def bindCN(self,
site_index,
molecule,
v,
CN_bond_length=1.16,
catC_bond_length=1.49):
"""
input:
molecule: (molSimplify mol class) molecule to modify in-place with O2
v: (np.array) coordinates to displace first O
output:
molecule modified with functional group OH
"""
site_coords = molecule.atoms[site_index].coords()
v_C = self.scale_vector(v, catC_bond_length)
v_N = self.scale_vector(v, catC_bond_length + CN_bond_length)
site_coords = molecule.atoms[site_index].coords()
molecule.addAtom(
mol3D.atom3D(
Sym='C',
xyz=[site_coords[c] + v_C[c]
for c in range(len(site_coords))]))
molecule.addAtom(
mol3D.atom3D(
Sym='N',
xyz=[site_coords[c] + v_N[c]
for c in range(len(site_coords))]))
#structgen.ffopt('MMFF94', molecule, [], 1, [], False, [], 200, False) # keeps failing
return molecule
def bindO2H(self,
site_index,
molecule,
v,
bond_angle=111.,
OO_bond_length=1.32,
catO_bond_length=1.55):
"""
input:
molecule: (molSimplify mol class) molecule to modify in-place with O2
v: (np.array) coordinates to displace first O
output:
molecule modified with functional group O2H
"""
site_coords = molecule.atoms[site_index].coords()
v_O1 = self.scale_vector(v, catO_bond_length)
v_O2 = self.scale_vector(
v, catO_bond_length +
OO_bond_length * math.cos(math.pi - math.radians(bond_angle)))
v_H = self.scale_vector(v, self.OH_bond_length)
theta_0 = 0 # arbitrarily chosen
v_perp = self.vec3_perp(
self.scale_vector(
v,
self.OO_bond_length *
math.sin(math.pi - math.radians(bond_angle))), theta_0)
if v_perp == None: # shouldn't happen
return None
site_coords = molecule.atoms[site_index].coords()
molecule.addAtom(
mol3D.atom3D(Sym='O',
xyz=[
site_coords[c] + v_O1[c]
for c in range(len(site_coords))
]))
molecule.addAtom(
mol3D.atom3D(Sym='O',
xyz=[
site_coords[c] + v_O2[c] + v_perp[c]
for c in range(len(site_coords))
]))
molecule.addAtom(
mol3D.atom3D(Sym='H',
xyz=[
site_coords[c] + v_O2[c] + (v_perp[c] + v_H[c])
for c in range(len(site_coords))
]))
#structgen.ffopt('MMFF94', molecule, [], 1, [], False, [], 200, False) # keeps failing
return molecule
def bind_OOH(infile, molecule, site_index, catO_bond_length, catOO_bond_angle,
OO_bond_length, OH_bond_length):
molecule_copy = mol3D.mol3D()
molecule_copy.copymol3D(molecule)
v = get_normal_vec(molecule_copy, site_index)
v_O1 = scale_vector(v, catO_bond_length)
v_O2 = scale_vector(
v, catO_bond_length +
OO_bond_length * math.cos(math.pi - math.radians(catOO_bond_angle)))
theta_0 = 0
v_perp = vec3_perp(
scale_vector(
v,
OO_bond_length *
math.sin(math.pi - math.radians(catOO_bond_angle))), theta_0)
if v_perp == None: # shouldn't happen
return None
v_H = scale_vector(v, OH_bond_length)
site_coords = molecule_copy.atoms[site_index].coords()
molecule_copy.addAtom(
mol3D.atom3D(
Sym='O',
xyz=[site_coords[c] + v_O1[c] for c in range(len(site_coords))]))
molecule_copy.addAtom(
mol3D.atom3D(Sym='O',
xyz=[
site_coords[c] + v_O2[c] + v_perp[c]
for c in range(len(site_coords))
]))
molecule_copy.addAtom(
mol3D.atom3D(Sym='H',
xyz=[
site_coords[c] + v_O2[c] + v_perp[c] + v_H[c]
for c in range(len(site_coords))
]))
file_name = infile.split('.')[0] + "OOH"
if not is_metal_catalyst: # metal catalysts assumed to have one active site
file_name += "-" + str(site_index) # still zero-indexed
molecule_copy.writexyz(file_name)
def bind_O(infile, molecule, site_index, catO_bond_length):
molecule_copy = mol3D.mol3D()
molecule_copy.copymol3D(molecule)
v = get_normal_vec(molecule_copy, site_index)
v_O = scale_vector(v, catO_bond_length)
site_coords = molecule_copy.atoms[site_index].coords()
molecule_copy.addAtom(
mol3D.atom3D(
Sym='O',
xyz=[site_coords[c] + v_O[c] for c in range(len(site_coords))]))
file_name = infile.split('.')[0] + "O"
if not is_metal_catalyst: # metal catalysts assumed to have one active site
file_name += "-" + str(site_index) # still zero-indexed
molecule_copy.writexyz(file_name)
oxo = mymol.getAtom(-1)
oxo_coord = oxo.coords()
metal_coord = mymol.getAtom(metalval[0]).coords()
bond1_coord = mymol.getAtom(bondedatoms[0]).coords()
bond2_coord = mymol.getAtom(bondedatoms[1]).coords()
oxo, dxyz = setPdistance(oxo, oxo_coord, metal_coord, 1.84)
metaloxo = np.array(oxo_coord) - np.array(metal_coord)
extra = getPointu(oxo_coord, 1.2, metaloxo)
moveup = np.array(extra) - metal_coord
val = midpt(bond1_coord, bond2_coord)
movevect = np.array(
normalize(
np.array(val) + moveup -
np.array(oxo_coord))) + oxo_coord
p = list(movevect)
newH = atom3D('H', p)
mymol.addAtom(newH)
hydrogen = mymol.getAtom(-1)
hydrogen, dxyz = setPdistance(hydrogen, hydrogen.coords(),
oxo.coords(), 1)
if not dry_run:
if not os.path.exists(
path_dictionary["initial_geo_path"] + modgeo1
) and (upperspin
in metal_spin_dictionary[metal][hydroxyl_ox]):
mymol.writexyz(
path_dictionary["initial_geo_path"] + modgeo1)
elif (upperspin not in metal_spin_dictionary[metal]
[hydroxyl_ox]):
print((str(upperspin) +
' spin not in dictionary for ' +
def bind_O2(self,
site_index,
catO_bond_length=1.8,
bond_angle=120,
OO_bond_length=1.3,
reposition_O2=False):
# binds O2 perpendicular to catalyst plane, then makes .xyz file
# does not modify input molecule
# bond lengths in angstroms, angle in degrees. Variables set to parameters for Fe
molecule_copy = mol3D.mol3D()
molecule_copy.copymol3D(self.molecule)
connection_list = molecule_copy.getBondedAtomsSmart(site_index,
oct=False)
#print("Active Site: %s Neighbors: %s" %(str(site_index), str(connection_list))) # for debugging
try:
v1 = molecule_copy.atoms[connection_list[0]].distancev(
molecule_copy.atoms[connection_list[1]])
v2 = molecule_copy.atoms[connection_list[0]].distancev(
molecule_copy.atoms[connection_list[2]])
v = np.cross(v1, v2)
except:
print("Error finding plane of catalyst.")
return None
v_O1 = self.scale_vector(v, catO_bond_length)
v_O2 = self.scale_vector(
v, catO_bond_length +
OO_bond_length * math.cos(math.pi - math.radians(bond_angle)))
theta_0 = 0 # arbitrarily chosen
v_perp = self.vec3_perp(
self.scale_vector(
v,
OO_bond_length * math.sin(math.pi - math.radians(bond_angle))),
theta_0)
if v_perp == None: # shouldn't happen
return None
site_coords = molecule_copy.atoms[site_index].coords()
molecule_copy.addAtom(
mol3D.atom3D(Sym='O',
xyz=[
site_coords[c] + v_O1[c]
for c in range(len(site_coords))
]))
molecule_copy.addAtom(
mol3D.atom3D(Sym='O',
xyz=[
site_coords[c] + v_O2[c] + v_perp[c]
for c in range(len(site_coords))
]))
#structgen.ffopt('MMFF94', molecule_copy, [], 1, [], False, [], 200, False) # keeps failing
if reposition_O2: # workaround for ffopt() failing to set up; nonmetal catalysts
theta = theta_0 + self.dtheta
position_OK = False
while not position_OK:
position_OK = True
for atom in molecule_copy.getAtoms():
if atom == molecule_copy.getAtoms(
)[-1] or atom == molecule_copy.getAtoms()[-2]:
continue
if atom.symbol() in self.bond_length_cutoffs:
cutoff = self.bond_length_cutoffs[atom.symbol()]
else: # won't happen if bond_length_cutoffs is kept up to date
cutoff = self.bond_length_cutoffs[max(
self.bond_length_cutoffs,
key=lambda key: self.bond_length_cutoffs[key])]
print("Using %f A as the bond length cutoff for %s" %
(cutoff, atom.symbol()))
if molecule_copy.getAtoms()[-1].distance(atom) < cutoff:
position_OK = False
break
if not position_OK:
if theta >= 360:
print("%s may have geometry issues after O2-binding." %
infile)
break
v_perp = self.vec3_perp(
self.scale_vector(
v,
OO_bond_length *
math.sin(math.pi - math.radians(bond_angle))),
theta)
if v_perp == None: # shouldn't happen
return None
molecule_copy.getAtoms()[-1].setcoords([
site_coords[c] + v_O2[c] + v_perp[c]
for c in range(len(site_coords))
])
theta += self.dtheta
file_name = self.infile.split('.')[0] + "O2"
if len(self.active_sites
) > 1: #only add active site in name if more than 1
file_name += "-" + str(site_index) # still zero-indexed
molecule_copy.writexyz(file_name)
def bind_XY(infile, molecule, site_index, X, Y, catX_bond_length, bond_angle,
XY_bond_length, reposition_XY, fn_suffix):
# XY is any diatomic species, with X closer to the active site
# positions XY perpendicular to catalyst plane, then makes .xyz file
# does not modify input molecule
# bond lengths in angstroms, angle in degrees
molecule_copy = mol3D.mol3D()
molecule_copy.copymol3D(molecule)
v = get_normal_vec(molecule_copy, site_index)
v_X = scale_vector(v, catX_bond_length)
v_Y = scale_vector(
v, catX_bond_length +
XY_bond_length * math.cos(math.pi - math.radians(bond_angle)))
theta_0 = 0 # arbitrarily chosen
v_perp = vec3_perp(
scale_vector(
v, XY_bond_length * math.sin(math.pi - math.radians(bond_angle))),
theta_0)
if v_perp == None: # shouldn't happen
return None
site_coords = molecule_copy.atoms[site_index].coords()
molecule_copy.addAtom(
mol3D.atom3D(
Sym=X,
xyz=[site_coords[c] + v_X[c] for c in range(len(site_coords))]))
molecule_copy.addAtom(
mol3D.atom3D(Sym=Y,
xyz=[
site_coords[c] + v_Y[c] + v_perp[c]
for c in range(len(site_coords))
]))
#structgen.ffopt('MMFF94', molecule_copy, [], 1, [], False, [], 200, False) # keeps failing
if reposition_XY: # workaround for ffopt() failing to set up; nonmetal catalysts
bond_length_cutoffs = {
'C': 1.953,
'H': 1.443,
'I': 2.543,
'Cl': 2.154,
'B': 2.027,
'N': 1.834,
'F': 1.707,
'Br': 2.423,
'P': 2.297,
'S': 2.198,
'O': 1.810
} # X-O (angstroms)
dtheta = 5 # change this if you want to
theta = theta_0 + dtheta
position_OK = False
while not position_OK:
position_OK = True
for atom in molecule_copy.getAtoms():
if atom == molecule_copy.getAtoms(
)[-1] or atom == molecule_copy.getAtoms()[-2]:
continue
if atom.symbol() in bond_length_cutoffs:
cutoff = bond_length_cutoffs[atom.symbol()]
else: # won't happen if bond_length_cutoffs is kept up to date
cutoff = bond_length_cutoffs[max(
bond_length_cutoffs,
key=lambda key: bond_length_cutoffs[key])]
print("Using %f A as the bond length cutoff for %s" %
(cutoff, atom.symbol()))
if molecule_copy.getAtoms()[-1].distance(atom) < cutoff:
position_OK = False
break
if not position_OK:
if theta >= 360:
print("%s may have geometry issues after O2-binding." %
infile)
break
v_perp = vec3_perp(
scale_vector(
v,
XY_bond_length *
math.sin(math.pi - math.radians(bond_angle))), theta)
if v_perp == None: # shouldn't happen
return None
molecule_copy.getAtoms()[-1].setcoords([
site_coords[c] + v_Y[c] + v_perp[c]
for c in range(len(site_coords))
])
theta += dtheta
file_name = infile.split('.')[0] + fn_suffix
if not is_metal_catalyst: # metal catalysts assumed to have one active site
file_name += "-" + str(site_index) # still zero-indexed
molecule_copy.writexyz(file_name)
