Output File

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.

Example IDs for the bonds, components, and binding sites

output.yaml

0: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [M1.a, X0.a]
  comp_id_to_kind: {L1: L, M1: M, X0: X}
1: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [M1.a, X0.a]
  - [M2.b, X1.a]
  comp_id_to_kind: {L1: L, M1: M, M2: M, X0: X, X1: X}
2: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L4.b, M1.a]
  comp_id_to_kind: {L1: L, L4: L, M1: M}
3: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [M1.a, X0.a]
  comp_id_to_kind: {L1: L, L2: L, M1: M, M2: M, X0: X}
4: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [M1.a, X0.a]
  - [M3.b, X1.a]
  comp_id_to_kind: {L1: L, L2: L, M1: M, M2: M, M3: M, X0: X, X1: X}
5: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L4.b, M1.a]
  comp_id_to_kind: {L1: L, L2: L, L4: L, M1: M, M2: M}
6: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [L3.a, M3.b]
  - [M1.a, X0.a]
  comp_id_to_kind: {L1: L, L2: L, L3: L, M1: M, M2: M, M3: M, X0: X}
7: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [L3.a, M3.b]
  - [L3.b, M4.a]
  - [M1.a, X0.a]
  - [M4.b, X1.a]
  comp_id_to_kind: {L1: L, L2: L, L3: L, M1: M, M2: M, M3: M, M4: M, X0: X, X1: X}
8: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [L3.a, M3.b]
  - [L4.b, M1.a]
  comp_id_to_kind: {L1: L, L2: L, L3: L, L4: L, M1: M, M2: M, M3: M}
9: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [L3.a, M3.b]
  - [L3.b, M4.a]
  - [L4.a, M4.b]
  - [M1.a, X0.a]
  comp_id_to_kind: {L1: L, L2: L, L3: L, L4: L, M1: M, M2: M, M3: M, M4: M, X0: X}
10: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [L3.a, M3.b]
  - [L3.b, M4.a]
  - [L4.a, M4.b]
  - [L4.b, M1.a]
  comp_id_to_kind: {L1: L, L2: L, L3: L, L4: L, M1: M, M2: M, M3: M, M4: M}

Explanation

0: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [M1.a, X0.a]
  comp_id_to_kind: {L1: L, M1: M, X0: X}

Each assembly is represented as a dictionary with the following fields:

• bonds: A list of binding site pairs.
• comp_id_to_kind: A dictionary where keys are component IDs and values are component kinds.

In the example above, the assembly has three components, L1, M1, and X0, whose kinds are L, M, and X, respectively. The assembly has two bonds: one between the binding sites a of L1 and b of M1, and another between the binding sites a of M1 and a of X0.

Structure of the assembly-0, i.e., MLX