def match_lig_list(file_in,
file_init_geo,
catoms_arr,
flag_loose,
flag_lbd=True,
debug=False,
depth=3,
BondedOct=False):
flag_match = True
my_mol = create_mol_with_xyz(_file_in=file_in)
init_mol = create_mol_with_xyz(_file_in=file_init_geo)
if flag_lbd: # Also do ligand breakdown for opt geo
my_mol_trunc = obtain_truncation_metal(my_mol, depth)
init_mol_trunc = obtain_truncation_metal(init_mol, depth)
my_mol_trunc.createMolecularGraph()
init_mol_trunc.createMolecularGraph()
init_mol_trunc.writexyz('init_trunc_tmp.xyz')
my_mol_trunc.writexyz('mymol_trunc_tmp.xyz')
liglist_init, ligdents_init, ligcons_init = ligand_breakdown(
init_mol_trunc)
liglist, ligdents, ligcons = ligand_breakdown(my_mol_trunc)
liglist_atom = [[my_mol_trunc.getAtom(x).symbol() for x in ele]
for ele in liglist]
liglist_init_atom = [[init_mol_trunc.getAtom(x).symbol() for x in ele]
for ele in liglist_init]
if debug:
print(('!!!!:', [x.symbol() for x in init_mol_trunc.getAtoms()]))
print(('liglist_init, ligdents_init, ligcons_init', liglist_init,
ligdents_init, ligcons_init))
# print('liglist, ligdents, ligcons', liglist, ligdents, ligcons)
else: # ceate/use the liglist, ligdents, ligcons of initial geo as we just wanna track them down
# _start = time.clock()
if debug:
print('Just inherit the ligand list from init structure.')
liglist_init, ligdents_init, ligcons_init = ligand_breakdown(
init_mol, flag_loose=flag_loose, BondedOct=BondedOct)
# _elapsed = (time.clock() - _start)
# print('time on lig_breakdoen:', _elapsed)
liglist, ligdents, ligcons = liglist_init[:], ligdents_init[:], ligcons_init[:]
liglist_atom = [[my_mol.getAtom(x).symbol() for x in ele]
for ele in liglist]
liglist_init_atom = [[init_mol.getAtom(x).symbol() for x in ele]
for ele in liglist_init]
if debug:
print(('ligand_list opt in symbols:', liglist_atom))
print(('ligand_list init in symbols: ', liglist_init_atom))
liglist_shifted = []
for ele in liglist_init_atom:
# posi = liglist_atom.index(ele)
# liglist_shifted.append(liglist[posi])
# liglist_atom.pop(posi)
try:
_flag = False
for idx, _ele in enumerate(liglist_atom):
if set(ele) == set(_ele) and len(ele) == len(_ele):
if debug:
print(('fragment in liglist_init', ele))
print(('fragment in liglist', _ele))
posi = idx
_flag = True
liglist_shifted.append(liglist[posi])
liglist_atom.pop(posi)
liglist.pop(posi)
if not _flag:
if debug:
print('Ligands cannot match!')
flag_match = False
except:
print('Ligands cannot match!')
flag_match = False
if debug:
print(('!!!!!returns', liglist_shifted, liglist_init))
return liglist_shifted, liglist_init, flag_match
def match_lig_list(file_in, file_init_geo, catoms_arr,
flag_loose, flag_lbd=True, debug=False,
depth=3, BondedOct=False):
flag_match = True
my_mol = create_mol_with_xyz(_file_in=file_in)
init_mol = create_mol_with_xyz(_file_in=file_init_geo)
if flag_lbd: ## Also do ligand breakdown for opt geo
my_mol_trunc = obtain_truncation_metal(my_mol, depth)
init_mol_trunc = obtain_truncation_metal(init_mol, depth)
my_mol_trunc.createMolecularGraph()
init_mol_trunc.createMolecularGraph()
init_mol_trunc.writexyz('init_trunc_tmp.xyz')
my_mol_trunc.writexyz('mymol_trunc_tmp.xyz')
liglist_init, ligdents_init, ligcons_init = ligand_breakdown(init_mol_trunc)
liglist, ligdents, ligcons = ligand_breakdown(my_mol_trunc)
liglist_atom = [[my_mol_trunc.getAtom(x).symbol() for x in ele]
for ele in liglist]
liglist_init_atom = [[init_mol_trunc.getAtom(x).symbol() for x in ele]
for ele in liglist_init]
if debug:
print('!!!!:', [x.symbol() for x in init_mol_trunc.getAtoms()])
print('liglist_init, ligdents_init, ligcons_init', liglist_init, ligdents_init, ligcons_init)
# print('liglist, ligdents, ligcons', liglist, ligdents, ligcons)
else: ## ceate/use the liglist, ligdents, ligcons of initial geo as we just wanna track them down
# _start = time.clock()
if debug:
print('Just inherit the ligand list from init structure.')
liglist_init, ligdents_init, ligcons_init = ligand_breakdown(init_mol,
flag_loose=flag_loose,
BondedOct=BondedOct)
# _elapsed = (time.clock() - _start)
# print('time on lig_breakdoen:', _elapsed)
liglist, ligdents, ligcons = liglist_init[:], ligdents_init[:], ligcons_init[:]
liglist_atom = [[my_mol.getAtom(x).symbol() for x in ele]
for ele in liglist]
liglist_init_atom = [[init_mol.getAtom(x).symbol() for x in ele]
for ele in liglist_init]
if debug:
print('ligand_list opt in symbols:', liglist_atom)
print('ligand_list init in symbols: ', liglist_init_atom)
liglist_shifted = []
for ele in liglist_init_atom:
# posi = liglist_atom.index(ele)
# liglist_shifted.append(liglist[posi])
# liglist_atom.pop(posi)
try:
_flag = False
for idx, _ele in enumerate(liglist_atom):
if set(ele) == set(_ele) and len(ele) == len(_ele):
if debug:
print('fragment in liglist_init', ele)
print('fragment in liglist', _ele)
posi = idx
_flag = True
liglist_shifted.append(liglist[posi])
liglist_atom.pop(posi)
liglist.pop(posi)
if not _flag:
if debug:
print('Ligands cannot match!')
flag_match = False
except:
print('Ligands cannot match!')
flag_match = False
if debug:
print('!!!!!returns', liglist_shifted, liglist_init)
return liglist_shifted, liglist_init, flag_match