def obtain_jobinfo(xyzfile, frame=-1, txt=False):
init_mol = read_geometry_to_mol(xyzfile, frame=frame, txt=txt)
natoms = init_mol.natoms
metal_ind = init_mol.findMetal()[0]
liglist, ligdents, ligcons = ligand_breakdown(init_mol, flag_loose=False, BondedOct=False)
# print(liglist)
# print(ligdents)
# print(ligcons)
### Old version
# _, _, _, _, _, _, ax_con, eq_con, _ = ligand_assign(init_mol, liglist,
# ligdents, ligcons)
# print("ax_con: ", ax_con)
# print("eq_con: ", eq_con)
# ax_con = np.squeeze(np.array(ax_con).reshape(2, -1))
# eq_con = np.squeeze(np.array(eq_con).reshape(4, -1))
_, _, _, _, _, _, _ax_con, _eq_con, _ = ligand_assign_consistent(init_mol, liglist,
ligdents, ligcons)
print(("ax_con: ", _ax_con))
print(("eq_con: ", _eq_con))
job_info = {}
info_list = ['ax_con', 'eq_con', 'ax_con_sym', 'eq_con_sym', 'catoms', 'natoms', 'metal_ind']
eq_con, ax_con = [], []
for x in _eq_con:
eq_con += x
for x in _ax_con:
ax_con += x
ax_con_sym = [init_mol.atoms[x].sym for x in ax_con]
eq_con_sym = [init_mol.atoms[x].sym for x in eq_con]
catoms = [x for x in eq_con] + [x for x in ax_con]
for info in info_list:
job_info.update({info: locals()[info]})
return job_info
def getLigFormulae(mol):
## This function gets
## ax and equitorial
## ligand names for octahedral complexes
axnames = []
eqnames = []
liglist, ligdents, ligcons = ligand_breakdown(mol)
ax_ligand_list, eq_ligand_list, ax_natoms_list, eq_natoms_list, ax_con_int_list, eq_con_int_list, ax_con_list, eq_con_list, built_ligand_list = ligand_assign_consistent(
mol, liglist, ligdents, ligcons, False, False)
for axl in ax_ligand_list:
axnames.append(axl.mol.make_formula())
for eql in eq_ligand_list:
eqnames.append(eql.mol.make_formula())
return axnames, eqnames
def getOctBondDistances(mol):
## This function gets
## ax and equitorial
## min and max bond lengths
liglist, ligdents, ligcons = ligand_breakdown(mol)
ax_ligand_list, eq_ligand_list, ax_natoms_list, eq_natoms_list, ax_con_int_list, eq_con_int_list, ax_con_list, eq_con_list, built_ligand_list = ligand_assign_consistent(
mol, liglist, ligdents, ligcons, False, False)
ax_dist = list()
eq_dist = list()
for ax_ligs in ax_con_list:
tempList = list()
for conatms in ax_ligs:
tempList.append(
distance(
mol.getAtom(mol.findMetal()[0]).coords(),
mol.getAtom(conatms).coords()))
ax_dist.append(tempList)
for eq_ligs in eq_con_list:
tempList = list()
for conatms in eq_ligs:
tempList.append(
distance(
mol.getAtom(mol.findMetal()[0]).coords(),
mol.getAtom(conatms).coords()))
eq_dist.append(tempList)
return ax_dist, eq_dist