Difference between revisions of "CONGA Parameter List"

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! Default Value
 
! Default Value
 
|-
 
|-
−
! ga_molecule_file
+
| ga_molecule_file
 
| Initial molecule ensemble in mol2 format || -  
 
| Initial molecule ensemble in mol2 format || -  
 
|-
 
|-
−
! ga_fraglib_scaffold_file
+
| ga_fraglib_scaffold_file
 
| Fragment library mol2 file containing scaffolds || -
 
| Fragment library mol2 file containing scaffolds || -
 
|-
 
|-
−
! ga_fraglib_linker_file
+
| ga_fraglib_linker_file
 
| Fragment library mol2 file containing linkers || -
 
| Fragment library mol2 file containing linkers || -
 
|-
 
|-
−
!ga_fraglib_sidechain_file
+
|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 || -
 
 
|-
 
|-
−
!ga_use_torenv_table
+
|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
+
|ga_torenv_table
 
| Path to the torsion environment table (.dat) || -
 
| Path to the torsion environment table (.dat) || -
 
|-
 
|-
−
!max_generations
+
|ga_max_generations
−
| Max number of generations || 1
+
| Max number of generations to be executed|| 100
 
|-
 
|-
−
!ga_xover_sampling_method_rand
+
|ga_xover_sampling_method_rand
−
| Crossover sampling method random || yes
+
| Selects the random or exhaustive crossover sampling methods (yes for random) || yes
 
|-
 
|-
−
!ga_xover_max
+
|ga_xover_max
 
| Max number of offspring generated from crossover events || 150
 
| Max number of offspring generated from crossover events || 150
 
|-
 
|-
−
!ga_bond_tolerance
+
|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
+
|ga_angle_cutoff
 
| User-specified cutoff for bond angles || 0.14
 
| User-specified cutoff for bond angles || 0.14
 
|-
 
|-
−
!ga_check_overlap
+
|ga_check_overlap
−
| Check the molecules that overlap || yes
+
| Output parent pairs involved in crossover in unique_xover.mol2 file || no
 
|-
 
|-
−
!ga_check_only
+
|ga_check_only
−
| Check for molecule generation || no
+
| Only check parent pairs for crossover (no offspring, mutations, or selection) || no
 
|-
 
|-
−
!ga_mutate_parents
+
|ga_mutate_parents
−
| Mutate the parents || yes
+
| Mutate the parents || no
 
|-
 
|-
−
!ga_pmut_rate
+
|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 || 0.3
 
|-
 
|-
−
!ga_omut_rate
+
|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
+
|ga_max_mut_cycles
 
| Max mutation attemps - for random mutation sampling || 5
 
| Max mutation attemps - for random mutation sampling || 5
 
|-
 
|-
−
!ga_mut_sampling_method
+
|ga_mut_sampling_method
 
| Type of sampling (rand, graph) || rand
 
| Type of sampling (rand, graph) || rand
 
|-
 
|-
−
!ga_num_random_picks
+
|ga_num_random_picks
 
| Number of random picks for random sampling || 10
 
| Number of random picks for random sampling || 10
 
|-
 
|-
−
!ga_max_root_size
+
|ga_max_root_size
−
| Max root size in de novo || 5
+
| Max root size in NOVA || 5
 
|-
 
|-
−
!ga_graph_max_picks
+
|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
+
|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 that are similar (using Tanimoto) to a successful fragment when graph method is turned on || 3
 
|-
 
|-
−
!ga_graph_depth
+
|ga_graph_depth
−
| The number of fragments chosen that are similar to successful mutations through Tanimoto when graph method is turned on || 2
+
| Parameter that controls the overall number of fragment attempted via the following formula: Total_attempts=(breadth)^(depth) || 2
 
|-
 
|-
−
!ga_graph_temperature
+
|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
+
|ga_energy_cutoff
 
| The upper bounds for energy pruning || 100
 
| The upper bounds for energy pruning || 100
 
|-
 
|-
−
!ga_heur_unmatched_num
+
|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
+
|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
+
|ga_constraint_mol_wt
 
| The upper bound for mol wt || 500
 
| The upper bound for mol wt || 500
 
|-
 
|-
−
!ga_constraint_rot_bon
+
|ga_constraint_rot_bon
 
| The upper bound for # rot bonds || 10
 
| The upper bound for # rot bonds || 10
 
|-
 
|-
−
!ga_constraint_H_accept
+
|ga_constraint_H_accept
 
| The upper bound for # of hydrogen acceptors || 10
 
| The upper bound for # of hydrogen acceptors || 10
 
|-
 
|-
−
!ga_constraint_H_donor
+
|ga_constraint_H_donor
 
| The upper bound for # of hydrogen donors || 5
 
| The upper bound for # of hydrogen donors || 5
 
|-
 
|-
−
!ga_constraint_formal_charge  
+
|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
+
|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
+
|ga_selection_method
 
| Type of selection (elitism, tournament, roulette) || elitism
 
| Type of selection (elitism, tournament, roulette) || elitism
 
|-
 
|-
−
!ga_elitism_combined
+
|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
+
|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
 
| 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
+
|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
+
|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
+
|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
+
|ga_niching
 
| Selection niching method || no
 
| Selection niching method || no
 
|-
 
|-
−
!ga_niching_method
+
|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
+
|ga_selection_extinction
 
| Turn on mass extinction? || no
 
| Turn on mass extinction? || no
 
|-
 
|-
−
!ga_extinction_frequency
+
|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
 
|-
 
|-
−
!ga_extinction_duration
+
|ga_extinction_duration
 
| 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
+
|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
+
|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
+
|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) || 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
 
| User-defined output name prefix || output
 
| User-defined output name prefix || output
 
|-
 
|-
 
|}
 
|}

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
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