Honeycomb¶

class
Honeycomb
(building_blocks, lattice_size, periodic=False, vertex_alignments=None, reaction_factory=GenericReactionFactory(), num_processes=1, optimizer=<stk.molecular.topology_graphs.topology_graph.optimizers.null.NullOptimizer object>)[source]¶ Bases:
stk.molecular.topology_graphs.cof.cof.Cof
Represents a honeycomb COF topology graph.
Unoptimized construction
Collapser(scale_steps=False)
optimized constructionBuilding blocks with three and two functional groups are required for this topology graph.
When using a
dict
for the building_blocks parameter, as in Examples: MultiBuilding Block COF Construction, aBuildingBlock
, with the following number of functional groups, needs to be assigned to each of the following vertex ids:3functional groups: 0 to 12functional groups: 2 to 4See
Cof
for more details and examples.Methods
clone
()Return a clone.
Construct a
ConstructedMolecule
.Yield the building blocks.
get_num_building_block
(building_block)Get the number of times building_block is present.
with_building_blocks
(building_block_map)Return a clone holding different building blocks.

__init__
(building_blocks, lattice_size, periodic=False, vertex_alignments=None, reaction_factory=GenericReactionFactory(), num_processes=1, optimizer=<stk.molecular.topology_graphs.topology_graph.optimizers.null.NullOptimizer object>)¶ Initialize a
Cof
instance. Parameters
building_blocks (
tuple
ordict
) –Can be a
tuple
ofBuildingBlock
instances, which should be placed on the topology graph.Can also be a
dict
which maps theBuildingBlock
instances to the ids of the vertices it should be placed on. Adict
is required when there are multiple building blocks with the same number of functional groups, because in this case the desired placement is ambiguous.lattice_size (
tuple
ofint
) – The size of the lattice in the x, y and z directions.periodic (
bool
, optional) – Toggle the construction of a periodic molecule. IfTrue
, periodic bonds will be made across the edges of the lattice.vertex_alignments (
dict
, optional) – A mapping from the id of aVertex
to anEdge
connected to it. TheEdge
is used to align the firstFunctionalGroup
of aBuildingBlock
placed on that vertex. Only vertices which need to have their default edge changed need to be present in thedict
. IfNone
then the default edge is used for each vertex. Changing whichEdge
is used will mean that the topology graph represents different structural isomers. The edge is referred to by a number between0
(inclusive) and the number of edges the vertex is connected to (exclusive).reaction_factory (
ReactionFactory
, optional) – The reaction factory to use for creating bonds between building blocks.num_processes (
int
, optional) – The number of parallel processes to create duringconstruct()
.optimizer (
Optimizer
, optional) – Used to optimize the structure of the constructed molecule.
 Raises
AssertionError – If the any building block does not have a valid number of functional groups.
ValueError – If the there are multiple building blocks with the same number of functional_groups in building_blocks, and they are not explicitly assigned to vertices. The desired placement of building blocks is ambiguous in this case.
UnoccupiedVertexError – If a vertex of the COF topology graph does not have a building block placed on it.
OverlyOccupiedVertexError – If a vertex of the COF topology graph has more than one building block placed on it.

clone
()¶ Return a clone.
 Returns
The clone. Has the same type as the original topology graph.
 Return type

construct
()¶ Construct a
ConstructedMolecule
. Returns
The data describing the
ConstructedMolecule
. Return type

get_building_blocks
()¶ Yield the building blocks.
Building blocks are yielded in an order based on their position in the topology graph. For two equivalent topology graphs, but with different building blocks, equivalently positioned building blocks will be yielded at the same time.
 Yields
BuildingBlock
– A building block of the topology graph.

get_num_building_block
(building_block)¶ Get the number of times building_block is present.
 Parameters
building_block (
BuildingBlock
) – The building block whose frequency in the topology graph is desired. Returns
The number of times building_block is present in the topology graph.
 Return type

with_building_blocks
(building_block_map)¶ Return a clone holding different building blocks.
 Parameters
building_block_map (
dict
) – Maps a building block in the current topology graph to the building block which should replace it in the clone. If a building block should be not replaced in the clone, it can be omitted from the map. Returns
The clone. Has the same type as the original topology graph.
 Return type
