Source code for stk.molecular.functional_groups.factories.terminal_alkene_factory

"""
Terminal Alkene Factory
=======================

"""

from ..functional_groups import Alkene
from .functional_group_factory import FunctionalGroupFactory
from .utilities import _get_atom_ids


[docs]class TerminalAlkeneFactory(FunctionalGroupFactory): # This docstring is a literal string, to silence a flake8 warning # about CH\ :sub:`2`. It's taking the backslash out of context. r""" Creates :class:`.Alkene` instances. Creates functional groups from substructures, which match the ``[*][C]([*])=[C]([H])[H]`` functional group string. Examples -------- *Creating Functional Groups with the Factory* You want to create a building block which has :class:`.Alkene` functional groups, but only if they are terminal. You want the non-terminal carbon atom in those functional groups to be the *bonder* atom, and the terminal CH\ :sub:`2` group to be the *deleter* atoms. .. testcode:: creating-functional-groups-with-the-factory import stk building_block = stk.BuildingBlock( smiles='C=CCCCCC=C', functional_groups=(stk.TerminalAlkeneFactory(), ), ) .. testcode:: creating-functional-groups-with-the-factory :hide: assert all( isinstance(functional_group, stk.Alkene) for functional_group in building_block.get_functional_groups() ) assert building_block.get_num_functional_groups() == 2 *Changing the Bonder and Deleter Atoms* You want to create a building block which has :class:`.Alkene` functional groups, but only if they are terminal. You want the carbon atoms to be the *bonder* atoms and you don't want any *deleter* atoms. .. testcode:: changing-the-bonder-and-deleter-atoms import stk terminal_alkene_factory = stk.TerminalAlkeneFactory( # The indices of the carbon atoms in the functional # group string (see docstring) are 1 and 3. bonders=(1, 3), deleters=(), ) building_block = stk.BuildingBlock( smiles='C=CCCCCC=C', functional_groups=(terminal_alkene_factory, ), ) .. testcode:: changing-the-bonder-and-deleter-atoms :hide: fg1, fg2 = building_block.get_functional_groups() assert fg1.get_num_bonders() == 2 assert sum(1 for _ in fg1.get_deleters()) == 0 assert fg2.get_num_bonders() == 2 assert sum(1 for _ in fg2.get_deleters()) == 0 assert all( isinstance(atom, stk.C) for functional_group in building_block.get_functional_groups() for atom in functional_group.get_bonders() ) See Also -------- :class:`.GenericFunctionalGroup` Defines *bonders* and *deleters*. """
[docs] def __init__( self, bonders=(1, ), deleters=(3, 4, 5), placers=None, ): """ Initialize a :class:`.TerminalAlkeneFactory` instance. Parameters ---------- bonders : :class:`tuple` of :class:`int` The indices of atoms in the functional group string, which are *bonder* atoms. deleters : :class:`tuple` of :class:`int` The indices of atoms in the functional group string, which are *deleter* atoms. placers : :class:`tuple` of :class:`int`, optional The indices of atoms in the functional group string, which are *placer* atoms. If ``None``, `bonders` will be used. """ self._bonders = bonders self._deleters = deleters self._placers = bonders if placers is None else placers
[docs] def get_functional_groups(self, molecule): ids = _get_atom_ids('[*][C]([*])=[C]([H])[H]', molecule) for atom_ids in ids: atoms = tuple(molecule.get_atoms(atom_ids)) yield Alkene( carbon1=atoms[1], atom1=atoms[0], atom2=atoms[2], carbon2=atoms[3], atom3=atoms[4], atom4=atoms[5], bonders=tuple(atoms[i] for i in self._bonders), deleters=tuple(atoms[i] for i in self._deleters), placers=tuple(atoms[i] for i in self._placers), )