Recipe File Reference

Recipe File Reference

FBTK’s Builder can load YAML-formatted recipe files that describe the composition of your system.

System Configuration (system)

Global settings for the entire system.

Key	Type	Description
density	float	Target density in g/cm³.
cell_shape	list[3]	[Optional] Explicit box dimensions [Lx, Ly, Lz] in Å.

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Component Configuration (components)

A list of molecules or polymers that make up the system.

Common Keys

Key	Type	Description
name	string	Identifier for the component.
role	enum	Either molecule or polymer.
input	nested	Input source configuration. Contains the following sub-fields:
count	int	[Role: molecule only] Number of molecules to place.

Input Source (input)

Key	Type	Description
smiles	string	SMILES string. Can include * as connection points.
file	string	Path to a structural file (.mol / .mol2).

Polymer Parameters (polymer_params)

Required when role: polymer is specified.

Key	Type	Description
degree	int	Degree of polymerization (DP).
n_chains	int	Number of polymer chains to generate.
head_index	int	[Optional] Heavy atom index (0-indexed) for the polymerization start site.
tail_index	int	[Optional] Heavy atom index (0-indexed) for the polymerization end site.

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Example Recipe

system:
  density: 0.9
components:
  - name: "PS"
    role: "polymer"
    input:
      smiles: "*C(C*)c1ccccc1"
    polymer_params:
      degree: 10
      n_chains: 50
  - name: "Toluene"
    role: "molecule"
    count: 100
    input:
      file: "toluene.mol"