def get_asa_fragments(qd: Molecule) -> Tuple[List[Molecule], Molecule]:
"""Construct the fragments for an activation strain analyses.
Parameters
----------
qd : |plams.Molecule|
A Molecule whose atoms' properties should be marked with `pdb_info.ResidueName`.
Atoms in the core should herein be marked with ``"COR"``.
Returns
-------
:class:`list` [|plams.Molecule|] and |plams.Molecule|
A list of ligands and the core.
Fragments are defined based on connectivity patterns (or lack thereof).
"""
# Delete all atoms within the core
mol_complete = qd.copy()
core = Molecule()
core.properties = mol_complete.properties.copy()
core_atoms = [at for at in mol_complete if at.properties.pdb_info.ResidueName == 'COR']
for atom in core_atoms:
mol_complete.delete_atom(atom)
atom.mol = core
core.atoms = core_atoms
mol_complete.properties.name += '_frags'
core.properties.name += '_core'
# Fragment the molecule
ligand_list = mol_complete.separate()
# Set atomic properties
for at1, at2 in zip(chain(*ligand_list), mol_complete):
at1.properties.symbol = at2.properties.symbol
at1.properties.charge_float = at2.properties.charge_float
for at1, at2 in zip(core, qd):
at1.properties.symbol = at2.properties.symbol
at1.properties.charge_float = at2.properties.charge_float
# Set the prm parameter which points to the created .prm file
name = mol_complete.properties.name[:-1]
path = mol_complete.properties.path
prm = mol_complete.properties.prm
for mol in ligand_list:
mol.properties.name = name
mol.properties.path = path
mol.properties.prm = prm
return ligand_list, core
def separate_mod(self) -> Tuple[Molecule]:
"""Modified PLAMS function: creates new molecules out of this instance rather than a copy of this instance. Atoms, bonds and properties are *not* copied.
Separate the molecule into connected components.
Returns is a list of new Molecule instrances (all atoms and bonds are disjoint with
the original molecule).
Each element of this list is identical to one connected component of the base molecule.
A connected component is a subset of atoms such that there exists a path
(along one or more bonds) between any two atoms.
Returns
-------
|tuple|_ [|plams.Molecule|_]
A list of molecules with atoms and bonds from **self**.
""" # noqa: E501
frags = ()
for at in self:
at._visited = False
def dfs(v, mol):
v._visited = True
v.mol = mol
for e in v.bonds:
e.mol = mol
u = e.other_end(v)
if not u._visited:
dfs(u, mol)
for src in self.atoms:
if not src._visited:
m = Molecule()
dfs(src, m)
frags += (m, )
m.properties = self.properties.copy()
for at in self.atoms:
del at._visited
at.mol.atoms.append(at)
for b in self.bonds:
b.mol.bonds.append(b)
return frags
