stk.molecular.topology_graphs package

Subpackages

• stk.molecular.topology_graphs.cage package
  • Subpackages
    • stk.molecular.topology_graphs.cage.metal_topologies package
      • Submodules
    • stk.molecular.topology_graphs.cage.three_plus_four package
      • Submodules
    • stk.molecular.topology_graphs.cage.three_plus_three package
      • Submodules
    • stk.molecular.topology_graphs.cage.two_plus_five package
      • Submodules
    • stk.molecular.topology_graphs.cage.two_plus_four package
      • Submodules
    • stk.molecular.topology_graphs.cage.two_plus_three package
      • Submodules
  • Submodules
    • Cage
      • Organic
      • Metal-Organic
    • Cage
      • Cage.__init__()
      • Cage.clone()
      • Cage.construct()
      • Cage.get_building_blocks()
      • Cage.get_num_building_block()
      • Cage.with_building_blocks()
    • OverlyOccupiedVertexError
      • OverlyOccupiedVertexError.add_note()
      • OverlyOccupiedVertexError.args
      • OverlyOccupiedVertexError.with_traceback()
    • UnoccupiedVertexError
      • UnoccupiedVertexError.add_note()
      • UnoccupiedVertexError.args
      • UnoccupiedVertexError.with_traceback()
    • Cage Construction State
    • Cage Vertices
    • AngledVertex
      • AngledVertex.__init__()
      • AngledVertex.clone()
      • AngledVertex.get_aligner_edge()
      • AngledVertex.get_cell()
      • AngledVertex.get_id()
      • AngledVertex.get_position()
      • AngledVertex.init_at_center()
      • AngledVertex.map_functional_groups_to_edges()
      • AngledVertex.place_building_block()
      • AngledVertex.use_neighbor_placement()
      • AngledVertex.with_aligner_edge()
      • AngledVertex.with_position()
      • AngledVertex.with_scale()
    • LinearVertex
      • LinearVertex.__init__()
      • LinearVertex.clone()
      • LinearVertex.get_aligner_edge()
      • LinearVertex.get_cell()
      • LinearVertex.get_id()
      • LinearVertex.get_position()
      • LinearVertex.init_at_center()
      • LinearVertex.map_functional_groups_to_edges()
      • LinearVertex.place_building_block()
      • LinearVertex.use_neighbor_placement()
      • LinearVertex.with_aligner_edge()
      • LinearVertex.with_position()
      • LinearVertex.with_scale()
    • NonLinearVertex
      • NonLinearVertex.__init__()
      • NonLinearVertex.clone()
      • NonLinearVertex.get_aligner_edge()
      • NonLinearVertex.get_cell()
      • NonLinearVertex.get_id()
      • NonLinearVertex.get_position()
      • NonLinearVertex.init_at_center()
      • NonLinearVertex.map_functional_groups_to_edges()
      • NonLinearVertex.place_building_block()
      • NonLinearVertex.use_neighbor_placement()
      • NonLinearVertex.with_aligner_edge()
      • NonLinearVertex.with_position()
      • NonLinearVertex.with_scale()
    • UnaligningVertex
      • UnaligningVertex.__init__()
      • UnaligningVertex.clone()
      • UnaligningVertex.get_aligner_edge()
      • UnaligningVertex.get_cell()
      • UnaligningVertex.get_id()
      • UnaligningVertex.get_position()
      • UnaligningVertex.init_at_center()
      • UnaligningVertex.map_functional_groups_to_edges()
      • UnaligningVertex.place_building_block()
      • UnaligningVertex.use_neighbor_placement()
      • UnaligningVertex.with_aligner_edge()
      • UnaligningVertex.with_position()
      • UnaligningVertex.with_scale()
• stk.molecular.topology_graphs.cof package
  • Submodules
    • Covalent Organic Framework
      • Hexagonal
      • Hexagonal
      • Honeycomb
      • Honeycomb
      • Kagome
      • Kagome
      • Linkerless Honeycomb
      • LinkerlessHoneycomb
      • Square
      • Square
      • Periodic Hexagonal
      • PeriodicHexagonal
      • Periodic Honeycomb
      • PeriodicHoneycomb
      • Periodic Kagome
      • PeriodicKagome
      • Periodic Linkerless Honeycomb
      • PeriodicLinkerlessHoneycomb
      • Periodic Square
      • PeriodicSquare
    • Cof
      • Cof.__init__()
      • Cof.clone()
      • Cof.construct()
      • Cof.get_building_blocks()
      • Cof.get_num_building_block()
      • Cof.with_building_blocks()
    • OverlyOccupiedVertexError
      • OverlyOccupiedVertexError.add_note()
      • OverlyOccupiedVertexError.args
      • OverlyOccupiedVertexError.with_traceback()
    • UnoccupiedVertexError
      • UnoccupiedVertexError.add_note()
      • UnoccupiedVertexError.args
      • UnoccupiedVertexError.with_traceback()
    • COF Edge
    • CofEdge
      • CofEdge.__init__()
      • CofEdge.clone()
      • CofEdge.get_id()
      • CofEdge.get_parent_id()
      • CofEdge.get_periodicity()
      • CofEdge.get_position()
      • CofEdge.get_vertex1_id()
      • CofEdge.get_vertex2_id()
      • CofEdge.get_vertex_ids()
      • CofEdge.is_periodic()
      • CofEdge.with_position()
      • CofEdge.with_scale()
    • Hexagonal
    • Hexagonal
      • Hexagonal.__init__()
      • Hexagonal.clone()
      • Hexagonal.construct()
      • Hexagonal.get_building_blocks()
      • Hexagonal.get_num_building_block()
      • Hexagonal.with_building_blocks()
    • Honeycomb
    • Honeycomb
      • Honeycomb.__init__()
      • Honeycomb.clone()
      • Honeycomb.construct()
      • Honeycomb.get_building_blocks()
      • Honeycomb.get_num_building_block()
      • Honeycomb.with_building_blocks()
    • Kagome
    • Kagome
      • Kagome.__init__()
      • Kagome.clone()
      • Kagome.construct()
      • Kagome.get_building_blocks()
      • Kagome.get_num_building_block()
      • Kagome.with_building_blocks()
    • Linkerless Honeycomb
    • LinkerlessHoneycomb
      • LinkerlessHoneycomb.__init__()
      • LinkerlessHoneycomb.clone()
      • LinkerlessHoneycomb.construct()
      • LinkerlessHoneycomb.get_building_blocks()
      • LinkerlessHoneycomb.get_num_building_block()
      • LinkerlessHoneycomb.with_building_blocks()
    • Periodic Hexagonal
    • PeriodicHexagonal
      • PeriodicHexagonal.__init__()
      • PeriodicHexagonal.clone()
      • PeriodicHexagonal.construct()
      • PeriodicHexagonal.get_building_blocks()
      • PeriodicHexagonal.get_num_building_block()
      • PeriodicHexagonal.with_building_blocks()
    • Periodic Honeycomb
    • PeriodicHoneycomb
      • PeriodicHoneycomb.__init__()
      • PeriodicHoneycomb.clone()
      • PeriodicHoneycomb.construct()
      • PeriodicHoneycomb.get_building_blocks()
      • PeriodicHoneycomb.get_num_building_block()
      • PeriodicHoneycomb.with_building_blocks()
    • Periodic Kagome
    • PeriodicKagome
      • PeriodicKagome.__init__()
      • PeriodicKagome.clone()
      • PeriodicKagome.construct()
      • PeriodicKagome.get_building_blocks()
      • PeriodicKagome.get_num_building_block()
      • PeriodicKagome.with_building_blocks()
    • Periodic Linkerless Honeycomb
    • PeriodicLinkerlessHoneycomb
      • PeriodicLinkerlessHoneycomb.__init__()
      • PeriodicLinkerlessHoneycomb.clone()
      • PeriodicLinkerlessHoneycomb.construct()
      • PeriodicLinkerlessHoneycomb.get_building_blocks()
      • PeriodicLinkerlessHoneycomb.get_num_building_block()
      • PeriodicLinkerlessHoneycomb.with_building_blocks()
    • Periodic Square
    • PeriodicSquare
      • PeriodicSquare.__init__()
      • PeriodicSquare.clone()
      • PeriodicSquare.construct()
      • PeriodicSquare.get_building_blocks()
      • PeriodicSquare.get_num_building_block()
      • PeriodicSquare.with_building_blocks()
    • Square
    • Square
      • Square.__init__()
      • Square.clone()
      • Square.construct()
      • Square.get_building_blocks()
      • Square.get_num_building_block()
      • Square.with_building_blocks()
    • COF Vertices
    • LinearVertex
      • LinearVertex.__init__()
      • LinearVertex.clone()
      • LinearVertex.get_aligner_edge()
      • LinearVertex.get_cell()
      • LinearVertex.get_id()
      • LinearVertex.get_position()
      • LinearVertex.init_at_center()
      • LinearVertex.init_at_shifted_center()
      • LinearVertex.map_functional_groups_to_edges()
      • LinearVertex.place_building_block()
      • LinearVertex.with_position()
      • LinearVertex.with_scale()
    • NonLinearVertex
      • NonLinearVertex.__init__()
      • NonLinearVertex.clone()
      • NonLinearVertex.get_aligner_edge()
      • NonLinearVertex.get_cell()
      • NonLinearVertex.get_id()
      • NonLinearVertex.get_position()
      • NonLinearVertex.init_at_center()
      • NonLinearVertex.init_at_shifted_center()
      • NonLinearVertex.map_functional_groups_to_edges()
      • NonLinearVertex.place_building_block()
      • NonLinearVertex.with_position()
      • NonLinearVertex.with_scale()
    • UnaligningVertex
      • UnaligningVertex.__init__()
      • UnaligningVertex.clone()
      • UnaligningVertex.get_aligner_edge()
      • UnaligningVertex.get_cell()
      • UnaligningVertex.get_id()
      • UnaligningVertex.get_position()
      • UnaligningVertex.init_at_center()
      • UnaligningVertex.init_at_shifted_center()
      • UnaligningVertex.map_functional_groups_to_edges()
      • UnaligningVertex.place_building_block()
      • UnaligningVertex.with_position()
      • UnaligningVertex.with_scale()
• stk.molecular.topology_graphs.host_guest package
  • Submodules
    • Host Guest Complex
    • Complex
      • Complex.__init__()
      • Complex.clone()
      • Complex.construct()
      • Complex.get_building_blocks()
      • Complex.get_num_building_block()
      • Complex.with_building_blocks()
    • Guest
      • Guest.__init__()
      • Guest.get_building_block()
      • Guest.get_displacement()
      • Guest.get_end_vector()
      • Guest.get_start_vector()
    • Host Guest Complex Vertices
    • GuestVertex
      • GuestVertex.__init__()
      • GuestVertex.clone()
      • GuestVertex.get_cell()
      • GuestVertex.get_id()
      • GuestVertex.get_position()
      • GuestVertex.map_functional_groups_to_edges()
      • GuestVertex.place_building_block()
      • GuestVertex.with_position()
      • GuestVertex.with_scale()
    • HostVertex
      • HostVertex.__init__()
      • HostVertex.clone()
      • HostVertex.get_cell()
      • HostVertex.get_id()
      • HostVertex.get_position()
      • HostVertex.map_functional_groups_to_edges()
      • HostVertex.place_building_block()
      • HostVertex.with_position()
      • HostVertex.with_scale()
• stk.molecular.topology_graphs.macrocycle package
  • Submodules
    • Macrocycle
    • Macrocycle
      • Macrocycle.__init__()
      • Macrocycle.clone()
      • Macrocycle.construct()
      • Macrocycle.get_building_blocks()
      • Macrocycle.get_num_building_block()
      • Macrocycle.with_building_blocks()
    • Macrocycle Vertices
    • CycleVertex
      • CycleVertex.__init__()
      • CycleVertex.clone()
      • CycleVertex.get_cell()
      • CycleVertex.get_flip()
      • CycleVertex.get_id()
      • CycleVertex.get_position()
      • CycleVertex.map_functional_groups_to_edges()
      • CycleVertex.place_building_block()
      • CycleVertex.with_position()
      • CycleVertex.with_scale()
• stk.molecular.topology_graphs.metal_complex package
  • Subpackages
    • stk.molecular.topology_graphs.metal_complex.octahedral package
      • Submodules
    • stk.molecular.topology_graphs.metal_complex.paddlewheel package
      • Submodules
    • stk.molecular.topology_graphs.metal_complex.porphyrin package
      • Submodules
    • stk.molecular.topology_graphs.metal_complex.square_planar package
      • Submodules
  • Submodules
    • Metal Complex
      • Paddlewheel
      • Paddlewheel
      • Porphyrin
      • Porphyrin
      • Octahedral
      • Octahedral
      • Octahedral Lambda
      • OctahedralLambda
      • Octahedral Delta
      • OctahedralDelta
      • Square Planar
      • SquarePlanar
      • Bidentate Square Planar
      • BidentateSquarePlanar
      • Cis Protected Square Planar
      • CisProtectedSquarePlanar
    • MetalComplex
      • MetalComplex.__init__()
      • MetalComplex.clone()
      • MetalComplex.construct()
      • MetalComplex.get_building_blocks()
      • MetalComplex.get_num_building_block()
      • MetalComplex.with_building_blocks()
    • Metal Complex Vertices
    • BiDentateLigandVertex
      • BiDentateLigandVertex.__init__()
      • BiDentateLigandVertex.clone()
      • BiDentateLigandVertex.get_cell()
      • BiDentateLigandVertex.get_id()
      • BiDentateLigandVertex.get_position()
      • BiDentateLigandVertex.map_functional_groups_to_edges()
      • BiDentateLigandVertex.place_building_block()
      • BiDentateLigandVertex.with_position()
      • BiDentateLigandVertex.with_scale()
    • MetalVertex
      • MetalVertex.__init__()
      • MetalVertex.clone()
      • MetalVertex.get_cell()
      • MetalVertex.get_id()
      • MetalVertex.get_position()
      • MetalVertex.map_functional_groups_to_edges()
      • MetalVertex.place_building_block()
      • MetalVertex.with_position()
      • MetalVertex.with_scale()
    • MonoDentateLigandVertex
      • MonoDentateLigandVertex.__init__()
      • MonoDentateLigandVertex.clone()
      • MonoDentateLigandVertex.get_cell()
      • MonoDentateLigandVertex.get_id()
      • MonoDentateLigandVertex.get_position()
      • MonoDentateLigandVertex.map_functional_groups_to_edges()
      • MonoDentateLigandVertex.place_building_block()
      • MonoDentateLigandVertex.with_position()
      • MonoDentateLigandVertex.with_scale()
    • UnaligningVertex
      • UnaligningVertex.__init__()
      • UnaligningVertex.clone()
      • UnaligningVertex.get_cell()
      • UnaligningVertex.get_id()
      • UnaligningVertex.get_position()
      • UnaligningVertex.map_functional_groups_to_edges()
      • UnaligningVertex.place_building_block()
      • UnaligningVertex.with_position()
      • UnaligningVertex.with_scale()
• stk.molecular.topology_graphs.polymer package
  • Polymer
  • Subpackages
    • stk.molecular.topology_graphs.polymer.linear package
      • Submodules
• stk.molecular.topology_graphs.rotaxane package
  • Rotaxane
  • Submodules
    • [n]Rotaxane
    • NRotaxane
      • NRotaxane.__init__()
      • NRotaxane.clone()
      • NRotaxane.construct()
      • NRotaxane.get_building_blocks()
      • NRotaxane.get_num_building_block()
      • NRotaxane.with_building_blocks()
    • Rotaxane Vertices
    • AxleVertex
      • AxleVertex.__init__()
      • AxleVertex.clone()
      • AxleVertex.get_cell()
      • AxleVertex.get_id()
      • AxleVertex.get_position()
      • AxleVertex.map_functional_groups_to_edges()
      • AxleVertex.place_building_block()
      • AxleVertex.with_position()
      • AxleVertex.with_scale()
    • CycleVertex
      • CycleVertex.__init__()
      • CycleVertex.clone()
      • CycleVertex.get_cell()
      • CycleVertex.get_flip()
      • CycleVertex.get_id()
      • CycleVertex.get_position()
      • CycleVertex.map_functional_groups_to_edges()
      • CycleVertex.place_building_block()
      • CycleVertex.with_position()
      • CycleVertex.with_scale()
• stk.molecular.topology_graphs.topology_graph package
  • Subpackages
    • stk.molecular.topology_graphs.topology_graph.construction_result package
      • Submodules
    • stk.molecular.topology_graphs.topology_graph.construction_state package
      • Subpackages
      • Submodules
    • stk.molecular.topology_graphs.topology_graph.optimizers package
      • Submodules
    • stk.molecular.topology_graphs.topology_graph.topology_graph package
      • Subpackages
      • Submodules
  • Submodules
    • Edge
    • Edge
      • Edge.__init__()
      • Edge.clone()
      • Edge.get_id()
      • Edge.get_periodicity()
      • Edge.get_position()
      • Edge.get_vertex1_id()
      • Edge.get_vertex2_id()
      • Edge.get_vertex_ids()
      • Edge.is_periodic()
      • Edge.with_position()
      • Edge.with_scale()
    • Edge Group
    • EdgeGroup
      • EdgeGroup.__init__()
      • EdgeGroup.get_edge_ids()
    • Vertex
    • Vertex
      • Vertex.__init__()
      • Vertex.clone()
      • Vertex.get_cell()
      • Vertex.get_id()
      • Vertex.get_position()
      • Vertex.map_functional_groups_to_edges()
      • Vertex.place_building_block()
      • Vertex.with_position()
      • Vertex.with_scale()
• stk.molecular.topology_graphs.utilities package
  • Submodules
    • Edge Sorter
    • Functional Group Sorter
    • Sorter