def get_representative_molecule(self, mode='minimal', update=True):
if mode == 'minimal':
# create a molecule from fragment.vertices.copy
mapping = self.copyAndMap()
# replace CuttingLabel with H
atoms = []
for vertex in self.vertices:
mapped_vertex = mapping[vertex]
if isinstance(mapped_vertex, CuttingLabel):
# replace cutting label with atom H
atom_H = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
for bondedAtom, bond in mapped_vertex.edges.iteritems():
new_bond = Bond(bondedAtom, atom_H, order=bond.order)
bondedAtom.edges[atom_H] = new_bond
del bondedAtom.edges[mapped_vertex]
atom_H.edges[bondedAtom] = new_bond
mapping[vertex] = atom_H
atoms.append(atom_H)
else:
atoms.append(mapped_vertex)
# Note: mapping is a dict with
# key: self.vertex and value: mol_repr.atom
mol_repr = Molecule()
mol_repr.atoms = atoms
if update:
mol_repr.update()
return mol_repr, mapping
def toSMILES(self):
cutting_label_list = []
for vertex in self.vertices:
if isinstance(vertex, CuttingLabel):
cutting_label_list.append(vertex.symbol)
SMILES_before = self.copy(deep=True)
final_vertices = []
for ind, atom in enumerate(SMILES_before.atoms):
element_symbol = atom.symbol
if isinstance(atom, CuttingLabel):
substi_name = 'Si'
substi = Atom(element=substi_name)
substi.label = element_symbol
for bondedAtom, bond in atom.edges.iteritems():
new_bond = Bond(bondedAtom, substi, order=bond.order)
bondedAtom.edges[substi] = new_bond
del bondedAtom.edges[atom]
substi.edges[bondedAtom] = new_bond
substi.radicalElectrons = 3
final_vertices.append(substi)
else:
final_vertices.append(atom)
SMILES_before.vertices = final_vertices
mol_repr = Molecule()
mol_repr.atoms = SMILES_before.vertices
SMILES_after = mol_repr.toSMILES()
import re
smiles = re.sub('\[Si\]', '', SMILES_after)
return smiles
def assign_representative_molecule(self):
# create a molecule from fragment.vertices.copy
mapping = self.copyAndMap()
# replace CuttingLabel with CC
atoms = []
additional_atoms = []
additional_bonds = []
for vertex in self.vertices:
mapped_vertex = mapping[vertex]
if isinstance(mapped_vertex, CuttingLabel):
# replace cutting label with atom C
atom_C1 = Atom(element=getElement('C'),
radicalElectrons=0,
charge=0,
lonePairs=0)
for bondedAtom, bond in mapped_vertex.edges.iteritems():
new_bond = Bond(bondedAtom, atom_C1, order=bond.order)
bondedAtom.edges[atom_C1] = new_bond
del bondedAtom.edges[mapped_vertex]
atom_C1.edges[bondedAtom] = new_bond
# add hydrogens and carbon to make it CC
atom_H1 = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atom_H2 = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atom_C2 = Atom(element=getElement('C'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atom_H3 = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atom_H4 = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atom_H5 = Atom(element=getElement('H'),
radicalElectrons=0,
charge=0,
lonePairs=0)
atoms.append(atom_C1)
additional_atoms.extend(
[atom_H1, atom_H2, atom_H3, atom_H4, atom_H5, atom_C2])
additional_bonds.extend([
Bond(atom_C1, atom_H1, 1),
Bond(atom_C1, atom_H2, 1),
Bond(atom_C2, atom_H3, 1),
Bond(atom_C2, atom_H4, 1),
Bond(atom_C2, atom_H5, 1),
Bond(atom_C1, atom_C2, 1)
])
else:
atoms.append(mapped_vertex)
mol_repr = Molecule()
mol_repr.atoms = atoms
for atom in additional_atoms:
mol_repr.addAtom(atom)
for bond in additional_bonds:
mol_repr.addBond(bond)
# update connectivity
mol_repr.update()
# create a species object from molecule
self.mol_repr = mol_repr
return mapping
