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Example

Use M4L4 assembly as an example, where M is a metal ion with two binding sites and L is a ditopic ligand with two binding sites.

M4L4 assembly

Example IDs for the bonds, components, and binding sites

input.yaml
bonds: [1, 2, 3, 4, 5, 6, 7, 8]
bond_adjacency:
  1: [8, 2]
  2: [1, 3]
  3: [2, 4]
  4: [3, 5]
  5: [4, 6]
  6: [5, 7]
  7: [6, 8]
  8: [7, 1]
sym_ops:
  C_4: [[1, 3, 5, 7], [2, 4, 6, 8]]
  C_2: [[1, 5], [2, 6], [3, 7], [4, 8]]
  C_4^3: [[1, 7, 5, 3], [2, 8, 6, 4]]
  C_2x: [[1, 2], [3, 8], [4, 7], [5, 6]]
  C_2y: [[1, 6], [2, 5], [3, 4], [7, 8]]
  C_2(1): [[1, 4], [2, 3], [5, 8], [6, 7]]
  C_2(2): [[1, 8], [2, 7], [3, 6], [4, 5]]
component_kinds:
  L: !Component
    binding_sites: [a, b]
  M: !Component
    binding_sites: [a, b]
  X: !Component
    binding_sites: [a]
components_and_their_kinds:
  M1: M
  M2: M
  M3: M
  M4: M
  L1: L
  L2: L
  L3: L
  L4: L
bonds_and_their_binding_sites:
  1: [M1.b, L1.a]
  2: [L1.b, M2.a]
  3: [M2.b, L2.a]
  4: [L2.b, M3.a]
  5: [M3.b, L3.a]
  6: [L3.b, M4.a]
  7: [M4.b, L4.a]
  8: [L4.b, M1.a]
capping_config:
  target_component_kind: M
  capping_component_kind: X
  capping_binding_site: a

Download the example input file: input.yaml

Fields

bonds field

bonds: [1, 2, 3, 4, 5, 6, 7, 8]

A list of bond IDs.

  • IDs must be unique. (Incorrect: [1, 1, 2])
  • IDs can be either integers or strings. (Correct: 1, a, bond1, "1")
  • ID type must be consistent. (Incorrect: [1, "a"])

bond_adjacency field

bond_adjacency:
  1: [8, 2]
  2: [1, 3]
  3: [2, 4]
  4: [3, 5]
  5: [4, 6]
  6: [5, 7]
  7: [6, 8]
  8: [7, 1]

A dictionary where keys are bond IDs and values are lists of adjacent bond IDs.

For example, 1: [8, 2] means that bond 1 is adjacent to bonds 8 and 2.

sym_ops field

sym_ops:
  C_4: [[1, 3, 5, 7], [2, 4, 6, 8]]
  C_2: [[1, 5], [2, 6], [3, 7], [4, 8]]
  C_4^3: [[1, 7, 5, 3], [2, 8, 6, 4]]
  C_2x: [[1, 2], [3, 8], [4, 7], [5, 6]]
  C_2y: [[1, 6], [2, 5], [3, 4], [7, 8]]
  C_2(1): [[1, 4], [2, 3], [5, 8], [6, 7]]
  C_2(2): [[1, 8], [2, 7], [3, 6], [4, 5]]

A dictionary where keys are symmetry operation names and values are symmetry operation definitions.

Names of symmetry operations can be any string.

Three types of definitions are supported:

1. Permutation of bond IDs

C_4: [[1, 3, 5, 7], [2, 4, 6, 8]]
This means that the symmetry operation C_4 maps 1 to 3, 3 to 5, 5 to 7, and 7 to 1. Similarly, 2 to 4, 4 to 6, 6 to 8, and 8 to 2.

Note

If there are bonds that do not move, represent them as a list containing only one element, like this:

sigma_x: [[1], [2, 3]]

This means that the symmetry operation sigma_x maps 1 to 1, 2 to 3, and 3 to 2, i.e., 1 remains at the same position.

2. Mapping of bond IDs:

C_4: {1: 3, 2: 4, 3: 5, 4: 6, 5: 7, 6: 8, 7: 1, 8: 2}

Symmetry operations can also be defined as a dictionary where keys are bond IDs and values are the bond IDs to which they are mapped.

3. Composition of other symmetry operations:

C_2y: [C_2x, C_2]

Symmetry operations can be defined as a product of other symmetry operations. In this case, C_2y is defined as the composition of C_2x and C_2.

Warning

The order of the symmetry operations in the composition is important. The symmetry operation on the right is applied first. For example, C_2y is defined as C_2 followed by C_2x.

Note

Composition of three or more symmetry operations is also supported. For example: 

C_4^3: [C_4, C_4, C_4]

Combination of representation types

The representation types can be mixed in the sym_ops field. For example: 

sym_ops:
  C_4: [[1, 3, 5, 7], [2, 4, 6, 8]]  # Permutation
  C_2: [C_4, C_4]  # Composition
  C_4^3: {1: 7, 2: 8, 3: 1, 4: 2, 5: 3, 6: 4, 7: 5, 8: 6}  # Mapping
  C_2x: [[1, 2], [3, 8], [4, 7], [5, 6]]
  C_2y: [C_2x, C_2]
  C_2(1): [C_4, C_2x]
  C_2(2): [C_2x, C_4]

component_kinds field

component_kinds:
  L: !Component
    binding_sites: [a, b]
  M: !Component
    binding_sites: [a, b]
  X: !Component
    binding_sites: [a]

A dictionary where keys are names of component kinds and values are component definitions.

Note

Component kinds can also have "auxiliary edges" defined. For example: 

component_kinds:
  M: !Component
    binding_sites: [a, b, c, d]
    aux_edges: [[a, b, cis], [b, c, cis], [c, d, cis], [d, a, cis]]
The auxiliary edges can be used to define the relative orientation of the binding sites in the component, which can be used to distinguish between different stereoisomers.

components_and_their_kinds field

components_and_their_kinds:
  M1: M
  M2: M
  M3: M
  M4: M
  L1: L
  L2: L
  L3: L
  L4: L

A dictionary where keys are component names and values are component kind names defined in the component_kinds field.

bonds_and_their_binding_sites field

bonds_and_their_binding_sites:
  1: [M1.b, L1.a]
  2: [L1.b, M2.a]
  3: [M2.b, L2.a]
  4: [L2.b, M3.a]
  5: [M3.b, L3.a]
  6: [L3.b, M4.a]
  7: [M4.b, L4.a]
  8: [L4.b, M1.a]

A dictionary where keys are bond IDs and values are lists of binding sites. For example, 1: [M1.b, L1.a] means that bond 1 connects the binding site b of component M1 to the binding site a of component L1. Here, M1.b refers to the binding site b of component M1.

capping_config field

capping_config:
  target_component_kind: M
  capping_component_kind: X
  capping_binding_site: a

A dictionary that defines the capping configuration.

  • target_component_kind: The component kind to be capped.
  • capping_component_kind: The component kind to be used for capping.
  • capping_binding_site: The binding site of the capping component to be connected to the target component.