Source code for stk.molecular.reactions.reactions.one_two_reaction

One-Two Reaction


import itertools as it

from ...bonds import Bond
from .reaction import Reaction

[docs]class OneTwoReaction(Reaction): """ A reaction between two functional groups. One functional group has 1 *bonder* atom, A, and the other has 2, B and C. Two bonds are created, one between A and B and one between A and C. Any deleter atoms are removed. """
[docs] def __init__( self, functional_group1, functional_group2, bond_order, periodicity, ): """ Initialize a :class:`.OneTwoReaction` instance. Parameters ---------- functional_group1 : :class:`.GenericFunctionalGroup` The first functional group in the reaction. functional_group2 : :class:`.GenericFunctionalGroup` The second functional group in the reaction. bond_order : :class:`int` The bond order of the bond created by the reaction. periodicity : :class:`tuple` of :class:`int` The periodicity of the bond created by the reaction. """ self._functional_group1 = functional_group1 self._functional_group2 = functional_group2 self._bond_order = bond_order self._periodicity = periodicity
def _get_new_atoms(self): return yield def _get_new_bonds(self): bonders1 = self._functional_group1.get_bonders() bonders2 = self._functional_group2.get_bonders() for bonder1, bonder2 in it.product(bonders1, bonders2): yield Bond( atom1=bonder1, atom2=bonder2, order=self._bond_order, periodicity=self._periodicity, ) def _get_deleted_atoms(self): yield from self._functional_group1.get_deleters() yield from self._functional_group2.get_deleters() def _get_deleted_bonds(self): return yield