CONGA Parameter List

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