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 testSubgraphIsomorphism(self):
# Simple test comparing C-C to C-C-C (no hydrogens)
mol = Molecule()
c1 = Atom(getElement(6))
c2 = c1.copy()
mol.addAtom(c1)
mol.addAtom(c2)
mol.addBond(Bond(c1, c2))
mol2 = Molecule()
c1 = c1.copy()
c2 = c1.copy()
c3 = c1.copy()
mol2.addAtom(c1)
mol2.addAtom(c2)
mol2.addAtom(c3)
mol2.addBond(Bond(c1, c2))
mol2.addBond(Bond(c2, c3))
self.assertTrue(self.vf3.isSubgraphIsomorphic(mol2, mol, None))
self.assertFalse(self.vf3.isSubgraphIsomorphic(mol, mol2, None))
# Ring membership is a semantic property of molecules,
# so straight chains are not considered sub graphs of rings
hexane = Molecule().fromSMILES("C1CCCCC1")
self.assertFalse(self.vf3.isSubgraphIsomorphic(hexane, mol, None))
self.assertFalse(self.vf3.isSubgraphIsomorphic(hexane, mol2, None))
# Benzene and hexane, while technically sharing the same shape,
# differ in semantic information.
benzene = Molecule().fromSMILES("C1=CC=CC=C1")
self.assertFalse(self.vf3.isSubgraphIsomorphic(hexane, benzene, None))
# Test sub graph isomorphism on rings
hexaneMinusH = hexane.copy(True)
hexaneMinusH.removeVertex(hexaneMinusH.vertices[6])
self.assertTrue(self.vf3.isSubgraphIsomorphic(hexane, hexaneMinusH, None))
self.assertFalse(self.vf3.isSubgraphIsomorphic(hexaneMinusH, hexane, None))
benzeneMinusH = benzene.copy(True)
benzeneMinusH.removeVertex(benzeneMinusH.vertices[6])
self.assertTrue(self.vf3.isSubgraphIsomorphic(benzene, benzeneMinusH, None))
self.assertFalse(self.vf3.isSubgraphIsomorphic(benzeneMinusH, hexane, None))
def testToAdjacencyListForNonIntegerBonds(self):
"""
Test the adjacency list can be created for molecules with bond orders
that don't fit into single, double, triple, or benzene
"""
from rmgpy.molecule.molecule import Atom, Bond, Molecule
atom1 = Atom(element='H', lonePairs=0)
atom2 = Atom(element='H', lonePairs=0)
bond = Bond(atom1, atom2, 0.5)
mol = Molecule(multiplicity=1)
mol.addAtom(atom1)
mol.addAtom(atom2)
mol.addBond(bond)
adjlist = mol.toAdjacencyList()
self.assertIn('H', adjlist)
self.assertIn('{1,0.5}', adjlist)
def testToAdjacencyListForNonIntegerBonds(self):
"""
Test the adjacency list can be created for molecules with bond orders
that don't fit into single, double, triple, or benzene
"""
from rmgpy.molecule.molecule import Atom, Bond, Molecule
atom1 = Atom(element='H',lonePairs=0)
atom2 = Atom(element='H',lonePairs=0)
bond = Bond(atom1, atom2, 0.5)
mol = Molecule(multiplicity=1)
mol.addAtom(atom1)
mol.addAtom(atom2)
mol.addBond(bond)
adjlist = mol.toAdjacencyList()
self.assertIn('H', adjlist)
self.assertIn('{1,0.5}',adjlist)
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
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
