Source code for stk.molecular.reactions.reactions.two_two_reaction

Two-Two Reaction


import itertools as it

from scipy.spatial.distance import euclidean

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

[docs]class TwoTwoReaction(Reaction): """ A reaction between two functional groups, each with 2 bonder atoms. The reaction creates the two shortest possible bonds between the *bonder* atoms of the two functional groups, and deletes any *deleter* atoms. """
[docs] def __init__( self, construction_state, functional_group1, functional_group2, bond_order, periodicity, ): """ Initialize a :class:`.TwoTwoReaction` instance. Parameters ---------- construction_state : :class:`.ConstructionState` The construction state of the molecule being constructed. 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 bonds created by the reaction. periodicity : :class:`tuple` of :class:`int` The periodicity of the bonds created by the reaction. """ self._position_matrix = ( construction_state.get_position_matrix() ) 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): for bonder1, bonder2 in self._get_bonder_pairs(): yield Bond( atom1=bonder1, atom2=bonder2, order=self._bond_order, periodicity=self._periodicity, ) def _get_bonder_pairs(self): pairs = it.product( self._functional_group1.get_bonders(), self._functional_group2.get_bonders(), ) sorted_pairs = sorted(pairs, key=self._pair_distance) bonded = set() for bonder1, bonder2 in sorted_pairs: if ( bonder1.get_id() not in bonded and bonder2.get_id() not in bonded ): bonded.add(bonder1.get_id()) bonded.add(bonder2.get_id()) yield bonder1, bonder2 def _pair_distance(self, bonders): bonder1, bonder2 = bonders return euclidean( self._position_matrix[bonder1.get_id()], self._position_matrix[bonder2.get_id()], ) 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