DOCK GA Parameters

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Parameter Description Default Value
ga_molecule_file Initial molecule ensemble in mol2 format -
ga_fraglib_scaffold_file Fragment library mol2 file containing scaffolds -
ga_fraglib_linker_file Fragment library mol2 file containing linkers -
ga_fraglib_sidechain_file Fragment library mol2 file containing side chains -
ga_use_torenv_table Is the user going to use a torsion environment table (.dat) yes
ga_torenv_table Path to the torsion environment table (.dat) -
ga_use_dn_roulette Is the user going to use a roulette acceptance for torsions no
ga_max_generations Max number of generations to be executed 100
ga_xover_sampling_method_rand Selects the random or exhaustive crossover sampling methods (yes for random) yes
ga_xover_max Max number of offspring generated from crossover events 150
ga_bond_tolerance User-specified cutoff for allowable atom sq dist 0.5
ga_angle_cutoff User-specified cutoff for bond angles 0.14
ga_check_overlap Output parent pairs involved in crossover in unique_xover.mol2 file no
ga_mutations Turn on mutations yes
ga_mutate_addition Turn on mutation type addition yes
ga_mutate_deletion Turn on mutation type deletion yes
ga_mutate_substitution Turn on mutation type substitution yes
ga_mutate_replacement Turn on mutation type replacement (also known as scaffold hopping) yes
ga_mutate_parents Mutate the parents no
ga_pmut_rate Parent mutation rate - only used when random parent mutation is turned on 0.3
ga_omut_rate Offspring mutation rate for random mutation sampling 0.7
ga_max_mut_cycles Max mutation attemps - for random mutation sampling 5
ga_mut_sampling_method Type of sampling (rand, graph) rand
ga_num_random_picks Number of random picks for random sampling 10
ga_max_root_size Max root size in NOVA 5
ga_graph_max_picks The number of fragment picks per round of mutation when grpah method is turned on 10
ga_graph_breadth The number of fragments that are similar (using Tanimoto) to a successful fragment when graph method is turned on 3
ga_graph_depth Parameter that controls the overall number of fragment attempted via the following formula: Total_attempts=(breadth)^(depth) 2
ga_graph_temperature The initial annealing temperature when the graph method is turned on 100
ga_energy_cutoff The upper bounds for energy pruning 100
ga_heur_unmatched_num The number of unmatched atoms for H. RMSD pruning 5
ga_heur_matched_rmsd The RMSD of matched atoms for H. RMSD pruning 2.0
ga_constraint_mol_wt The upper bound for mol wt 500
ga_constraint_rot_bon The upper bound for # rot bonds 10
ga_constraint_H_accept The upper bound for # of hydrogen acceptors 10
ga_constraint_H_donor The upper bound for # of hydrogen donors 5
ga_constraint_formal_charge The upper and lower bound for formal charge 4
ga_ensemble_size The number of survivors to carry to next generation 200
ga_selection_method Type of selection (elitism, tournament, roulette) elitism
ga_elitism_combined Combine the parent and offspring populations for the elitism selection method? no
ga_elitism_option Type of selection: max, percent (perc), or number(num) when elitism is the selection method max
ga_elitism_number The number of top scored parents to pass to the next generation when elitism number is the selection method 20
ga_elitism_percent The top percent of the ensemble(s) to be carried tot he next generation when elitism percent is the selection method 0.2
ga_tournament_p_vs_c Select the top scored molecules between parents and offspring separately when tournament selection method is used yes
ga_roulette_separate Select the top scored molecule between parents and offspring separately when roulette selection method is used yes
ga_niching Selection niching method no
ga_niching_method Type of selection (sharing crowding) when niching is turned on sharing
ga_selection_extinction Turn on mass extinction? no
ga_extinction_frequency Number of generations to turn on when mass extinction is used 200
ga_extinction_duration Number of generations to remain on when mass extinction is used 50
ga_extinction_keep Number of generations to remain on when mass extinction is used 20
ga_extinction_switch_selection Change selection type when mass extinction is used no
ga_secondary_selection_method Secondary selection when ga_extinction_switch_selection = yes (Options: elitism, roulette, tournament) roulette
ga_max_num_gen_with_no_crossover The max generation of allowable growth without a crossover event 5
ga_output_prefix User-defined output name prefix output