def dfs(at1: Atom, atom_set: Set[Atom]):
at1._visited = True
atom_set.add(at1)
for at2 in at1.neighbors():
if at2._visited:
continue
dfs(at2, atom_set)
def set_dihed(self,
angle: float,
anchor: Atom,
cap: Sequence[Atom],
opt: bool = True,
unit: str = 'degree') -> None:
"""Change all valid dihedral angles into a specific value.
Performs an inplace update of this instance.
Parameters
----------
angle : :class:`float`
The desired dihedral angle.
anchor : |plams.Atom|
The ligand anchor atom.
opt : :class:`bool`
Whether or not the dihedral adjustment should be followed up by an RDKit UFF optimization.
unit : :class:`str`
The input unit.
"""
cap_atnum = []
for at in cap:
cap_atnum.append(at.atnum)
at.atnum = 0
angle = Units.convert(angle, unit, 'degree')
bond_iter = (bond for bond in self.bonds
if bond.atom1.atnum != 1 and bond.atom2.atnum != 1
and bond.order == 1 and not self.in_ring(bond))
# Correction factor for, most importantly, tri-valent anchors (e.g. P(R)(R)R)
dihed_cor = angle / 2
neighbors = anchor.neighbors()
if len(neighbors) > 2:
atom_list = [anchor] + sorted(neighbors, key=lambda at: -at.atnum)[:3]
improper = get_dihed(atom_list)
dihed_cor *= np.sign(improper)
for bond in bond_iter:
# Gather lists of all non-hydrogen neighbors
n1, n2 = self.neighbors_mod(bond.atom1), self.neighbors_mod(bond.atom2)
# Remove all atoms in `bond`
n1 = [atom for atom in n1 if atom is not bond.atom2]
n2 = [atom for atom in n2 if atom is not bond.atom1]
# Remove all non-subsituted atoms
# A special case consists of anchor atoms; they can stay
if len(n1) > 1:
n1 = [
atom for atom in n1 if (len(self.neighbors_mod(atom)) > 1
or atom is anchor or atom.atnum == 0)
]
if len(n2) > 1:
n2 = [
atom for atom in n2 if (len(self.neighbors_mod(atom)) > 1
or atom is anchor or atom.atnum == 0)
]
# Set `bond` in an anti-periplanar conformation
if n1 and n2:
dihed = get_dihed((n1[0], bond.atom1, bond.atom2, n2[0]))
if anchor not in bond:
self.rotate_bond(bond,
bond.atom1,
angle - dihed,
unit='degree')
else:
dihed -= dihed_cor
self.rotate_bond(bond, bond.atom1, -dihed, unit='degree')
dihed_cor *= -1
for at, atnum in zip(cap, cap_atnum):
at.atnum = atnum
if opt:
rdmol = molkit.to_rdmol(self)
UFF(rdmol).Minimize()
self.from_rdmol(rdmol)
def _besides_ring(atom: Atom) -> bool:
"""Check if any neighboring atoms are part of a ring system."""
return any(plams_mol.in_ring(at) for at in atom.neighbors())