def apply(self, mol: RWMol) -> RWMol:
num_atoms = mol.GetNumAtoms()
if self.detach:
for i, a in enumerate(mol.GetAtoms()):
m = a.GetAtomMapNum()
if m == self.atom_map2:
for bond in a.GetBonds():
mol.RemoveBond(bond.GetBeginAtomIdx(),
bond.GetEndAtomIdx())
mol.RemoveAtom(i)
num_atoms -= 1
break
atom_ind = get_atom_ind(mol, self.atom_map1)
b_type = rdchem.BondType.values[self.bond_type]
b_stereo = rdchem.BondStereo.values[self.bond_stereo]
old_atom = mol.GetAtomWithIdx(atom_ind)
if old_atom.HasProp('in_reactant'):
self.new_a.SetBoolProp('in_reactant',
old_atom.GetBoolProp('in_reactant'))
if old_atom.HasProp('mol_id'):
self.new_a.SetIntProp('mol_id', old_atom.GetIntProp('mol_id'))
mol.AddAtom(self.new_a)
new_atom_ind = num_atoms
bond_ind = mol.AddBond(atom_ind, new_atom_ind, order=b_type) - 1
new_bond = mol.GetBondWithIdx(bond_ind)
new_bond.SetStereo(b_stereo)
new_bond.SetBoolProp('is_edited', True)
return mol
def apply(self, mol: RWMol) -> RWMol:
atom1 = get_atom_ind(mol, self.atom_map1)
atom2 = get_atom_ind(mol, self.atom_map2)
if self.bond_type is None: # delete bond
bond = mol.GetBondBetweenAtoms(atom1, atom2)
if bond is not None:
mol.RemoveBond(atom1, atom2)
else:
b_type = rdchem.BondType.values[self.bond_type]
b_stereo = rdchem.BondStereo.values[self.bond_stereo]
bond = mol.GetBondBetweenAtoms(atom1, atom2)
if bond is None: # add new bond
bond_ind = mol.AddBond(atom1, atom2, order=b_type) - 1
bond = mol.GetBondWithIdx(bond_ind)
else: # change an existing bond
bond.SetBondType(b_type)
bond.SetStereo(b_stereo)
bond.SetBoolProp('is_edited', True)
if b_type == BondType.AROMATIC:
bond.SetIsAromatic(True)
mol.GetAtomWithIdx(atom1).SetIsAromatic(True)
mol.GetAtomWithIdx(atom2).SetIsAromatic(True)
return mol
def fragment(self, scaffold):
"""Fragment a scaffold into its next set of Murcko fragments.
Parameters
----------
scaffold : scaffoldgraph.core.Scaffold
Child scaffold to be fragmented.
Returns
-------
list
A list of parent scaffolds representing the next hierarchy.
"""
parents = [] # container for parent scaffolds
rings = scaffold.rings # ring information
for rix, ring in enumerate(rings): # Loop through all rings and remove
edit = RWMol(scaffold.mol) # Editable molecule
# Collect all removable atoms in the molecule
remove_atoms = set()
for index, atom in zip(ring.aix, ring.atoms):
if rings.info.NumAtomRings(index) == 1:
if atom.GetDegree() > 2: # Evoke linker collection
collect_linker_atoms(edit.GetAtomWithIdx(index),
remove_atoms)
else: # Add ring atom to removable set
remove_atoms.add(index)
else: # Atom is shared between multiple rings
correct_atom_props(edit.GetAtomWithIdx(index))
# Collect removable bonds (this needs to be done to prevent the case where when deleting
# a ring two atoms belonging to the same bond are also part of separate other rings.
# This bond must be broken to prevent an incorrect output)
remove_bonds = set()
for bix in {
x
for x in ring.bix if rings.info.NumBondRings(x) == 1
}:
bond = edit.GetBondWithIdx(bix)
b_x, b_y = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
if b_x not in remove_atoms and b_y not in remove_atoms:
remove_bonds.add((b_x, b_y))
correct_atom_props(edit.GetAtomWithIdx(b_x))
correct_atom_props(edit.GetAtomWithIdx(b_y))
# Scheme 4 (scaffold tree rule)
if self.use_scheme_4 is not False and len(ring) == 3:
atomic_nums = [a.GetAtomicNum() for a in ring.atoms]
if len([a for a in atomic_nums if a != 1 and a != 6]) == 1:
shared = {
x
for x in ring.bix if rings.info.NumBondRings(x) > 1
}
if len(shared) == 1:
bond = edit.GetBondWithIdx(shared.pop())
bond.SetBondType(BondType.DOUBLE)
# Remove collected atoms and bonds
for bix in remove_bonds:
edit.RemoveBond(*bix)
for aix in sorted(remove_atoms, reverse=True):
edit.RemoveAtom(aix)
# Add new parent scaffolds to parent list
for parent in get_scaffold_frags(edit):
if parent.rings.count == len(rings) - 1:
parent.removed_ring_idx = rix
parents.append(parent)
return parents