def reactants_graph(tsg):
""" get a graph of the reactants from a transition state graph
"""
frm_bnd_keys = forming_bond_keys(tsg)
ord_dct = dict_.transform_values(bond_orders(tsg), func=round)
gra = set_bond_orders(tsg, ord_dct)
gra = remove_bonds(gra, frm_bnd_keys)
return gra
def one_resonance_dominant_bond_orders(rgr):
""" resonance-dominant bond orders, by bond
"""
rgr = without_fractional_bonds(rgr)
bnd_keys = list(bond_keys(rgr))
bnd_ords_by_res = [
dict_.values_by_key(bond_orders(dom_rgr), bnd_keys)
for dom_rgr in dominant_resonances(rgr)
]
first_bnd_ords = [bnd_ords_by_res[0]]
bnd_ords_lst = list(map(frozenset, zip(*first_bnd_ords)))
bnd_dom_res_ords_dct = dict(zip(bnd_keys, bnd_ords_lst))
return bnd_dom_res_ords_dct
def resonance_avg_bond_orders(rgr):
""" resonance-dominant bond orders, by bond
"""
rgr = without_fractional_bonds(rgr)
bnd_keys = list(bond_keys(rgr))
bnd_ords_by_res = [
dict_.values_by_key(bond_orders(dom_rgr), bnd_keys)
for dom_rgr in dominant_resonances(rgr)
]
nres = len(bnd_ords_by_res)
bnd_ords_lst = zip(*bnd_ords_by_res)
avg_bnd_ord_lst = [sum(bnd_ords) / nres for bnd_ords in bnd_ords_lst]
avg_bnd_ord_dct = dict(zip(bnd_keys, avg_bnd_ord_lst))
return avg_bnd_ord_dct
def from_graph(gra):
""" networkx graph object from a molecular graph
"""
nxg = networkx.Graph()
nxg.add_nodes_from(atom_keys(gra))
nxg.add_edges_from(bond_keys(gra))
networkx.set_node_attributes(nxg, atom_symbols(gra), 'symbol')
networkx.set_node_attributes(nxg, atom_implicit_hydrogen_valences(gra),
'implicit_hydrogen_valence')
networkx.set_node_attributes(nxg, atom_stereo_parities(gra),
'stereo_parity')
networkx.set_edge_attributes(nxg, bond_orders(gra), 'order')
networkx.set_edge_attributes(nxg, bond_stereo_parities(gra),
'stereo_parity')
return nxg
def inchi_with_sort_from_geometry(gra, geo=None, geo_idx_dct=None):
""" Generate an InChI string from a molecular graph.
If coordinates are passed in, they are used to determine stereo.
:param gra: molecular graph
:type gra: automol graph data structure
:param geo: molecular geometry
:type geo: automol geometry data structure
:param geo_idx_dct:
:type geo_idx_dct: dict[:]
:rtype: (str, tuple(int))
"""
gra = without_dummy_atoms(gra)
gra = dominant_resonance(gra)
atm_keys = sorted(atom_keys(gra))
bnd_keys = list(bond_keys(gra))
atm_syms = dict_.values_by_key(atom_symbols(gra), atm_keys)
atm_bnd_vlcs = dict_.values_by_key(atom_bond_valences(gra), atm_keys)
atm_rad_vlcs = dict_.values_by_key(atom_unsaturated_valences(gra),
atm_keys)
bnd_ords = dict_.values_by_key(bond_orders(gra), bnd_keys)
if geo is not None:
assert geo_idx_dct is not None
atm_xyzs = coordinates(geo)
atm_xyzs = [
atm_xyzs[geo_idx_dct[atm_key]] if atm_key in geo_idx_dct else
(0., 0., 0.) for atm_key in atm_keys
]
else:
atm_xyzs = None
mlf, key_map_inv = _molfile.from_data(atm_keys,
bnd_keys,
atm_syms,
atm_bnd_vlcs,
atm_rad_vlcs,
bnd_ords,
atm_xyzs=atm_xyzs)
rdm = _rdkit.from_molfile(mlf)
ich, aux_info = _rdkit.to_inchi(rdm, with_aux_info=True)
nums = _parse_sort_order_from_aux_info(aux_info)
nums = tuple(map(key_map_inv.__getitem__, nums))
return ich, nums
def bonds_of_order(gra, mbond=1):
""" Determine the indices of all bonds in a molecule with
the specified bond order.
:param gra: molecular graph
:type gra: molecular graph data structure
:param mbond: bond order of desired bond type
:type mbond: int
"""
# Build resonance graph to get the bond orders
gra = dominant_resonance(gra)
bond_order_dct = bond_orders(gra)
mbond_idxs = tuple()
for bond, order in bond_order_dct.items():
if order == mbond:
bnd1, bnd2 = bond
mbond_idxs += ((bnd1, bnd2), )
return mbond_idxs
def breaking_bond_keys(tsg):
""" get the forming bonds from a transition state graph
"""
ord_dct = bond_orders(tsg)
brk_bnd_keys = [k for k, o in ord_dct.items() if round(o, 1) == 0.9]
return frozenset(map(frozenset, brk_bnd_keys))
