relax Namespace Reference

Namespaces
	centroid
	range

Functions
BooleanOptionKey const	relax ("relax")
BooleanOptionKey const	fast ("relax:fast")
BooleanOptionKey const	thorough ("relax:thorough")
BooleanOptionKey const	centroid_mode ("relax:centroid_mode")
IntegerOptionKey const	default_repeats ("relax:default_repeats")
BooleanOptionKey const	dualspace ("relax:dualspace")
BooleanOptionKey const	cyclic_peptide ("relax:cyclic_peptide")
BooleanOptionKey const	ramady ("relax:ramady")
RealOptionKey const	ramady_rms_limit ("relax:ramady_rms_limit")
RealOptionKey const	ramady_cutoff ("relax:ramady_cutoff")
IntegerOptionKey const	ramady_max_rebuild ("relax:ramady_max_rebuild")
BooleanOptionKey const	ramady_force ("relax:ramady_force")
FileOptionKey const	script ("relax:script")
IntegerOptionKey const	script_max_accept ("relax:script_max_accept")
BooleanOptionKey const	superimpose_to_native ("relax:superimpose_to_native")
FileOptionKey const	superimpose_to_file ("relax:superimpose_to_file")
BooleanOptionKey const	constrain_relax_to_native_coords ("relax:constrain_relax_to_native_coords")
BooleanOptionKey const	constrain_relax_to_start_coords ("relax:constrain_relax_to_start_coords")
BooleanOptionKey const	coord_constrain_sidechains ("relax:coord_constrain_sidechains")
RealOptionKey const	sc_cst_maxdist ("relax:sc_cst_maxdist")
BooleanOptionKey const	limit_aroma_chi2 ("relax:limit_aroma_chi2")
BooleanOptionKey const	respect_resfile ("relax:respect_resfile")
BooleanOptionKey const	use_explicit_water ("relax:use_explicit_water")
BooleanOptionKey const	movemap_disables_packing_of_fixed_chi_positions ("relax:movemap_disables_packing_of_fixed_chi_positions")
BooleanOptionKey const	bb_move ("relax:bb_move")
BooleanOptionKey const	chi_move ("relax:chi_move")
BooleanOptionKey const	jump_move ("relax:jump_move")
BooleanOptionKey const	dna_move ("relax:dna_move")
BooleanOptionKey const	fix_omega ("relax:fix_omega")
BooleanOptionKey const	minimize_bond_lengths ("relax:minimize_bond_lengths")
BooleanOptionKey const	minimize_bond_angles ("relax:minimize_bond_angles")
IntegerOptionKey const	minimize_bondlength_subset ("relax:minimize_bondlength_subset")
IntegerOptionKey const	minimize_bondangle_subset ("relax:minimize_bondangle_subset")
StringOptionKey const	min_type ("relax:min_type")
BooleanOptionKey const	cartesian ("relax:cartesian")
RealOptionKey const	chainbreak_weight ("relax:chainbreak_weight")
RealOptionKey const	linear_chainbreak_weight ("relax:linear_chainbreak_weight")
RealOptionKey const	overlap_chainbreak_weight ("relax:overlap_chainbreak_weight")
BooleanOptionKey const	classic ("relax:classic")
FileOptionKey const	sequence_file ("relax:sequence_file")
BooleanOptionKey const	quick ("relax:quick")
BooleanOptionKey const	sequence ("relax:sequence")
IntegerOptionKey const	minirelax_repeats ("relax:minirelax_repeats")
RealOptionKey const	minirelax_sdev ("relax:minirelax_sdev")
BooleanOptionKey const	wobblemoves ("relax:wobblemoves")
FileOptionKey const	constrain_relax_segments ("relax:constrain_relax_segments")
RealOptionKey const	coord_cst_width ("relax:coord_cst_width")
RealOptionKey const	coord_cst_stdev ("relax:coord_cst_stdev")
BooleanOptionKey const	ramp_constraints ("relax:ramp_constraints")
RealOptionKey const	energycut ("relax:energycut")
BooleanOptionKey const	mini ("relax:mini")
IntegerOptionKey const	stage1_ramp_cycles ("relax:stage1_ramp_cycles")
IntegerOptionKey const	stage1_ramp_inner_cycles ("relax:stage1_ramp_inner_cycles")
IntegerOptionKey const	stage2_repack_period ("relax:stage2_repack_period")
IntegerOptionKey const	stage2_cycles ("relax:stage2_cycles")
RealOptionKey const	min_tolerance ("relax:min_tolerance")
IntegerOptionKey const	stage3_cycles ("relax:stage3_cycles")
RealOptionKey const	cycle_ratio ("relax:cycle_ratio")
RealOptionKey const	filter_stage2_beginning ("relax:filter_stage2_beginning")
RealOptionKey const	filter_stage2_quarter ("relax:filter_stage2_quarter")
RealOptionKey const	filter_stage2_half ("relax:filter_stage2_half")
RealOptionKey const	filter_stage2_end ("relax:filter_stage2_end")

Function Documentation

bb_move()

BooleanOptionKey const relax::bb_move

(

"relax:bb_move"

)

cartesian()

BooleanOptionKey const relax::cartesian

(

"relax:cartesian"

)

centroid_mode()

BooleanOptionKey const relax::centroid_mode

(

"relax:centroid_mode"

)

chainbreak_weight()

RealOptionKey const relax::chainbreak_weight

(

"relax:chainbreak_weight"

)

chi_move()

BooleanOptionKey const relax::chi_move

(

"relax:chi_move"

)

classic()

BooleanOptionKey const relax::classic

(

"relax:classic"

)

constrain_relax_segments()

FileOptionKey const relax::constrain_relax_segments

(

"relax:constrain_relax_segments"

)

constrain_relax_to_native_coords()

BooleanOptionKey const relax::constrain_relax_to_native_coords

(

"relax:constrain_relax_to_native_coords"

)

constrain_relax_to_start_coords()

BooleanOptionKey const relax::constrain_relax_to_start_coords

(

"relax:constrain_relax_to_start_coords"

)

coord_constrain_sidechains()

BooleanOptionKey const relax::coord_constrain_sidechains

(

"relax:coord_constrain_sidechains"

)

coord_cst_stdev()

RealOptionKey const relax::coord_cst_stdev

(

"relax:coord_cst_stdev"

)

coord_cst_width()

RealOptionKey const relax::coord_cst_width

(

"relax:coord_cst_width"

)

cycle_ratio()

RealOptionKey const relax::cycle_ratio

(

"relax:cycle_ratio"

)

cyclic_peptide()

BooleanOptionKey const relax::cyclic_peptide

(

"relax:cyclic_peptide"

)

default_repeats()

IntegerOptionKey const relax::default_repeats

(

"relax:default_repeats"

)

Referenced by CenRelaxMover::apply(), CenRotRelaxMover::apply(), and CenRotRBRelaxMover::apply().

dna_move()

BooleanOptionKey const relax::dna_move

(

"relax:dna_move"

)

dualspace()

BooleanOptionKey const relax::dualspace

(

"relax:dualspace"

)

energycut()

RealOptionKey const relax::energycut

(

"relax:energycut"

)

fast()

BooleanOptionKey const relax::fast

(

"relax:fast"

)

Referenced by main(), and register_options().

filter_stage2_beginning()

RealOptionKey const relax::filter_stage2_beginning

(

"relax:filter_stage2_beginning"

)

filter_stage2_end()

RealOptionKey const relax::filter_stage2_end

(

"relax:filter_stage2_end"

)

filter_stage2_half()

RealOptionKey const relax::filter_stage2_half

(

"relax:filter_stage2_half"

)

filter_stage2_quarter()

RealOptionKey const relax::filter_stage2_quarter

(

"relax:filter_stage2_quarter"

)

fix_omega()

BooleanOptionKey const relax::fix_omega

(

"relax:fix_omega"

)

jump_move()

BooleanOptionKey const relax::jump_move

(

"relax:jump_move"

)

limit_aroma_chi2()

BooleanOptionKey const relax::limit_aroma_chi2

(

"relax:limit_aroma_chi2"

)

linear_chainbreak_weight()

RealOptionKey const relax::linear_chainbreak_weight

(

"relax:linear_chainbreak_weight"

)

min_tolerance()

RealOptionKey const relax::min_tolerance

(

"relax:min_tolerance"

)

min_type()

StringOptionKey const relax::min_type

(

"relax:min_type"

)

mini()

BooleanOptionKey const relax::mini

(

"relax:mini"

)

minimize_bond_angles()

BooleanOptionKey const relax::minimize_bond_angles

(

"relax:minimize_bond_angles"

)

minimize_bond_lengths()

BooleanOptionKey const relax::minimize_bond_lengths

(

"relax:minimize_bond_lengths"

)

minimize_bondangle_subset()

IntegerOptionKey const relax::minimize_bondangle_subset

(

"relax:minimize_bondangle_subset"

)

minimize_bondlength_subset()

IntegerOptionKey const relax::minimize_bondlength_subset

(

"relax:minimize_bondlength_subset"

)

minirelax_repeats()

IntegerOptionKey const relax::minirelax_repeats

(

"relax:minirelax_repeats"

)

minirelax_sdev()

RealOptionKey const relax::minirelax_sdev

(

"relax:minirelax_sdev"

)

movemap_disables_packing_of_fixed_chi_positions()

BooleanOptionKey const relax::movemap_disables_packing_of_fixed_chi_positions

(

"relax:movemap_disables_packing_of_fixed_chi_positions"

)

overlap_chainbreak_weight()

RealOptionKey const relax::overlap_chainbreak_weight

(

"relax:overlap_chainbreak_weight"

)

quick()

BooleanOptionKey const relax::quick

(

"relax:quick"

)

ramady()

BooleanOptionKey const relax::ramady

(

"relax:ramady"

)

ramady_cutoff()

RealOptionKey const relax::ramady_cutoff

(

"relax:ramady_cutoff"

)

ramady_force()

BooleanOptionKey const relax::ramady_force

(

"relax:ramady_force"

)

ramady_max_rebuild()

IntegerOptionKey const relax::ramady_max_rebuild

(

"relax:ramady_max_rebuild"

)

ramady_rms_limit()

RealOptionKey const relax::ramady_rms_limit

(

"relax:ramady_rms_limit"

)

ramp_constraints()

BooleanOptionKey const relax::ramp_constraints

(

"relax:ramp_constraints"

)

relax()

BooleanOptionKey const relax::relax

(

"relax"

)

respect_resfile()

BooleanOptionKey const relax::respect_resfile

(

"relax:respect_resfile"

)

sc_cst_maxdist()

RealOptionKey const relax::sc_cst_maxdist

(

"relax:sc_cst_maxdist"

)

script()

FileOptionKey const relax::script

(

"relax:script"

)

script_max_accept()

IntegerOptionKey const relax::script_max_accept

(

"relax:script_max_accept"

)

sequence()

BooleanOptionKey const relax::sequence

(

"relax:sequence"

)

sequence_file()

FileOptionKey const relax::sequence_file

(

"relax:sequence_file"

)

stage1_ramp_cycles()

IntegerOptionKey const relax::stage1_ramp_cycles

(

"relax:stage1_ramp_cycles"

)

stage1_ramp_inner_cycles()

IntegerOptionKey const relax::stage1_ramp_inner_cycles

(

"relax:stage1_ramp_inner_cycles"

)

stage2_cycles()

IntegerOptionKey const relax::stage2_cycles

(

"relax:stage2_cycles"

)

stage2_repack_period()

IntegerOptionKey const relax::stage2_repack_period

(

"relax:stage2_repack_period"

)

stage3_cycles()

IntegerOptionKey const relax::stage3_cycles

(

"relax:stage3_cycles"

)

superimpose_to_file()

FileOptionKey const relax::superimpose_to_file

(

"relax:superimpose_to_file"

)

Referenced by RelaxJobQueen::RelaxJobQueen().

superimpose_to_native()

BooleanOptionKey const relax::superimpose_to_native

(

"relax:superimpose_to_native"

)

Referenced by RelaxJobQueen::RelaxJobQueen().

thorough()

BooleanOptionKey const relax::thorough

(

"relax:thorough"

)

use_explicit_water()

BooleanOptionKey const relax::use_explicit_water

(

"relax:use_explicit_water"

)

wobblemoves()

BooleanOptionKey const relax::wobblemoves

(

"relax:wobblemoves"

)