Difference between revisions of "CONGA Parameter List"
From Rizzo_Lab
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! Default Value | ! Default Value | ||
|- | |- | ||
| − | + | | ga_molecule_file | |
| Initial molecule ensemble in mol2 format || - | | Initial molecule ensemble in mol2 format || - | ||
|- | |- | ||
| − | + | | ga_fraglib_scaffold_file | |
| Fragment library mol2 file containing scaffolds || - | | Fragment library mol2 file containing scaffolds || - | ||
|- | |- | ||
| − | + | | ga_fraglib_linker_file | |
| Fragment library mol2 file containing linkers || - | | Fragment library mol2 file containing linkers || - | ||
|- | |- | ||
| − | + | |ga_fraglib_sidechain_file | |
| Fragment library mol2 file containing side chains || - | | Fragment library mol2 file containing side chains || - | ||
|- | |- | ||
| − | + | |ga_fraglib_rigid_file | |
| Fragment library mol2 file containing completely rigid molecules || - | | Fragment library mol2 file containing completely rigid molecules || - | ||
|- | |- | ||
| − | + | |ga_use_torenv_table | |
| Is the user going to use a torsion environment table (.dat) || yes | | Is the user going to use a torsion environment table (.dat) || yes | ||
|- | |- | ||
| − | + | |ga_torenv_table | |
| Path to the torsion environment table (.dat) || - | | Path to the torsion environment table (.dat) || - | ||
|- | |- | ||
| − | + | |max_generations | |
| Max number of generations || 1 | | Max number of generations || 1 | ||
|- | |- | ||
| − | + | |ga_xover_sampling_method_rand | |
| Crossover sampling method random || yes | | Crossover sampling method random || yes | ||
|- | |- | ||
| − | + | |ga_xover_max | |
| Max number of offspring generated from crossover events || 150 | | Max number of offspring generated from crossover events || 150 | ||
|- | |- | ||
| − | + | |ga_bond_tolerance | |
| User-specified cutoff for allowable atom sq dist || 0.5 | | User-specified cutoff for allowable atom sq dist || 0.5 | ||
|- | |- | ||
| − | + | |ga_angle_cutoff | |
| User-specified cutoff for bond angles || 0.14 | | User-specified cutoff for bond angles || 0.14 | ||
|- | |- | ||
| − | + | |ga_check_overlap | |
| Check the molecules that overlap || yes | | Check the molecules that overlap || yes | ||
|- | |- | ||
| − | + | |ga_check_only | |
| Check for molecule generation || no | | Check for molecule generation || no | ||
|- | |- | ||
| − | + | |ga_mutate_parents | |
| Mutate the parents || yes | | Mutate the parents || yes | ||
|- | |- | ||
| − | + | |ga_pmut_rate | |
| Parent mutation rate - only used when random parent mutation is turned on || 0.4 | | Parent mutation rate - only used when random parent mutation is turned on || 0.4 | ||
|- | |- | ||
| − | + | |ga_omut_rate | |
| Offspring mutation rate for random mutation sampling || 0.7 | | Offspring mutation rate for random mutation sampling || 0.7 | ||
|- | |- | ||
| − | + | |ga_max_mut_cycles | |
| Max mutation attemps - for random mutation sampling || 5 | | Max mutation attemps - for random mutation sampling || 5 | ||
|- | |- | ||
| − | + | |ga_mut_sampling_method | |
| Type of sampling (rand, graph) || rand | | Type of sampling (rand, graph) || rand | ||
|- | |- | ||
| − | + | |ga_num_random_picks | |
| Number of random picks for random sampling || 10 | | Number of random picks for random sampling || 10 | ||
|- | |- | ||
| − | + | |ga_max_root_size | |
| Max root size in de novo || 5 | | Max root size in de novo || 5 | ||
|- | |- | ||
| − | + | |ga_graph_max_picks | |
| The number of fragment picks per round of mutation when grpah method is turned on || 10 | | The number of fragment picks per round of mutation when grpah method is turned on || 10 | ||
|- | |- | ||
| − | + | |ga_graph_breadth | |
| The number of fragments chosen that are similar to successful mutations through Tanimoto when graph method is turned on || 3 | | The number of fragments chosen that are similar to successful mutations through Tanimoto when graph method is turned on || 3 | ||
|- | |- | ||
| − | + | |ga_graph_depth | |
| The number of fragments chosen that are similar to successful mutations through Tanimoto when graph method is turned on || 2 | | The number of fragments chosen that are similar to successful mutations through Tanimoto when graph method is turned on || 2 | ||
|- | |- | ||
| − | + | |ga_graph_temperature | |
| The initial annealing temperature when the graph method is turned on || 100 | | The initial annealing temperature when the graph method is turned on || 100 | ||
|- | |- | ||
| − | + | |ga_energy_cutoff | |
| The upper bounds for energy pruning || 100 | | The upper bounds for energy pruning || 100 | ||
|- | |- | ||
| − | + | |ga_heur_unmatched_num | |
| The number of unmatched atoms for H. RMSD pruning || 5 | | 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 | | The RMSD of matched atoms for H. RMSD pruning || 2.0 | ||
|- | |- | ||
| − | + | |ga_constraint_mol_wt | |
| The upper bound for mol wt || 500 | | The upper bound for mol wt || 500 | ||
|- | |- | ||
| − | + | |ga_constraint_rot_bon | |
| The upper bound for # rot bonds || 10 | | The upper bound for # rot bonds || 10 | ||
|- | |- | ||
| − | + | |ga_constraint_H_accept | |
| The upper bound for # of hydrogen acceptors || 10 | | The upper bound for # of hydrogen acceptors || 10 | ||
|- | |- | ||
| − | + | |ga_constraint_H_donor | |
| The upper bound for # of hydrogen donors || 5 | | The upper bound for # of hydrogen donors || 5 | ||
|- | |- | ||
| − | + | |ga_constraint_formal_charge | |
| The upper and lower bound for formal charge || 4 | | The upper and lower bound for formal charge || 4 | ||
|- | |- | ||
| − | + | |ga_ensemble_size | |
| The number of survivors to carry to next generation || 200 | | The number of survivors to carry to next generation || 200 | ||
|- | |- | ||
| − | + | |ga_selection_method | |
| Type of selection (elitism, tournament, roulette) || elitism | | Type of selection (elitism, tournament, roulette) || elitism | ||
|- | |- | ||
| − | + | |ga_elitism_combined | |
| Combine the parent and offspring populations for the elitism selection method? || no | | 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 | | 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 | | 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 | | 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 | | 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 | | Select the top scored molecule between parents and offspring separately when roulette selection method is used || yes | ||
|- | |- | ||
| − | + | |ga_niching | |
| Selection niching method || no | | Selection niching method || no | ||
|- | |- | ||
| − | + | |ga_niching_method | |
| Type of selection (sharing crowding) when niching is turned on || sharing | | Type of selection (sharing crowding) when niching is turned on || sharing | ||
|- | |- | ||
| − | + | |ga_selection_extinction | |
| Turn on mass extinction? || no | | Turn on mass extinction? || no | ||
|- | |- | ||
| − | + | |ga_extinction_frequency | |
| Number of generations to turn on when mass extinction is used || 200 | | Number of generations to turn on when mass extinction is used || 200 | ||
|- | |- | ||
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| Number of generations to remain on when mass extinction is used || 50 | | 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 | | 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 | | 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) || elitism | | Secondary selection when ga_extinction_switch_selection = yes (Options: elitism, roulette, tournament) || elitism | ||
|- | |- | ||
| − | + | |ga_output_prefix | |
| User-defined output name prefix || output | | User-defined output name prefix || output | ||
|- | |- | ||
|} | |} | ||
Revision as of 11:03, 21 February 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_fraglib_rigid_file | Fragment library mol2 file containing completely rigid molecules | - |
| 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) | - |
| max_generations | Max number of generations | 1 |
| ga_xover_sampling_method_rand | Crossover sampling method 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 | Check the molecules that overlap | yes |
| ga_check_only | Check for molecule generation | no |
| ga_mutate_parents | Mutate the parents | yes |
| ga_pmut_rate | Parent mutation rate - only used when random parent mutation is turned on | 0.4 |
| 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 de novo | 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 chosen that are similar to successful mutations through Tanimoto when graph method is turned on | 3 |
| ga_graph_depth | The number of fragments chosen that are similar to successful mutations through Tanimoto when graph method is turned on | 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) | elitism |
| ga_output_prefix | User-defined output name prefix | output |
