_path: input_clashes.yaml
ga:         # Section to configure the Genetic Algorithm parameters
    mut_pb: 0.8
    cx_pb: 0.2
    mut_indpb: 1
    generations: 500
    population: 12
genes:      # Section to configure the genes
-   module: gpath.genes.molecule
    name: Ligand
    path: ./mol_files/ligand.mol2 #optionally could be the ligand with H
-   module: gpath.genes.molecule
    name: Protein
    path: ./mol_files/protein.mol2 #optionally could be the ligand with H 
-   module: gpath.genes.path_torsion
    name: T
    target: Ligand
    anchor: Ligand/3 # This anchor atom has to be set in function of the concrete ligand (see tutorial section for more information)
-   module: gpath.genes.path_rotamers
    name: R
-   module: gpath.genes.path_normalmodes
    name: NM
    target: Protein
    modes: [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19]
    group_by: residues
    group_lambda: 15
    n_samples: 100
    write_modes: True
    write_samples: True
-   module: gpath.genes.path
    name: Pathway
    ligand: Ligand
    protein: Protein
    torsion_gene: T
    rotamers_gene: R
    nm_gene: NM
    min_step_increment: 0.8
objectives:     # Section to configure the evaluation of the pathways
-   module: gpath.objectives.path_scoring
    name: Clashes
    probe: Pathway
    which: clashes
    method: max
    weight: -1.0
output:
    check_every: 0
    name: 2ace_clashes     
    pareto: False   #there is only one objective
    path: ./results_clashes
similarity:
    args:
    - Pathway
    - 1.0
    kwargs: {}
    module: gpath.path_similarity.pathways_rmsd