packing Namespace Reference

Namespaces
	ex1
	ex1aro
	ex1aro_exposed
	ex2
	ex2aro
	ex2aro_exposed
	ex3
	ex4
	exdna
	packer_palette

Functions
BooleanOptionKey const	packing ("packing")
BooleanOptionKey const	repack_only ("packing:repack_only")
BooleanOptionKey const	prevent_repacking ("packing:prevent_repacking")
RealOptionKey const	cenrot_cutoff ("packing:cenrot_cutoff")
BooleanOptionKey const	ignore_ligand_chi ("packing:ignore_ligand_chi")
BooleanOptionKey const	quasisymmetry ("packing:quasisymmetry")
IntegerOptionKey const	ndruns ("packing:ndruns")
BooleanOptionKey const	soft_rep_design ("packing:soft_rep_design")
RealOptionKey const	mainchain_h_rebuild_threshold ("packing:mainchain_h_rebuild_threshold")
BooleanOptionKey const	use_electrostatic_repulsion ("packing:use_electrostatic_repulsion")
BooleanOptionKey const	dump_rotamer_sets ("packing:dump_rotamer_sets")
RealOptionKey const	dunbrack_prob_buried ("packing:dunbrack_prob_buried")
RealOptionKey const	dunbrack_prob_nonburied ("packing:dunbrack_prob_nonburied")
RealOptionKey const	dunbrack_prob_buried_semi ("packing:dunbrack_prob_buried_semi")
RealOptionKey const	dunbrack_prob_nonburied_semi ("packing:dunbrack_prob_nonburied_semi")
BooleanOptionKey const	no_optH ("packing:no_optH")
BooleanOptionKey const	optH_MCA ("packing:optH_MCA")
BooleanOptionKey const	pack_missing_sidechains ("packing:pack_missing_sidechains")
BooleanOptionKey const	preserve_c_beta ("packing:preserve_c_beta")
BooleanOptionKey const	flip_HNQ ("packing:flip_HNQ")
IntegerVectorOptionKey const	fix_his_tautomer ("packing:fix_his_tautomer")
BooleanOptionKey const	print_pymol_selection ("packing:print_pymol_selection")
IntegerOptionKey const	extrachi_cutoff ("packing:extrachi_cutoff")
FileVectorOptionKey const	resfile ("packing:resfile")
BooleanOptionKey const	sc_branch_rotamers ("packing:sc_branch_rotamers")
RealOptionKey const	outeriterations_scaling ("packing:outeriterations_scaling")
RealOptionKey const	inneriterations_scaling ("packing:inneriterations_scaling")
StringVectorOptionKey const	adducts ("packing:adducts")
BooleanOptionKey const	use_input_sc ("packing:use_input_sc")
FileVectorOptionKey const	unboundrot ("packing:unboundrot")
RealOptionKey const	max_rotbump_energy ("packing:max_rotbump_energy")
BooleanOptionKey const	lazy_ig ("packing:lazy_ig")
BooleanOptionKey const	double_lazy_ig ("packing:double_lazy_ig")
IntegerOptionKey const	linmem_ig ("packing:linmem_ig")
BooleanOptionKey const	precompute_ig ("packing:precompute_ig")
IntegerOptionKey const	multi_cool_annealer ("packing:multi_cool_annealer")
BooleanOptionKey const	sequence_symmetric_annealer ("packing:sequence_symmetric_annealer")
BooleanOptionKey const	smart_annealer ("packing:smart_annealer")
StringOptionKey const	smart_annealer_model ("packing:smart_annealer_model")
RealOptionKey const	smart_annealer_cutoff ("packing:smart_annealer_cutoff")
BooleanOptionKey const	smart_annealer_pick_again ("packing:smart_annealer_pick_again")
BooleanOptionKey const	smart_annealer_disable_during_quench ("packing:smart_annealer_disable_during_quench")
RealVectorOptionKey const	minpack_temp_schedule ("packing:minpack_temp_schedule")
IntegerOptionKey const	minpack_inner_iteration_scale ("packing:minpack_inner_iteration_scale")
BooleanOptionKey const	minpack_disable_bumpcheck ("packing:minpack_disable_bumpcheck")

Function Documentation

adducts()

StringVectorOptionKey const packing::adducts

(

"packing:adducts"

)

cenrot_cutoff()

RealOptionKey const packing::cenrot_cutoff

(

"packing:cenrot_cutoff"

)

double_lazy_ig()

BooleanOptionKey const packing::double_lazy_ig

(

"packing:double_lazy_ig"

)

dump_rotamer_sets()

BooleanOptionKey const packing::dump_rotamer_sets

(

"packing:dump_rotamer_sets"

)

dunbrack_prob_buried()

RealOptionKey const packing::dunbrack_prob_buried

(

"packing:dunbrack_prob_buried"

)

dunbrack_prob_buried_semi()

RealOptionKey const packing::dunbrack_prob_buried_semi

(

"packing:dunbrack_prob_buried_semi"

)

dunbrack_prob_nonburied()

RealOptionKey const packing::dunbrack_prob_nonburied

(

"packing:dunbrack_prob_nonburied"

)

dunbrack_prob_nonburied_semi()

RealOptionKey const packing::dunbrack_prob_nonburied_semi

(

"packing:dunbrack_prob_nonburied_semi"

)

extrachi_cutoff()

IntegerOptionKey const packing::extrachi_cutoff

(

"packing:extrachi_cutoff"

)

Referenced by main().

fix_his_tautomer()

IntegerVectorOptionKey const packing::fix_his_tautomer

(

"packing:fix_his_tautomer"

)

flip_HNQ()

BooleanOptionKey const packing::flip_HNQ

(

"packing:flip_HNQ"

)

Referenced by main().

ignore_ligand_chi()

BooleanOptionKey const packing::ignore_ligand_chi

(

"packing:ignore_ligand_chi"

)

inneriterations_scaling()

RealOptionKey const packing::inneriterations_scaling

(

"packing:inneriterations_scaling"

)

lazy_ig()

BooleanOptionKey const packing::lazy_ig

(

"packing:lazy_ig"

)

linmem_ig()

IntegerOptionKey const packing::linmem_ig

(

"packing:linmem_ig"

)

mainchain_h_rebuild_threshold()

RealOptionKey const packing::mainchain_h_rebuild_threshold

(

"packing:mainchain_h_rebuild_threshold"

)

max_rotbump_energy()

RealOptionKey const packing::max_rotbump_energy

(

"packing:max_rotbump_energy"

)

minpack_disable_bumpcheck()

BooleanOptionKey const packing::minpack_disable_bumpcheck

(

"packing:minpack_disable_bumpcheck"

)

minpack_inner_iteration_scale()

IntegerOptionKey const packing::minpack_inner_iteration_scale

(

"packing:minpack_inner_iteration_scale"

)

minpack_temp_schedule()

RealVectorOptionKey const packing::minpack_temp_schedule

(

"packing:minpack_temp_schedule"

)

multi_cool_annealer()

IntegerOptionKey const packing::multi_cool_annealer

(

"packing:multi_cool_annealer"

)

ndruns()

IntegerOptionKey const packing::ndruns

(

"packing:ndruns"

)

Referenced by main().

no_optH()

BooleanOptionKey const packing::no_optH

(

"packing:no_optH"

)

Referenced by main().

optH_MCA()

BooleanOptionKey const packing::optH_MCA

(

"packing:optH_MCA"

)

outeriterations_scaling()

RealOptionKey const packing::outeriterations_scaling

(

"packing:outeriterations_scaling"

)

pack_missing_sidechains()

BooleanOptionKey const packing::pack_missing_sidechains

(

"packing:pack_missing_sidechains"

)

packing()

BooleanOptionKey const packing::packing

(

"packing"

)

precompute_ig()

BooleanOptionKey const packing::precompute_ig

(

"packing:precompute_ig"

)

preserve_c_beta()

BooleanOptionKey const packing::preserve_c_beta

(

"packing:preserve_c_beta"

)

prevent_repacking()

BooleanOptionKey const packing::prevent_repacking

(

"packing:prevent_repacking"

)

print_pymol_selection()

BooleanOptionKey const packing::print_pymol_selection

(

"packing:print_pymol_selection"

)

quasisymmetry()

BooleanOptionKey const packing::quasisymmetry

(

"packing:quasisymmetry"

)

repack_only()

BooleanOptionKey const packing::repack_only

(

"packing:repack_only"

)

resfile()

FileVectorOptionKey const packing::resfile

(

"packing:resfile"

)

Referenced by LDConverterMover::apply(), byres_analysis(), CrystDesign::design_cycle(), protocols::jd2::RECONMPIJobDistributor::go_hardcoded(), FloppyTailMover::init_on_new_input(), main(), my_main(), A3BHbsCreatorMover::repack(), RotamerAnalysis(), sequence_tolerance_main(), sequence_tolerance_mf_main(), HECTMover::set_up_taskfactory(), and SymFixbbMover::SymFixbbMover().

sc_branch_rotamers()

BooleanOptionKey const packing::sc_branch_rotamers

(

"packing:sc_branch_rotamers"

)

sequence_symmetric_annealer()

BooleanOptionKey const packing::sequence_symmetric_annealer

(

"packing:sequence_symmetric_annealer"

)

smart_annealer()

BooleanOptionKey const packing::smart_annealer

(

"packing:smart_annealer"

)

smart_annealer_cutoff()

RealOptionKey const packing::smart_annealer_cutoff

(

"packing:smart_annealer_cutoff"

)

smart_annealer_disable_during_quench()

BooleanOptionKey const packing::smart_annealer_disable_during_quench

(

"packing:smart_annealer_disable_during_quench"

)

smart_annealer_model()

StringOptionKey const packing::smart_annealer_model

(

"packing:smart_annealer_model"

)

smart_annealer_pick_again()

BooleanOptionKey const packing::smart_annealer_pick_again

(

"packing:smart_annealer_pick_again"

)

soft_rep_design()

BooleanOptionKey const packing::soft_rep_design

(

"packing:soft_rep_design"

)

unboundrot()

FileVectorOptionKey const packing::unboundrot

(

"packing:unboundrot"

)

Referenced by main().

use_electrostatic_repulsion()

BooleanOptionKey const packing::use_electrostatic_repulsion

(

"packing:use_electrostatic_repulsion"

)

use_input_sc()

BooleanOptionKey const packing::use_input_sc

(

"packing:use_input_sc"

)