Difference between revisions of "CONGA Parameter List"
From Rizzo_Lab
| (6 intermediate revisions by the same user not shown) | |||
| Line 19: | Line 19: | ||
|ga_fraglib_sidechain_file | |ga_fraglib_sidechain_file | ||
| Fragment library mol2 file containing side chains || - | | Fragment library mol2 file containing side chains || - | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
|ga_use_torenv_table | |ga_use_torenv_table | ||
| Line 29: | Line 26: | ||
| Path to the torsion environment table (.dat) || - | | Path to the torsion environment table (.dat) || - | ||
|- | |- | ||
| − | | | + | |ga_max_generations |
| − | | Max number of generations || | + | | Max number of generations to be executed|| 100 |
|- | |- | ||
|ga_xover_sampling_method_rand | |ga_xover_sampling_method_rand | ||
| − | | | + | | Selects the random or exhaustive crossover sampling methods (yes for random) || yes |
|- | |- | ||
|ga_xover_max | |ga_xover_max | ||
| Line 45: | Line 42: | ||
|- | |- | ||
|ga_check_overlap | |ga_check_overlap | ||
| − | | | + | | Output parent pairs involved in crossover in unique_xover.mol2 file || no |
|- | |- | ||
|ga_check_only | |ga_check_only | ||
| − | | | + | | Only check parent pairs for crossover (no offspring, mutations, or selection) || no |
|- | |- | ||
|ga_mutate_parents | |ga_mutate_parents | ||
| − | | Mutate the parents || | + | | Mutate the parents || no |
|- | |- | ||
|ga_pmut_rate | |ga_pmut_rate | ||
| − | | Parent mutation rate - only used when random parent mutation is turned on || 0. | + | | Parent mutation rate - only used when random parent mutation is turned on || 0.3 |
|- | |- | ||
|ga_omut_rate | |ga_omut_rate | ||
| Line 69: | Line 66: | ||
|- | |- | ||
|ga_max_root_size | |ga_max_root_size | ||
| − | | Max root size in | + | | Max root size in NOVA || 5 |
|- | |- | ||
|ga_graph_max_picks | |ga_graph_max_picks | ||
| Line 75: | Line 72: | ||
|- | |- | ||
|ga_graph_breadth | |ga_graph_breadth | ||
| − | | The number of fragments | + | | The number of fragments that are similar (using Tanimoto) to a successful fragment when graph method is turned on || 3 |
|- | |- | ||
|ga_graph_depth | |ga_graph_depth | ||
| − | | | + | | Parameter that controls the overall number of fragment attempted via the following formula: Total_attempts=(breadth)^(depth) || 2 |
|- | |- | ||
|ga_graph_temperature | |ga_graph_temperature | ||
| Line 117: | Line 114: | ||
|- | |- | ||
|ga_elitism_option | |ga_elitism_option | ||
| − | | Type of selection:max, percent (perc), or number(num) when elitism is the selection method || max | + | | Type of selection: max, percent (perc), or number(num) when elitism is the selection method || max |
|- | |- | ||
|ga_elitism_number | |ga_elitism_number | ||
| Line 153: | Line 150: | ||
|- | |- | ||
|ga_secondary_selection_method | |ga_secondary_selection_method | ||
| − | | Secondary selection when ga_extinction_switch_selection = yes (Options: elitism, roulette, tournament) || | + | | 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 | |ga_output_prefix | ||
Latest revision as of 14:11, 28 August 2018
| 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 |
