stk.DiolFactory
- class stk.DiolFactory(bonders=(2, 3), deleters=(0, 1, 4, 5), placers=None)[source]
Bases:
FunctionalGroupFactory
Creates
Diol
instances.Creates functional groups from substructures, which match the
[H][O][#6]~[#6][O][H]
functional group string.Examples
Creating Functional Groups with the Factory
You want to create a building block which has
Diol
functional groups. You want the carbon atoms in those functional groups to be the bonder atoms, and the OH groups to be a leaving groups.import stk building_block = stk.BuildingBlock( smiles='CCCC(O)C(O)CCCC', functional_groups=(stk.DiolFactory(), ), )
Changing the Bonder and Deleter Atoms
You want to create a building block which has
Diol
functional groups. You want the oxygen atoms to be the bonder atoms and the hydrogen atoms to be the deleter atoms.import stk diol_factory = stk.DiolFactory( # The indices of the oxygen atoms in the functional # group string (see docstring) are 1 and 4. bonders=(1, 4), # The indices of the hydrogen atoms in the functional # group string (see docstring) are 0 and 5. deleters=(0, 5), ) building_block = stk.BuildingBlock( smiles='CCCC(O)C(O)CCCC', functional_groups=(diol_factory, ), )
See also
GenericFunctionalGroup
Defines bonders and deleters.
Initialize a
DiolFactory
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