def getSubstructureFromPath(refmol: Molecule, path: np.ndarray) -> Molecule:
"""Create a molecules object from a substructure of given molecule."""
# initialize
refat = refmol.get_atomic_numbers()
refxyz = refmol.get_positions()
# atoms from complex excluding old substrate
atoms = []
for elem in path:
atom = Atom(symbol=refat[elem], position=refxyz[elem, :])
atoms.append(atom)
# create molecule from atoms
return Molecule(symbols=atoms)
def exchangeSubstructure(
n: int,
center: int,
subnr: int,
bonds: np.ndarray,
ref: Molecule,
newsub: Molecule,
newSubBonds: np.ndarray,
name: str,
rotate: int,
exclude: bool,
):
"""Exchange substructure (subnr) from ref with substrate."""
# setup initial complex
refxyz = ref.get_positions()
refat = ref.get_atomic_numbers()
refnat = ref.get_number_of_atoms()
# match new and old substrate
newat = newsub.get_atomic_numbers()
newnat = newsub.get_number_of_atoms()
# extract coordinates of central atom
centralAtom = np.zeros(shape=(1, 3), dtype=np.float64)
centralAtom = refxyz[center, :]
for i in range(len(bonds[center])):
if i == subnr:
path = np.zeros(shape=(n, ), dtype=np.int32)
# set all elements to -1
path.fill(-1)
partner = bonds[center][i]
count = Counter() # type: ignore
count["step"] = -1
getSubstructures(n, bonds, center, partner, path, count=count)
# get rid of -1 elements
path = [x for x in path if x != -1]
path = np.array(path)
# create molecule from given path
oldsub = getSubstructureFromPath(ref, path)
# get all bonding partner
oldSubBonds = oldsub.get_bonds(partner="X")
outxyz = np.zeros(shape=(newnat, 3), dtype=np.float64)
outxyz = matchSubstrates(
bonds,
newsub,
newSubBonds,
oldsub,
oldSubBonds,
centralAtom,
)
# atoms from complex excluding old substrate
atoms = []
for i in range(refnat):
if i in path:
continue
atom = Atom(symbol=refat[i], position=refxyz[i, :])
atoms.append(atom)
# atoms from new substrate
# Should we rotate the substrate around covalent bond?
if rotate:
theta = rotate
origin = refxyz[center, :]
partner = outxyz[0, :]
outxyz2 = np.zeros(shape=outxyz.shape, dtype=np.float64)
# reference shift
refShift = getRodriguezRotation(partner, origin, partner,
theta)
shift = outxyz[0, :] - refShift
for i in range(newnat):
outxyz2[i, :] = getRodriguezRotation(
outxyz[i, :],
origin,
partner,
theta,
)
outxyz2[i, :] += shift
atom = Atom(symbol=newat[i], position=outxyz2[i, :])
atoms.append(atom)
else:
for i in range(newnat):
atom = Atom(symbol=newat[i], position=outxyz[i, :])
atoms.append(atom)
# create molecule from atoms
mol = Molecule(symbols=atoms)
# write new structure in xyz format
mol.writeMolecule(name + ".xyz")
# write constrain file
refnat = ref.get_number_of_atoms()
oldnat = oldsub.get_number_of_atoms()
nat = refnat - oldnat
writeTransitionMetalConstrains(nat, newnat, newSubBonds, exclude)
