def string(rotor_lst):
""" Write a list torsions to a string
"""
def _encode_idxs(idxs):
if len(idxs) == 1:
idx_str = idxs[0] + 1
else:
idx_str = '-'.join(str(val + 1) for val in idxs)
return idx_str
tors_dct = {}
for rotor in rotor_lst:
for torsion in rotor:
_axis = torsion.axis
_grps = torsion.groups
tors_dct[torsion.name] = {
'axis1': _axis[0] + 1,
'group1': _encode_idxs(_grps[0]),
'axis2': _axis[1] + 1,
'group2': _encode_idxs(_grps[1]),
'symmetry': torsion.symmetry,
}
sort_tors_dct = {}
tors_names = sort_tors_names(list(tors_dct.keys()))
for name in tors_names:
sort_tors_dct[name] = tors_dct[name]
tors_str = yaml.dump(sort_tors_dct, sort_keys=False)
return tors_str
def reaction_torsion_lst(zma, zrxn):
""" torsions from zrxn obj
"""
zbnd_keys = automol.reac.rotational_bond_keys(zrxn)
tors_axes = tuple(tuple(keys) for keys in zbnd_keys)
tors_names = tuple(
automol.zmat.torsion_coordinate_name(zma, *keys) for keys in tors_axes)
grxn = automol.reac.relabel_for_geometry(zrxn)
gbnd_keys = automol.reac.rotational_bond_keys(grxn)
tors_axes = tuple(tuple(keys) for keys in gbnd_keys)
# Get the sorted tors names for building the list
name_dct = dict(zip(tors_names, tors_axes))
tors_obj_lst = ()
sorted_tors_names = sort_tors_names(tuple(name_dct.keys()))
for name in sorted_tors_names:
gaxis = name_dct[name]
gaxis = tuple(sorted(gaxis))
ggrps = automol.reac.rotational_groups(grxn, *gaxis)
symm = automol.reac.rotational_symmetry_number(grxn, *gaxis)
# not for filesys
# zgrps = tuple(automol.zmat.shift_up(zma, grp)
# for grp in ggrps)
# zaxis = automol.zmat.shift_up(zma, gaxis)
# Build the torsion object and add to the list
tors_obj_lst += (Torsion(zma, name, gaxis, ggrps, symm), )
return tors_obj_lst
def torsion_lst(zma):
""" Build a list of torsion objects
"""
# Get the necessary graph and lin keys
gra = automol.zmat.graph(zma, stereo=True, dummy=True)
lin_keys = sorted(
automol.graph.dummy_atoms_neighbor_atom_key(gra).values())
# Build the torsion objects
_name_axis_dct = name_axis_dct(zma, gra, lin_keys)
# Get the sorted tors names for building the list
sorted_tors_names = sort_tors_names(tuple(_name_axis_dct.keys()))
tors_obj_lst = ()
for name in sorted_tors_names:
# Determine constituent rotor pieces in graph system
axis = _name_axis_dct[name]
grps = torsion_groups(gra, axis)
symm = torsion_symmetry(gra, axis, lin_keys)
# Build the torsion object and add to the list
tors_obj_lst += (Torsion(zma, name, axis, grps, symm), )
return tors_obj_lst
def torsion_lst(zma, gra, lin_keys):
""" Build a list of torsion objects
"""
# Build the torsion objects
_name_axis_dct = name_axis_dct(zma, gra, lin_keys)
# Get the sorted tors names for building the list
sorted_tors_names = sort_tors_names(tuple(_name_axis_dct.keys()))
tors_obj_lst = ()
for name in sorted_tors_names:
# Determine constituent rotor pieces in graph system
axis = _name_axis_dct[name]
grps = torsion_groups(gra, axis)
symm = torsion_symmetry(gra, axis, lin_keys)
# Build the torsion object and add to the list
tors_obj_lst += (Torsion(zma, name, axis, grps, symm), )
return tors_obj_lst