basic::options::OptionKeys::enzdes Namespace Reference

Variables
BooleanOptionKey const	enzdes
StringOptionKey const	checkpoint
BooleanOptionKey const	enz_score
BooleanOptionKey const	enz_repack
BooleanOptionKey const	cst_opt
BooleanOptionKey const	cst_predock
RealOptionKey const	trans_magnitude
RealOptionKey const	rot_magnitude
RealOptionKey const	dock_trials
BooleanOptionKey const	cst_min
BooleanOptionKey const	cst_design
IntegerOptionKey const	design_min_cycles
BooleanOptionKey const	make_consensus_mutations
BooleanOptionKey const	bb_min
RealOptionKey const	bb_min_allowed_dev
RealOptionKey const	loop_bb_min_allowed_dev
RealOptionKey const	minimize_ligand_torsions
RealOptionKey const	minimize_all_ligand_torsions
BooleanOptionKey const	chi_min
BooleanOptionKey const	min_all_jumps
BooleanOptionKey const	cst_dock
BooleanOptionKey const	run_ligand_motifs
BooleanOptionKey const	enz_debug
FileOptionKey const	cstfile
FileOptionKey const	enz_loops_file
BooleanOptionKey const	flexbb_protocol
BooleanOptionKey const	remodel_protocol
BooleanOptionKey const	kic_loop_sampling
StringOptionKey const	dump_loop_samples
BooleanOptionKey const	fix_catalytic_aa
IntegerOptionKey const	additional_packing_ligand_rb_confs
IntegerOptionKey const	ex_catalytic_rot
IntegerOptionKey const	single_loop_ensemble_size
IntegerOptionKey const	loop_generator_trials
BooleanOptionKey const	no_catres_min_in_loopgen
RealOptionKey const	mc_kt_low
RealOptionKey const	mc_kt_high
RealOptionKey const	min_cacb_deviation
RealOptionKey const	max_bb_deviation
RealOptionKey const	max_bb_deviation_from_startstruct
IntegerOptionKey const	remodel_trials
BooleanOptionKey const	remodel_secmatch
BooleanOptionKey const	dump_inverse_rotamers
RealOptionKey const	remodel_aggressiveness
RealOptionKey const	favor_native_res
BooleanOptionKey const	detect_design_interface
BooleanOptionKey const	include_catres_in_interface_detection
BooleanOptionKey const	arg_sweep_interface
RealOptionKey const	arg_sweep_cutoff
RealOptionKey const	cut1
RealOptionKey const	cut2
RealOptionKey const	cut3
RealOptionKey const	cut4
RealOptionKey const	lig_packer_weight
BooleanOptionKey const	no_unconstrained_repack
RealOptionKey const	secmatch_Ecutoff
FileOptionKey const	change_lig
StringOptionKey const	process_ligrot_separately
BooleanOptionKey const	start_from_random_rb_conf
RealOptionKey const	bb_bump_cutoff
RealOptionKey const	sc_sc_bump_cutoff
BooleanOptionKey const	no_packstat_calculation
StringOptionKey const	compare_native
BooleanOptionKey const	final_repack_without_ligand
BooleanOptionKey const	dump_final_repack_without_ligand_pdb
BooleanOptionKey const	parser_read_cloud_pdb

Variable Documentation

additional_packing_ligand_rb_confs

IntegerOptionKey const basic::options::OptionKeys::enzdes::additional_packing_ligand_rb_confs

extern

arg_sweep_cutoff

RealOptionKey const basic::options::OptionKeys::enzdes::arg_sweep_cutoff

extern

arg_sweep_interface

BooleanOptionKey const basic::options::OptionKeys::enzdes::arg_sweep_interface

extern

bb_bump_cutoff

RealOptionKey const basic::options::OptionKeys::enzdes::bb_bump_cutoff

extern

bb_min

BooleanOptionKey const basic::options::OptionKeys::enzdes::bb_min

extern

bb_min_allowed_dev

RealOptionKey const basic::options::OptionKeys::enzdes::bb_min_allowed_dev

extern

change_lig

FileOptionKey const basic::options::OptionKeys::enzdes::change_lig

extern

checkpoint

StringOptionKey const basic::options::OptionKeys::enzdes::checkpoint

extern

chi_min

BooleanOptionKey const basic::options::OptionKeys::enzdes::chi_min

extern

compare_native

StringOptionKey const basic::options::OptionKeys::enzdes::compare_native

extern

cst_design

BooleanOptionKey const basic::options::OptionKeys::enzdes::cst_design

extern

cst_dock

BooleanOptionKey const basic::options::OptionKeys::enzdes::cst_dock

extern

cst_min

BooleanOptionKey const basic::options::OptionKeys::enzdes::cst_min

extern

cst_opt

BooleanOptionKey const basic::options::OptionKeys::enzdes::cst_opt

extern

cst_predock

BooleanOptionKey const basic::options::OptionKeys::enzdes::cst_predock

extern

cstfile

FileOptionKey const basic::options::OptionKeys::enzdes::cstfile

extern

Referenced by add_user_constraints(), ligand_dock_main_jd1(), and main().

cut1

RealOptionKey const basic::options::OptionKeys::enzdes::cut1

extern

cut2

RealOptionKey const basic::options::OptionKeys::enzdes::cut2

extern

Referenced by CloseContactWithResidue::apply().

cut3

RealOptionKey const basic::options::OptionKeys::enzdes::cut3

extern

cut4

RealOptionKey const basic::options::OptionKeys::enzdes::cut4

extern

design_min_cycles

IntegerOptionKey const basic::options::OptionKeys::enzdes::design_min_cycles

extern

detect_design_interface

BooleanOptionKey const basic::options::OptionKeys::enzdes::detect_design_interface

extern

dock_trials

RealOptionKey const basic::options::OptionKeys::enzdes::dock_trials

extern

dump_final_repack_without_ligand_pdb

BooleanOptionKey const basic::options::OptionKeys::enzdes::dump_final_repack_without_ligand_pdb

extern

Referenced by main().

dump_inverse_rotamers

BooleanOptionKey const basic::options::OptionKeys::enzdes::dump_inverse_rotamers

extern

dump_loop_samples

StringOptionKey const basic::options::OptionKeys::enzdes::dump_loop_samples

extern

enz_debug

BooleanOptionKey const basic::options::OptionKeys::enzdes::enz_debug

extern

enz_loops_file

FileOptionKey const basic::options::OptionKeys::enzdes::enz_loops_file

extern

enz_repack

BooleanOptionKey const basic::options::OptionKeys::enzdes::enz_repack

extern

enz_score

BooleanOptionKey const basic::options::OptionKeys::enzdes::enz_score

extern

Referenced by main().

enzdes

BooleanOptionKey const basic::options::OptionKeys::enzdes::enzdes

extern

ex_catalytic_rot

IntegerOptionKey const basic::options::OptionKeys::enzdes::ex_catalytic_rot

extern

favor_native_res

RealOptionKey const basic::options::OptionKeys::enzdes::favor_native_res

extern

Referenced by setup_favor_native(), and HDdesignMover::task_constraint_setup().

final_repack_without_ligand

BooleanOptionKey const basic::options::OptionKeys::enzdes::final_repack_without_ligand

extern

Referenced by main().

fix_catalytic_aa

BooleanOptionKey const basic::options::OptionKeys::enzdes::fix_catalytic_aa

extern

flexbb_protocol

BooleanOptionKey const basic::options::OptionKeys::enzdes::flexbb_protocol

extern

Referenced by main().

include_catres_in_interface_detection

BooleanOptionKey const basic::options::OptionKeys::enzdes::include_catres_in_interface_detection

extern

kic_loop_sampling

BooleanOptionKey const basic::options::OptionKeys::enzdes::kic_loop_sampling

extern

lig_packer_weight

RealOptionKey const basic::options::OptionKeys::enzdes::lig_packer_weight

extern

loop_bb_min_allowed_dev

RealOptionKey const basic::options::OptionKeys::enzdes::loop_bb_min_allowed_dev

extern

loop_generator_trials

IntegerOptionKey const basic::options::OptionKeys::enzdes::loop_generator_trials

extern

make_consensus_mutations

BooleanOptionKey const basic::options::OptionKeys::enzdes::make_consensus_mutations

extern

max_bb_deviation

RealOptionKey const basic::options::OptionKeys::enzdes::max_bb_deviation

extern

max_bb_deviation_from_startstruct

RealOptionKey const basic::options::OptionKeys::enzdes::max_bb_deviation_from_startstruct

extern

mc_kt_high

RealOptionKey const basic::options::OptionKeys::enzdes::mc_kt_high

extern

mc_kt_low

RealOptionKey const basic::options::OptionKeys::enzdes::mc_kt_low

extern

min_all_jumps

BooleanOptionKey const basic::options::OptionKeys::enzdes::min_all_jumps

extern

min_cacb_deviation

RealOptionKey const basic::options::OptionKeys::enzdes::min_cacb_deviation

extern

minimize_all_ligand_torsions

RealOptionKey const basic::options::OptionKeys::enzdes::minimize_all_ligand_torsions

extern

minimize_ligand_torsions

RealOptionKey const basic::options::OptionKeys::enzdes::minimize_ligand_torsions

extern

no_catres_min_in_loopgen

BooleanOptionKey const basic::options::OptionKeys::enzdes::no_catres_min_in_loopgen

extern

no_packstat_calculation

BooleanOptionKey const basic::options::OptionKeys::enzdes::no_packstat_calculation

extern

no_unconstrained_repack

BooleanOptionKey const basic::options::OptionKeys::enzdes::no_unconstrained_repack

extern

parser_read_cloud_pdb

BooleanOptionKey const basic::options::OptionKeys::enzdes::parser_read_cloud_pdb

extern

process_ligrot_separately

StringOptionKey const basic::options::OptionKeys::enzdes::process_ligrot_separately

extern

Referenced by main().

remodel_aggressiveness

RealOptionKey const basic::options::OptionKeys::enzdes::remodel_aggressiveness

extern

remodel_protocol

BooleanOptionKey const basic::options::OptionKeys::enzdes::remodel_protocol

extern

Referenced by main().

remodel_secmatch

BooleanOptionKey const basic::options::OptionKeys::enzdes::remodel_secmatch

extern

remodel_trials

IntegerOptionKey const basic::options::OptionKeys::enzdes::remodel_trials

extern

rot_magnitude

RealOptionKey const basic::options::OptionKeys::enzdes::rot_magnitude

extern

run_ligand_motifs

BooleanOptionKey const basic::options::OptionKeys::enzdes::run_ligand_motifs

extern

sc_sc_bump_cutoff

RealOptionKey const basic::options::OptionKeys::enzdes::sc_sc_bump_cutoff

extern

secmatch_Ecutoff

RealOptionKey const basic::options::OptionKeys::enzdes::secmatch_Ecutoff

extern

single_loop_ensemble_size

IntegerOptionKey const basic::options::OptionKeys::enzdes::single_loop_ensemble_size

extern

start_from_random_rb_conf

BooleanOptionKey const basic::options::OptionKeys::enzdes::start_from_random_rb_conf

extern

trans_magnitude

RealOptionKey const basic::options::OptionKeys::enzdes::trans_magnitude

extern

Referenced by PhDocking::calc_energies(), abbinding::calc_energies_and_sasa(), and calculateInterfaceScore().