_path: /path/to/this/input/file/param.yaml
ga:         # Section to configure the Genetic Algorithm parameters
    mut_pb: 0.8
    cx_pb: 0.2
    mut_indpb: 1
    generations: 750
    population: 12
genes:      # Section to configure the genes
-   module: gpath.genes.molecule
    name: Ligand
    path: ./mol_files/ligand_with_H.mol2
-   module: gpath.genes.molecule
    name: Protein
    path: ./mol_files/protein_with_H.mol2 
-   module: gpath.genes.path_torsion
    name: T
    target: Ligand
    anchor: Ligand/1 # 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
    minimize: True
    #forcefields: [/path/to/protein.prmtop] #Should be used when non-standard residues are present
-   module: gpath.genes.path
    name: Pathway
    ligand: Ligand
    protein: Protein
    torsion_gene: T
    rotamers_gene: R
    nm_gene: NM
    min_step_increment: 0.8
    origin: [X.xxx, Y.yyy, Z.zzz]  #Coordinates of the initial point of the pathway object of study (referred to protein .mol2 file system of coordinates)
    destination: [X.xxx, Y.yyy, Z.zzz]  #Coordinates of the final point of the pathway object of study (referred to protein .mol2 file system of coordinates)
objectives:     # Section to configure the evaluation of the pathways
-   module: gpath.objectives.path_scoring
    name: Clashes
    probe: Pathway
    which: clashes
    method: average
    weight: -1.0
-   module: gpath.objectives.path_scoring
    name: Vina
    probe: Pathway
    which: vina
    method: average
    weight: -1.0
output:
    check_every: 0
    name: param     
    pareto: True   #there are more than one objectives
    path: /path/to/the/results/folder
similarity:
    args:
    - Pathway
    - 1.0
    kwargs: {}
    module: gpath.path_similarity.pathways_rmsd

# Input file to be used with GPathFinder version >= 1.0.1