stk.AmideFactory
- class stk.AmideFactory(bonders=(1,), deleters=(3, 4, 5), placers=None)[source]
Bases:
FunctionalGroupFactory
Creates
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
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.import stk building_block = stk.BuildingBlock( smiles='NC(=O)CC(=O)N', functional_groups=(stk.AmideFactory(), ), )
Changing the Bonder and Deleter Atoms
You want to create a building block which has
Amide
functional groups. You want the carbon atom to be the bonder atom and the oxygen atom to be the deleter atom.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, ), )
See also
GenericFunctionalGroup
Defines bonders and deleters.
Initialize a
AmideFactory
instance.- Parameters:
bonders (
tuple
ofint
) – The indices of atoms in the functional group string, which are bonder atoms.deleters (
tuple
ofint
) – The indices of atoms in the functional group string, which are deleter atoms.placers (
tuple
ofint
, optional) – The indices of atoms in the functional group string, which are placer atoms. IfNone
, bonders will be used.
Methods
Yield functional groups in molecule.
- get_functional_groups(molecule)[source]
Yield functional groups in molecule.
- Parameters:
molecule (
Molecule
) – The molecule, whose functional groups are to be found.- Yields:
FunctionalGroup
– A functional group in molecule.
Examples