def modified_minimum_scan_rdkit(ligand: Molecule, bond_tuple: Tuple[int, int],
anchor: Atom) -> None:
"""A modified version of the :func:`.global_minimum_scan_rdkit` function.
* Uses the ligand vector as criteria rather than the energy.
* Geometry optimizations are constrained during the conformation search.
* Finish with a final unconstrained geometry optimization.
See Also
--------
:func:`global_minimum_scan_rdkit<scm.plams.recipes.global_minimum.minimum_scan_rdkit>`:
Optimize the molecule (RDKit UFF) with 3 different values for the given dihedral angle and
find the lowest energy conformer.
:param |Molecule| mol: The input molecule
:param tuple bond_tuple: A 2-tuples containing the atomic indices of valid bonds
:return |Molecule|: A copy of *mol* with a newly optimized geometry
"""
# Define a number of variables and create 3 copies of the ligand
angles = (-120, 0, 120)
mol_list = [ligand.copy() for _ in range(3)]
for angle, mol in zip(angles, mol_list):
bond = mol[bond_tuple]
atom = mol[bond_tuple[0]]
mol.rotate_bond(bond, atom, angle, unit='degree')
rdmol_list = [molkit.to_rdmol(mol, properties=False) for mol in mol_list]
# Optimize the (constrained) geometry for all dihedral angles in angle_list
# The geometry that yields the minimum energy is returned
fixed = _find_idx(mol, bond)
for rdmol in rdmol_list:
ff = UFF(rdmol)
for f in fixed:
ff.AddFixedPoint(f)
ff.Minimize()
# Find the conformation with the optimal ligand vector
cost_list = []
try:
i = ligand.atoms.index(anchor)
except ValueError:
i = -1 # Default to the origin as anchor
for rdmol in rdmol_list:
xyz = rdmol_as_array(rdmol)
if i == -1: # Default to the origin as anchor
xyz = np.vstack([xyz, [0, 0, 0]])
rotmat = optimize_rotmat(xyz, i)
xyz[:] = xyz @ rotmat.T
xyz -= xyz[i]
cost = np.exp(xyz[:, 1:]).sum()
cost_list.append(cost)
# Perform an unconstrained optimization on the best geometry and update the geometry of ligand
j = np.argmin(cost_list)
rdmol_best = rdmol_list[j]
UFF(rdmol).Minimize()
ligand.from_rdmol(rdmol_best)
def fix_h(mol: Molecule) -> None:
"""If a C=C-H angle is smaller than :math:`20` degrees, set it back to :math:`120` degrees.
Performs an inplace update of **plams_mol**.
Parameters
----------
plams_mol : |plams.Molecule|_
A PLAMS molecule.
"""
h_list = [
atom for atom in mol if atom.atnum == 1
and 2.0 in [bond.order for bond in mol.neighbors(atom)[0].bonds]
]
rdmol = molkit.to_rdmol(mol)
conf = rdmol.GetConformer()
get_idx = mol.atoms.index
set_angle = rdMolTransforms.SetAngleDeg
get_angle = rdMolTransforms.GetAngleDeg
update = False
for atom in h_list:
at1 = atom # Central atom
at2 = mol.neighbors(at1)[0] # Neighbours
at3 = [atom for atom in mol.neighbors(at2)
if atom != at1] # Neighbours of neighbours
# Create 2 sets of 3 atomic indices for defining angles: at1-at2=at3
idx_tup1 = get_idx(at3[0]), get_idx(at2), get_idx(at1)
idx_tup2 = get_idx(at3[1]), get_idx(at2), get_idx(at1)
if get_angle(conf, *idx_tup1) <= 20.0:
set_angle(conf, *idx_tup1, 120.0)
update = True
elif get_angle(conf, *idx_tup2) <= 20.0:
set_angle(conf, *idx_tup2, 120.0)
update = True
if update:
mol.from_rdmol(rdmol)
def fix_carboxyl(mol: Molecule) -> None:
"""Resets carboxylate OCO angles if it is smaller than :math:`60` degrees.
Performs an inplace update of **plams_mol**.
Parameters
----------
plams_mol : |plams.Molecule|_
A PLAMS molecule.
"""
rdmol = molkit.to_rdmol(mol)
conf = rdmol.GetConformer()
matches = rdmol.GetSubstructMatches(_CARBOXYLATE)
if matches:
get_angle = rdMolTransforms.GetAngleDeg
set_angle = rdMolTransforms.SetAngleDeg
for idx in matches:
if get_angle(conf, idx[3], idx[1], idx[0]) < 60:
set_angle(conf, idx[2], idx[1], idx[3], 180.0)
set_angle(conf, idx[0], idx[1], idx[3], 120.0)
mol.from_rdmol(rdmol)
