Source code for stk.molecular.reactions.reactions.one_one_reaction

One-One Reaction


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

[docs]class OneOneReaction(Reaction): """ A reaction between two functional groups, each with 1 bonder atom. The reaction creates a bond between the *bonder* atoms, and deletes any *deleter* atoms. """
[docs] def __init__( self, functional_group1, functional_group2, bond_order, periodicity, ): """ Initialize a :class:`.OneOneReaction` 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): bonder1 = next(self._functional_group1.get_bonders()) bonder2 = next(self._functional_group2.get_bonders()) 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