def standard_keys_for_sequence(gras):
""" assigns non-overlapping keys to a sequence of graphs
(returns a series of key maps for each)
"""
atm_key_dcts = []
shift = 0
for gra in gras:
natms = atom_count(gra, dummy=True, with_implicit=False)
atm_key_dct = {
atm_key: idx + shift
for idx, atm_key in enumerate(sorted(atom_keys(gra)))
}
atm_key_dcts.append(atm_key_dct)
shift += natms
gras = [
relabel(gra, atm_key_dct)
for gra, atm_key_dct in zip(gras, atm_key_dcts)
]
return gras, atm_key_dcts
def insert_bonded_atom(gra,
sym,
atm_key,
bnd_atm_key=None,
imp_hyd_vlc=None,
atm_ste_par=None,
bnd_ord=None,
bnd_ste_par=None):
""" insert a single atom with a bond to an atom already in the graph
Keys will be standardized upon insertion
"""
keys = sorted(atom_keys(gra))
bnd_atm_key_ = max(keys) + 1
gra = add_bonded_atom(gra,
sym,
atm_key,
bnd_atm_key=bnd_atm_key_,
imp_hyd_vlc=imp_hyd_vlc,
atm_ste_par=atm_ste_par,
bnd_ord=bnd_ord,
bnd_ste_par=bnd_ste_par)
if bnd_atm_key != bnd_atm_key_:
assert bnd_atm_key in keys
idx = keys.index(bnd_atm_key)
key_dct = {}
key_dct.update({k: k for k in keys[:idx]})
key_dct[bnd_atm_key_] = bnd_atm_key
key_dct.update({k: k + 1 for k in keys[idx:]})
gra = relabel(gra, key_dct)
return gra
def _shift_remove_dummy_atom(gra, dummy_key):
keys = sorted(automol.graph.atom_keys(gra))
idx = keys.index(dummy_key)
key_dct = {}
key_dct.update({k: k for k in keys[:idx]})
key_dct.update({k: k - 1 for k in keys[(idx + 1):]})
gra = remove_atoms(gra, [dummy_key])
gra = relabel(gra, key_dct)
return gra
def relabel_for_zmatrix(gra, zma_keys, dummy_key_dct):
""" relabel a geometry graph to line up with a z-matrix
Inserts dummy atoms and sorts/relabels in z-matrix order.
Graph keys should correspond to the geometry used for conversion.
:param gra: the graph
:param zma_keys: graph keys in the order they appear in the z-matrix
:param dummy_key_dct: dummy keys introduced on z-matrix conversion, by atom
they are attached to
"""
gra = add_dummy_atoms(gra, dummy_key_dct)
key_dct = dict(map(reversed, enumerate(zma_keys)))
gra = relabel(gra, key_dct)
return gra
def from_yaml_dictionary(yaml_gra_dct, one_indexed=True):
""" read the graph from a yaml dictionary
"""
atm_dct = yaml_gra_dct['atoms']
bnd_dct = yaml_gra_dct['bonds']
atm_dct = dict_.transform_values(
atm_dct, lambda x: tuple(map(x.__getitem__, ATM_PROP_NAMES)))
bnd_dct = dict_.transform_keys(bnd_dct,
lambda x: frozenset(map(int, x.split('-'))))
bnd_dct = dict_.transform_values(
bnd_dct, lambda x: tuple(map(x.__getitem__, BND_PROP_NAMES)))
gra = _create.from_atoms_and_bonds(atm_dct, bnd_dct)
if one_indexed:
# revert one-indexing if the input is one-indexed
atm_key_dct = {atm_key: atm_key - 1 for atm_key in atom_keys(gra)}
gra = relabel(gra, atm_key_dct)
return gra
def standard_keys(gra):
""" replace the current atom keys with standard indices, counting from zero
"""
atm_key_dct = dict(map(reversed, enumerate(sorted(atom_keys(gra)))))
return relabel(gra, atm_key_dct)
def transform_keys(gra, atm_key_func):
""" transform atom keys with a function
"""
atm_keys = atom_keys(gra)
atm_key_dct = dict(zip(atm_keys, map(atm_key_func, atm_keys)))
return relabel(gra, atm_key_dct)