_path: input_clashes.yaml
ga:
    cx_eta: 5
    cx_pb: 0.2
    generations: 500
    lambda_: 1
    mu: 1
    mut_eta: 5
    mut_indpb: 1.0
    mut_pb: 0.8
    population: 12
genes:
-   module: gpath.genes.molecule
    name: Ligand
    path: ./mol_files/ligand.mol2
-   module: gpath.genes.molecule
    name: Protein
    path: ./mol_files/protein.mol2
-   anchor: Ligand/3
    module: gpath.genes.path_torsion
    name: T
    target: Ligand
-   module: gpath.genes.path_rotamers
    name: R
-   group_by: residues
    group_lambda: 15
    modes:
    - 0
    - 1
    - 2
    - 3
    - 4
    - 5
    - 6
    - 7
    - 8
    - 9
    - 10
    - 11
    - 12
    - 13
    - 14
    - 15
    - 16
    - 17
    - 18
    - 19
    module: gpath.genes.path_normalmodes
    n_samples: 100
    name: NM
    target: Protein
    write_modes: true
    write_samples: true
-   ligand: Ligand
    min_step_increment: 0.8
    module: gpath.genes.path
    name: Pathway
    nm_gene: NM
    protein: Protein
    rotamers_gene: R
    torsion_gene: T
objectives:
-   method: max
    module: gpath.objectives.path_scoring
    name: Clashes
    probe: Pathway
    weight: -1.0
    which: clashes
output:
    check_every: 0
    compress: true
    history: false
    name: 2ace_clashes
    pareto: false
    path: results_clashes
    precision: 3
    prompt_on_exception: true
    verbose: true
similarity:
    args:
    - Pathway
    - 1.0
    kwargs: {}
    module: gpath.path_similarity.pathways_rmsd
