View source for DOCK GA Parameter List



{| class="wikitable" 
|+ 
|-
! 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_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_check_only
| Only check parent pairs for crossover (no offspring, mutations, or selection) || no
|-
|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
|-
|}