stk.ThiolFactory
- class stk.ThiolFactory(bonders=(1,), deleters=(2,), placers=None)[source]
Bases:
FunctionalGroupFactory
Creates
Thiol
instances.Creates functional groups from substructures, which match the
[*][S][H]
functional group string.Examples
Creating Functional Groups with the Factory
You want to create a building block which has
Thiol
functional groups. You want the sulfur atom in those functional groups to be the bonder atom, and the hydrogen atom to be the deleter atom.import stk building_block = stk.BuildingBlock( smiles='SCCCCS', functional_groups=(stk.ThiolFactory(), ), )
Changing the Bonder and Deleter Atoms
You want to create a building block which has
Thiol
functional groups. You want the non-hydrogen atom bonded to the sulfur to be the bonder atom and the SH group to be deleter atoms.import stk thiol_factory = stk.ThiolFactory( # The index of the atom bonded to sulfur is 0 in the # functional group string (see docstring). bonders=(0, ), # The indices of the sulfur and hydrogen atoms in the # functional group string (see docstring) is 1 and 2, # respectively. deleters=(1, 2), ) building_block = stk.BuildingBlock( smiles='SCCCCS', functional_groups=(thiol_factory, ), )
See also
GenericFunctionalGroup
Defines bonders and deleters.
Initialize a
ThiolFactory
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