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

"""
Amide Factory
=============

"""

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


[docs]class AmideFactory(FunctionalGroupFactory): """ Creates :class:`.Amide` instances. Creates functional groups from substructures, which match the ``[*][C](=[O])[N]([H])[H]`` functional group string. Examples -------- *Creating Functional Groups with the Factory* You want to create a building block which has :class:`.Amide` functional groups. You want the carbon atom in those functional groups to be the bonder atom, and the amino group to be a leaving group. .. testcode:: creating-functional-groups-with-the-factory import stk building_block = stk.BuildingBlock( smiles='NC(=O)CC(=O)N', functional_groups=(stk.AmideFactory(), ), ) .. testcode:: creating-functional-groups-with-the-factory :hide: assert all( isinstance(functional_group, stk.Amide) 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:`.Amide` functional groups. You want the carbon atom to be the bonder atom and the oxygen atom to be the deleter atom. .. testcode:: changing-the-bonder-and-deleter-atoms import stk amide_factory = stk.AmideFactory( # The index of the carbon atom in the functional # group string (see docstring) is 1. bonders=(1, ), # The index of the oxygen atom in the functional # group string (see docstring) is 2. deleters=(2, ), ) building_block = stk.BuildingBlock( smiles='NC(=O)CC(=O)N', functional_groups=(amide_factory, ), ) .. testcode:: changing-the-bonder-and-deleter-atoms :hide: fg1, fg2 = building_block.get_functional_groups() assert fg1.get_num_bonders() == 1 assert sum(1 for _ in fg1.get_deleters()) == 1 assert fg2.get_num_bonders() == 1 assert sum(1 for _ in fg2.get_deleters()) == 1 assert all( isinstance(atom, stk.C) for functional_group in building_block.get_functional_groups() for atom in functional_group.get_bonders() ) assert all( isinstance(atom, stk.O) for functional_group in building_block.get_functional_groups() for atom in functional_group.get_deleters() ) See Also -------- :class:`.GenericFunctionalGroup` Defines *bonders* and *deleters*. """
[docs] def __init__( self, bonders=(1, ), deleters=(3, 4, 5), placers=None, ): """ Initialize a :class:`.AmideFactory` 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](=[O])[N]([H])[H]', molecule) for atom_ids in ids: atoms = tuple(molecule.get_atoms(atom_ids)) yield Amide( carbon=atoms[1], oxygen=atoms[2], nitrogen=atoms[3], hydrogen1=atoms[4], hydrogen2=atoms[5], atom=atoms[0], 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), )