formula dictionary from a molecular geometry.
:param geo: molecular geometry
:type geo: automol geometry data structure
:type: dict[str: int]
"""
symbs = symbols(geo)
fml = _util.formula(symbs)
return fml
def connectivity_graph(geo,
rqq_bond_max=3.45,
rqh_bond_max=2.6,
rhh_bond_max=1.9):
""" Generate a molecular graph from the molecular geometry that has information
about bond connectivity.
:param rqq_bond_max: maximum distance between heavy atoms
:type rqq_bond_max: float
:param rqh_bond_max: maximum distance between heavy atoms and hydrogens
:type rqh_bond_max: float
:param rhh_bond_max: maximum distance between hydrogens
:type rhh_bond_max: float
:rtype: automol molecular graph structure
"""
symbs = symbols(geo)
xyzs = coordinates(geo)
def _distance(idx_pair):
xyz1, xyz2 = map(xyzs.__getitem__, idx_pair)
dist = numpy.linalg.norm(numpy.subtract(xyz1, xyz2))
return dist
def _are_bonded(idx_pair):
sym1, sym2 = map(symbs.__getitem__, idx_pair)
dist = _distance(idx_pair)
return (False if 'X' in (sym1, sym2) else
(dist < rqh_bond_max) if 'H' in (sym1, sym2) else
(dist < rhh_bond_max) if (sym1 == 'H' and sym2 == 'H') else
(dist < rqq_bond_max))
idxs = range(len(xyzs))
atm_symb_dct = dict(enumerate(symbs))
bnd_keys = tuple(
map(frozenset, filter(_are_bonded, itertools.combinations(idxs, r=2))))
bnd_ord_dct = {bnd_key: 1 for bnd_key in bnd_keys}
gra = create.graph.from_data(atom_symbols=atm_symb_dct,
bond_keys=bnd_keys,
bond_orders=bnd_ord_dct)
return gra
def from_subset(geo, idxs):
""" Generate a new molecular geometry from a subset of the atoms in an
input geometry.
(Rename this and put it under operations?)
:param geo: molecular geometry
:type geo: automol molecular geometry data structure
:param idxs: indices representing the subset of atoms
:type idxs: tuple(int)
:rtype: automol moleculer geometry data structure
"""
symbs = symbols(geo)
xyzs = coordinates(geo)
symbs = list(map(symbs.__getitem__, idxs))
xyzs = list(map(xyzs.__getitem__, idxs))
return automol.create.geom.from_data(symbs, xyzs)
def insert(geo, symb, xyz, idx=None, angstrom=False):
""" Insert an atom into a molecular geometry.
:param geo: molecular geometry
:type geo: automol molecular geometry data structure
:param symb: symbol of atom to add
:type symb: str
:param xyz: xyz coordinates of atom to add
:type xyz: tuple(float)
:param idx: index of geometry to place atom
:type idx: int
:rtype: automol geometry date structure
"""
symbs = list(symbols(geo))
xyzs = list(coordinates(geo, angstrom=angstrom))
idx = idx if idx is not None else len(symbs)
symbs.insert(idx, symb)
xyzs.insert(idx, xyz)
return automol.create.geom.from_data(symbs, xyzs, angstrom=angstrom)