Source code for stk.molecular.reactions.reactions.dative_reaction.dative_reaction

Dative Reaction


from ....bonds import Bond
from ..reaction import Reaction
from .utilities import is_metal

[docs]class DativeReaction(Reaction): """ A reaction between two functional groups. The reaction creates a dative bond between the *bonder* atoms, and deletes any *deleter* atoms. Importantly, the direction of the bond is set to run from the non-metal atom to the metal atom. """
[docs] def __init__(self, reaction): """ Initialize a :class:`.DativeReaction` instance. Parameters ---------- reaction : :class:`.Reaction` A reaction which should be made dative. """ self._reaction = reaction
def _get_new_atoms(self): return self._reaction._get_new_atoms() def _get_new_bonds(self): for bond in self._reaction._get_new_bonds(): if bond.get_order() == 9 and is_metal(bond.get_atom1()): yield Bond( atom1=bond.get_atom2(), atom2=bond.get_atom1(), order=bond.get_order(), periodicity=bond.get_periodicity(), ) else: yield bond def _get_deleted_atoms(self): return self._reaction._get_deleted_atoms() def _get_deleted_bonds(self): return self._reaction._get_deleted_bonds()