def substplaceff_mode3(core, substr, substreact, compreact, cpoint, args, connected, frozenats):
enc = 0
# align substrate according to connection atom and shadow atom
substr.alignmol(substr.getAtom(substreact), atom3D('H', cpoint))
# perform rotations
Bcoords = core.getAtomCoords(compreact)
adjsidx = substr.getBondedAtoms(substreact)[0]
if substr.natoms > 1:
# align ligand center of symmetry
substr = align_lig_centersym(Bcoords, substr, substreact, core, False)
if substr.natoms > 2:
# check for linear molecule and align
substr = check_rotate_linear_lig(Bcoords, substr, substreact)
# check for symmetric molecule
substr = check_rotate_symm_lig(Bcoords, substr, substreact, core)
# rotate around M-L axis to minimize steric repulsion
substr = rotate_MLaxis_minimize_steric(
Bcoords, substr, substreact, core)
# distort substrate molecule
adjsidx = substr.getBondedAtoms(substreact)[0]
XYBL = XYcoeff*(substr.getAtom(substreact).rad +
substr.getAtom(adjsidx).rad)
substr.BCM(adjsidx, substreact, XYBL)
# combine molecules
ts3D = mol3D()
ts3D.copymol3D(core)
ts3D = ts3D.combine(substr)
ts3D.charge += substr.charge
if 'a' in args.ffoption or args.substplaceff:
ts3D, enc = ffopt(args.ff, ts3D, connected, 1,
frozenats, False, [], 'Adaptive')
return ts3D, enc
def remove_TEMPMETAL(dir):
dir = dir.rstrip("/")
for file in os.listdir(dir):
if file.split('.')[-1] != "xyz" or "TEMPMETAL" not in file:
continue
molecule = mol3D.mol3D()
molecule.OBMol = molecule.getOBMol(dir + "/" + file, "xyz", ffclean = False)
molecule.convert2mol3D()
for i in molecule.findMetal(): # len(molecule.findMetal()) should initially be 1
molecule.deleteatom(i)
structgen.ffopt('UFF', molecule, [], 1, [], False, [], 200, False)
# MMFF94/ffopt() in general can cause segfaults
# you should still check the structures in Avogadro and optimize manually if necessary
molecule.writexyz(dir + "/" + file[:file.index("TEMPMETAL")])
def substplaceff_mode1(core, substr, substreact, compreact, cpoint, ligalignpt, args, connected, frozenats):
enc = 0
Mcoords = core.getAtomCoords(compreact)
adjsidx = substr.getBondedAtoms(substreact)[0]
theta, u = rotation_params(
substr.getAtomCoords(adjsidx), cpoint, ligalignpt)
substr = rotate_around_axis(substr, cpoint, u, 180-theta)
if substr.natoms > 2:
# same as aligning an equilibrium ligand
substr = check_rotate_linear_lig(Mcoords, substr, substreact)
substr = check_rotate_symm_lig(Mcoords, substr, substreact, core)
substr = rotate_MLaxis_minimize_steric(
Mcoords, substr, substreact, core)
ts3D = mol3D()
ts3D.copymol3D(core)
ts3D = ts3D.combine(substr)
if 'a' in args.ffoption or args.substplaceff:
print('FF optimizing remainder of substrate')
ts3D, enc = ffopt(args.ff, ts3D, connected, 1,
frozenats, False, [], 'Adaptive')
return ts3D, enc
def decorate_ligand(args, ligand_to_decorate, decoration, decoration_index):
# structgen depends on decoration_manager, and decoration_manager depends on structgen.ffopt
# Thus, this import needs to be placed here to avoid a circular dependence
from molSimplify.Scripts.structgen import ffopt
# INPUT
# - args: placeholder for input arguments
# - ligand_to_decorate: mol3D ligand
# - decoration: list of smiles/decorations
# - decoration_index: list of ligand atoms to replace
# OUTPUT
# - new_ligand: built ligand
# - complex3D: list of all mol3D ligands and core
# - emsg: error messages
#if args.debug:
# print 'decorating ligand'
lig = ligand_to_decorate
## reorder to ensure highest atom index
## removed first
sort_order = [
i[0] for i in sorted(enumerate(decoration_index), key=lambda x: x[1])
]
sort_order = sort_order[::-1] ## reverse
decoration_index = [decoration_index[i] for i in sort_order]
decoration = [decoration[i] for i in sort_order]
if args.debug:
print(('decoration_index is ' + str(decoration_index)))
licores = getlicores()
if not isinstance(lig, mol3D):
lig, emsg = lig_load(lig, licores)
else:
lig.convert2OBMol()
lig.charge = lig.OBMol.GetTotalCharge()
lig.convert2mol3D() # convert to mol3D
## create new ligand
merged_ligand = mol3D()
merged_ligand.copymol3D(lig)
for i, dec in enumerate(decoration):
print(('** decoration number ' + str(i) + ' attaching ' + dec +
' at site ' + str(decoration_index[i]) + '**\n'))
dec, emsg = lig_load(dec, licores)
# dec.OBMol.AddHydrogens()
dec.convert2mol3D() # convert to mol3D
if args.debug:
print(i)
print(decoration_index)
print((merged_ligand.getAtom(decoration_index[i]).symbol()))
print((merged_ligand.getAtom(decoration_index[i]).coords()))
merged_ligand.writexyz('basic.xyz')
#dec.writexyz('dec' + str(i) + '.xyz')
Hs = dec.getHsbyIndex(0)
if len(Hs) > 0 and (not len(dec.cat)):
dec.deleteatom(Hs[0])
dec.charge = dec.charge - 1
#dec.writexyz('dec_noH' + str(i) + '.xyz')
if len(dec.cat) > 0:
decind = dec.cat[0]
else:
decind = 0
dec.alignmol(dec.getAtom(decind),
merged_ligand.getAtom(decoration_index[i]))
r1 = dec.getAtom(decind).coords()
r2 = dec.centermass() # center of mass
rrot = r1
decb = mol3D()
decb.copymol3D(dec)
####################################
# center of mass of local environment (to avoid bad placement of bulky ligands)
auxmol = mol3D()
for at in dec.getBondedAtoms(decind):
auxmol.addAtom(dec.getAtom(at))
if auxmol.natoms > 0:
r2 = auxmol.centermass() # overwrite global with local centermass
####################################
# rotate around axis and get both images
theta, u = rotation_params(merged_ligand.centermass(), r1, r2)
#print('u = ' + str(u) + ' theta = ' + str(theta))
dec = rotate_around_axis(dec, rrot, u, theta)
if args.debug:
dec.writexyz('dec_ARA' + str(i) + '.xyz')
decb = rotate_around_axis(decb, rrot, u, theta - 180)
if args.debug:
decb.writexyz('dec_ARB' + str(i) + '.xyz')
d1 = distance(dec.centermass(), merged_ligand.centermass())
d2 = distance(decb.centermass(), merged_ligand.centermass())
dec = dec if (d2 < d1) else decb # pick best one
#####################################
# check for linear molecule
auxm = mol3D()
for at in dec.getBondedAtoms(decind):
auxm.addAtom(dec.getAtom(at))
if auxm.natoms > 1:
r0 = dec.getAtom(decind).coords()
r1 = auxm.getAtom(0).coords()
r2 = auxm.getAtom(1).coords()
if checkcolinear(r1, r0, r2):
theta, urot = rotation_params(
r1,
merged_ligand.getAtom(decoration_index[i]).coords(), r2)
theta = vecangle(
vecdiff(
r0,
merged_ligand.getAtom(decoration_index[i]).coords()),
urot)
dec = rotate_around_axis(dec, r0, urot, theta)
## get the default distance between atoms in question
connection_neighbours = merged_ligand.getAtom(
merged_ligand.getBondedAtomsnotH(decoration_index[i])[0])
new_atom = dec.getAtom(decind)
target_distance = connection_neighbours.rad + new_atom.rad
position_to_place = vecdiff(new_atom.coords(),
connection_neighbours.coords())
old_dist = norm(position_to_place)
missing = (target_distance - old_dist) / 2
dec.translate([missing * position_to_place[j] for j in [0, 1, 2]])
r1 = dec.getAtom(decind).coords()
u = vecdiff(r1, merged_ligand.getAtom(decoration_index[i]).coords())
dtheta = 2
optmax = -9999
totiters = 0
decb = mol3D()
decb.copymol3D(dec)
# check for minimum distance between atoms and center of mass distance
while totiters < 180:
#print('totiters '+ str(totiters))
dec = rotate_around_axis(dec, r1, u, dtheta)
d0 = dec.mindist(
merged_ligand) # try to maximize minimum atoms distance
d0cm = dec.distance(
merged_ligand) # try to maximize center of mass distance
iteropt = d0cm + d0 # optimization function
if (iteropt > optmax): # if better conformation, keep
decb = mol3D()
decb.copymol3D(dec)
optmax = iteropt
#temp = mol3D()
#temp.copymol3D(merged_ligand)
#temp.combine(decb)
#temp.writexyz('opt_iter_'+str(totiters)+'.xyz')
#print('new max! ' + str(iteropt) )
totiters += 1
dec = decb
if args.debug:
dec.writexyz('dec_aligned' + str(i) + '.xyz')
print(('natoms before delete ' + str(merged_ligand.natoms)))
print(('obmol before delete at ' + str(decoration_index[i]) +
' is ' + str(merged_ligand.OBMol.NumAtoms())))
## store connectivity for deleted H
BO_mat = merged_ligand.populateBOMatrix()
row_deleted = BO_mat[decoration_index[i]]
bonds_to_add = []
# find where to put the new bonds ->>> Issue here.
for j, els in enumerate(row_deleted):
if els > 0:
# if there is a bond with an atom number
# before the deleted atom, all is fine
# else, we subtract one as the row will be be removed
if j < decoration_index[i]:
bond_partner = j
else:
bond_partner = j - 1
if len(dec.cat) > 0:
bonds_to_add.append(
(bond_partner, (merged_ligand.natoms - 1) + dec.cat[0],
els))
else:
bonds_to_add.append(
(bond_partner, merged_ligand.natoms - 1, els))
## perfrom delete
merged_ligand.deleteatom(decoration_index[i])
merged_ligand.convert2OBMol()
if args.debug:
merged_ligand.writexyz('merged del ' + str(i) + '.xyz')
## merge and bond
merged_ligand.combine(dec, bond_to_add=bonds_to_add)
merged_ligand.convert2OBMol()
if args.debug:
merged_ligand.writexyz('merged' + str(i) + '.xyz')
merged_ligand.printxyz()
print('************')
merged_ligand.convert2OBMol()
merged_ligand, emsg = ffopt('MMFF94', merged_ligand, [], 0, [], False, [],
100)
BO_mat = merged_ligand.populateBOMatrix()
if args.debug:
merged_ligand.writexyz('merged_relaxed.xyz')
print(BO_mat)
return (merged_ligand)