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

"""
Secondary Amino Factory
=======================

"""

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


[docs]class SecondaryAminoFactory(FunctionalGroupFactory): """ Creates :class:`.SecondaryAmino` instances. Creates functional groups from substructures, which match the ``[H][N]([#6])[#6]`` functional group string. Examples -------- *Creating Functional Groups with the Factory* You want to create a building block which has :class:`.SecondaryAmino` functional groups. You want the nitrogen atom in those functional groups to be the *bonder* atom, and the hydrogen atom to be the *deleter* atom. .. testcode:: creating-functional-groups-with-the-factory import stk building_block = stk.BuildingBlock( smiles='N(CCCC)CCCC', functional_groups=(stk.SecondaryAminoFactory(), ), ) .. testcode:: creating-functional-groups-with-the-factory :hide: assert all( isinstance(functional_group, stk.SecondaryAmino) for functional_group in building_block.get_functional_groups() ) assert building_block.get_num_functional_groups() == 1 *Changing the Bonder and Deleter Atoms* You want to create a building block which has :class:`.SecondaryAmino` functional groups. You want the nitrogen atom to be the *bonder* atom and one of the carbon atoms to be the *deleter* atom. .. testcode:: changing-the-bonder-and-deleter-atoms import stk secondary_amino_factory = stk.SecondaryAminoFactory( # The index of the nitrogen atom in the functional # group string (see docstring) is 1. bonders=(1, ), # The index of one of the carbon atoms in the functional # group string (see docstring) is 2. deleters=(2, ), ) building_block = stk.BuildingBlock( smiles='N(CCCC)CCCC', functional_groups=(secondary_amino_factory, ), ) .. testcode:: changing-the-bonder-and-deleter-atoms :hide: fg1, = building_block.get_functional_groups() assert fg1.get_num_bonders() == 1 assert sum(1 for _ in fg1.get_deleters()) == 1 assert all( isinstance(atom, stk.N) for functional_group in building_block.get_functional_groups() for atom in functional_group.get_bonders() ) assert all( isinstance(atom, stk.C) 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=(0, ), placers=None): """ Initialize a :class:`.SecondaryAminoFactory` 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): for atom_ids in _get_atom_ids('[H][N]([#6])[#6]', molecule): atoms = tuple(molecule.get_atoms(atom_ids)) yield SecondaryAmino( nitrogen=atoms[1], hydrogen=atoms[0], atom1=atoms[2], atom2=atoms[3], 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), )