def update_molecule(mol, to_single_bonds=False):
"""
Returns a copy of the current molecule with updated atomTypes
if to_single_bonds is True, the returned mol contains only single bonds.
This is useful for isomorphism comparison
"""
new_mol = Molecule()
try:
atoms = mol.atoms
except AttributeError:
return None
atom_mapping = dict()
for atom1 in atoms:
new_atom = new_mol.addAtom(Atom(atom1.element))
atom_mapping[atom1] = new_atom
for atom1 in atoms:
for atom2 in atom1.bonds.keys():
bond_order = 1.0 if to_single_bonds else atom1.bonds[
atom2].getOrderNum()
bond = Bond(atom_mapping[atom1], atom_mapping[atom2], bond_order)
new_mol.addBond(bond)
try:
new_mol.updateAtomTypes()
except AtomTypeError:
pass
new_mol.multiplicity = mol.multiplicity
return new_mol
def testPickle(self):
"""
Test that a Molecule object can be successfully pickled and
unpickled with no loss of information.
"""
molecule0 = Molecule().fromSMILES('C=CC=C[CH2]C')
molecule0.updateAtomTypes()
molecule0.updateConnectivityValues()
import cPickle
molecule = cPickle.loads(cPickle.dumps(molecule0))
self.assertEqual(len(molecule0.atoms), len(molecule.atoms))
self.assertEqual(molecule0.getFormula(), molecule.getFormula())
self.assertTrue(molecule0.isIsomorphic(molecule))
self.assertTrue(molecule.isIsomorphic(molecule0))
def testPickle(self):
"""
Test that a Molecule object can be successfully pickled and
unpickled with no loss of information.
"""
molecule0 = Molecule().fromSMILES('C=CC=C[CH2]C')
molecule0.updateAtomTypes()
molecule0.updateConnectivityValues()
import cPickle
molecule = cPickle.loads(cPickle.dumps(molecule0))
self.assertEqual(len(molecule0.atoms), len(molecule.atoms))
self.assertEqual(molecule0.getFormula(), molecule.getFormula())
self.assertTrue(molecule0.isIsomorphic(molecule))
self.assertTrue(molecule.isIsomorphic(molecule0))
def getResonanceHybrid(self):
"""
Returns a molecule object with bond orders that are the average
of all the resonance structures.
"""
# get labeled resonance isomers
self.generate_resonance_structures(keep_isomorphic=True)
# only consider reactive molecules as representative structures
molecules = [mol for mol in self.molecule if mol.reactive]
# return if no resonance
if len(molecules) == 1:
return molecules[0]
# create a sorted list of atom objects for each resonance structure
cython.declare(atomsFromStructures = list, oldAtoms = list, newAtoms = list,
numResonanceStructures=cython.short, structureNum = cython.short,
oldBondOrder = cython.float,
index1 = cython.short, index2 = cython.short,
newMol=Molecule, oldMol = Molecule,
atom1=Atom, atom2=Atom,
bond=Bond,
atoms=list,)
atomsFromStructures = []
for newMol in molecules:
newMol.atoms.sort(key=lambda atom: atom.id)
atomsFromStructures.append(newMol.atoms)
numResonanceStructures = len(molecules)
# make original structure with no bonds
newMol = Molecule()
originalAtoms = atomsFromStructures[0]
for atom1 in originalAtoms:
atom = newMol.addAtom(Atom(atom1.element))
atom.id = atom1.id
newAtoms = newMol.atoms
# initialize bonds to zero order
for index1, atom1 in enumerate(originalAtoms):
for atom2 in atom1.bonds:
index2 = originalAtoms.index(atom2)
bond = Bond(newAtoms[index1],newAtoms[index2], 0)
newMol.addBond(bond)
# set bonds to the proper value
for structureNum, oldMol in enumerate(molecules):
oldAtoms = atomsFromStructures[structureNum]
for index1, atom1 in enumerate(oldAtoms):
# make bond orders average of resonance structures
for atom2 in atom1.bonds:
index2 = oldAtoms.index(atom2)
newBond = newMol.getBond(newAtoms[index1], newAtoms[index2])
oldBondOrder = oldMol.getBond(oldAtoms[index1], oldAtoms[index2]).getOrderNum()
newBond.applyAction(('CHANGE_BOND',None,oldBondOrder / numResonanceStructures / 2))
# set radicals in resonance hybrid to maximum of all structures
if atom1.radicalElectrons > 0:
newAtoms[index1].radicalElectrons = max(atom1.radicalElectrons,
newAtoms[index1].radicalElectrons)
newMol.updateAtomTypes(logSpecies = False, raiseException=False)
return newMol
def getResonanceHybrid(self):
"""
Returns a molecule object with bond orders that are the average
of all the resonance structures.
"""
# get labeled resonance isomers
self.generate_resonance_structures(keep_isomorphic=True)
# only consider reactive molecules as representative structures
molecules = [mol for mol in self.molecule if mol.reactive]
# return if no resonance
if len(molecules) == 1:
return molecules[0]
# create a sorted list of atom objects for each resonance structure
cython.declare(atomsFromStructures = list, oldAtoms = list, newAtoms = list,
numResonanceStructures=cython.short, structureNum = cython.short,
oldBondOrder = cython.float,
index1 = cython.short, index2 = cython.short,
newMol=Molecule, oldMol = Molecule,
atom1=Atom, atom2=Atom,
bond=Bond,
atoms=list,)
atomsFromStructures = []
for newMol in molecules:
newMol.atoms.sort(key=lambda atom: atom.id)
atomsFromStructures.append(newMol.atoms)
numResonanceStructures = len(molecules)
# make original structure with no bonds
newMol = Molecule()
originalAtoms = atomsFromStructures[0]
for atom1 in originalAtoms:
atom = newMol.addAtom(Atom(atom1.element))
atom.id = atom1.id
newAtoms = newMol.atoms
# initialize bonds to zero order
for index1, atom1 in enumerate(originalAtoms):
for atom2 in atom1.bonds:
index2 = originalAtoms.index(atom2)
bond = Bond(newAtoms[index1],newAtoms[index2], 0)
newMol.addBond(bond)
# set bonds to the proper value
for structureNum, oldMol in enumerate(molecules):
oldAtoms = atomsFromStructures[structureNum]
for index1, atom1 in enumerate(oldAtoms):
# make bond orders average of resonance structures
for atom2 in atom1.bonds:
index2 = oldAtoms.index(atom2)
newBond = newMol.getBond(newAtoms[index1], newAtoms[index2])
oldBondOrder = oldMol.getBond(oldAtoms[index1], oldAtoms[index2]).getOrderNum()
newBond.applyAction(('CHANGE_BOND',None,oldBondOrder / numResonanceStructures / 2))
# set radicals in resonance hybrid to maximum of all structures
if atom1.radicalElectrons > 0:
newAtoms[index1].radicalElectrons = max(atom1.radicalElectrons,
newAtoms[index1].radicalElectrons)
newMol.updateAtomTypes(logSpecies = False, raiseException=False)
return newMol
