jumps Namespace Reference

Functions
BooleanOptionKey const	jumps ("jumps")
BooleanOptionKey const	evaluate ("jumps:evaluate")
FileOptionKey const	extra_frags_for_ss ("jumps:extra_frags_for_ss")
BooleanOptionKey const	fix_chainbreak ("jumps:fix_chainbreak")
FileOptionKey const	fix_jumps ("jumps:fix_jumps")
FileOptionKey const	jump_lib ("jumps:jump_lib")
FileOptionKey const	loop_definition_from_file ("jumps:loop_definition_from_file")
BooleanOptionKey const	no_chainbreak_in_relax ("jumps:no_chainbreak_in_relax")
FileOptionKey const	pairing_file ("jumps:pairing_file")
IntegerVectorOptionKey const	random_sheets ("jumps:random_sheets")
FileOptionKey const	residue_pair_jump_file ("jumps:residue_pair_jump_file")
IntegerVectorOptionKey const	sheets ("jumps:sheets")
FileOptionKey const	topology_file ("jumps:topology_file")
BooleanOptionKey const	bb_moves ("jumps:bb_moves")
BooleanOptionKey const	no_wobble ("jumps:no_wobble")
BooleanOptionKey const	no_shear ("jumps:no_shear")
BooleanOptionKey const	no_sample_ss_jumps ("jumps:no_sample_ss_jumps")
IntegerOptionKey const	invrate_jump_move ("jumps:invrate_jump_move")
RealOptionKey const	chainbreak_weight_stage1 ("jumps:chainbreak_weight_stage1")
RealOptionKey const	chainbreak_weight_stage2 ("jumps:chainbreak_weight_stage2")
RealOptionKey const	chainbreak_weight_stage3 ("jumps:chainbreak_weight_stage3")
RealOptionKey const	chainbreak_weight_stage4 ("jumps:chainbreak_weight_stage4")
BooleanOptionKey const	ramp_chainbreaks ("jumps:ramp_chainbreaks")
RealOptionKey const	increase_chainbreak ("jumps:increase_chainbreak")
BooleanOptionKey const	overlap_chainbreak ("jumps:overlap_chainbreak")
RealOptionKey const	sep_switch_accelerate ("jumps:sep_switch_accelerate")
BooleanOptionKey const	dump_frags ("jumps:dump_frags")
IntegerOptionKey const	njumps ("jumps:njumps")
IntegerOptionKey const	max_strand_gap_allowed ("jumps:max_strand_gap_allowed")
RealOptionKey const	contact_score ("jumps:contact_score")
BooleanOptionKey const	filter_templates ("jumps:filter_templates")

Function Documentation

bb_moves()

BooleanOptionKey const jumps::bb_moves

(

"jumps:bb_moves"

)

chainbreak_weight_stage1()

RealOptionKey const jumps::chainbreak_weight_stage1

(

"jumps:chainbreak_weight_stage1"

)

chainbreak_weight_stage2()

RealOptionKey const jumps::chainbreak_weight_stage2

(

"jumps:chainbreak_weight_stage2"

)

chainbreak_weight_stage3()

RealOptionKey const jumps::chainbreak_weight_stage3

(

"jumps:chainbreak_weight_stage3"

)

chainbreak_weight_stage4()

RealOptionKey const jumps::chainbreak_weight_stage4

(

"jumps:chainbreak_weight_stage4"

)

contact_score()

RealOptionKey const jumps::contact_score

(

"jumps:contact_score"

)

dump_frags()

BooleanOptionKey const jumps::dump_frags

(

"jumps:dump_frags"

)

evaluate()

BooleanOptionKey const jumps::evaluate

(

"jumps:evaluate"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::process_decoy(), and protocols::abinitio::JumpSpecificAbrelax::register_options().

extra_frags_for_ss()

FileOptionKey const jumps::extra_frags_for_ss

(

"jumps:extra_frags_for_ss"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_jumps().

filter_templates()

BooleanOptionKey const jumps::filter_templates

(

"jumps:filter_templates"

)

fix_chainbreak()

BooleanOptionKey const jumps::fix_chainbreak

(

"jumps:fix_chainbreak"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options().

fix_jumps()

FileOptionKey const jumps::fix_jumps

(

"jumps:fix_jumps"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_jumps().

increase_chainbreak()

RealOptionKey const jumps::increase_chainbreak

(

"jumps:increase_chainbreak"

)

invrate_jump_move()

IntegerOptionKey const jumps::invrate_jump_move

(

"jumps:invrate_jump_move"

)

jump_lib()

FileOptionKey const jumps::jump_lib

(

"jumps:jump_lib"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_jumps().

jumps()

BooleanOptionKey const jumps::jumps

(

"jumps"

)

loop_definition_from_file()

FileOptionKey const jumps::loop_definition_from_file

(

"jumps:loop_definition_from_file"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_jumps().

max_strand_gap_allowed()

IntegerOptionKey const jumps::max_strand_gap_allowed

(

"jumps:max_strand_gap_allowed"

)

njumps()

IntegerOptionKey const jumps::njumps

(

"jumps:njumps"

)

no_chainbreak_in_relax()

BooleanOptionKey const jumps::no_chainbreak_in_relax

(

"jumps:no_chainbreak_in_relax"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), and protocols::abinitio::JumpSpecificAbrelax::register_options().

no_sample_ss_jumps()

BooleanOptionKey const jumps::no_sample_ss_jumps

(

"jumps:no_sample_ss_jumps"

)

no_shear()

BooleanOptionKey const jumps::no_shear

(

"jumps:no_shear"

)

no_wobble()

BooleanOptionKey const jumps::no_wobble

(

"jumps:no_wobble"

)

overlap_chainbreak()

BooleanOptionKey const jumps::overlap_chainbreak

(

"jumps:overlap_chainbreak"

)

pairing_file()

FileOptionKey const jumps::pairing_file

(

"jumps:pairing_file"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_jumps().

ramp_chainbreaks()

BooleanOptionKey const jumps::ramp_chainbreaks

(

"jumps:ramp_chainbreaks"

)

random_sheets()

IntegerVectorOptionKey const jumps::random_sheets

(

"jumps:random_sheets"

)

residue_pair_jump_file()

FileOptionKey const jumps::residue_pair_jump_file

(

"jumps:residue_pair_jump_file"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_jumps().

sep_switch_accelerate()

RealOptionKey const jumps::sep_switch_accelerate

(

"jumps:sep_switch_accelerate"

)

sheets()

IntegerVectorOptionKey const jumps::sheets

(

"jumps:sheets"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_jumps().

topology_file()

FileOptionKey const jumps::topology_file

(

"jumps:topology_file"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::add_constraints(), protocols::abinitio::JumpSpecificAbrelax::register_options(), and protocols::abinitio::JumpSpecificAbrelax::setup_jumps().