abinitio Namespace Reference

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Functions
BooleanOptionKey const	abinitio ("abinitio")
BooleanOptionKey const	membrane ("abinitio:membrane")
BooleanOptionKey const	use_loophash_filter ("abinitio:use_loophash_filter")
RealOptionKey const	loophash_filter_acceptance_rate ("abinitio:loophash_filter_acceptance_rate")
FileOptionKey const	kill_hairpins ("abinitio:kill_hairpins")
RealOptionKey const	kill_hairpins_frequency ("abinitio:kill_hairpins_frequency")
BooleanOptionKey const	smooth_cycles_only ("abinitio:smooth_cycles_only")
BooleanOptionKey const	relax ("abinitio:relax")
BooleanOptionKey const	final_clean_relax ("abinitio:final_clean_relax")
BooleanOptionKey const	fastrelax ("abinitio:fastrelax")
BooleanOptionKey const	multifastrelax ("abinitio:multifastrelax")
BooleanOptionKey const	debug ("abinitio:debug")
BooleanOptionKey const	clear_pose_cache ("abinitio:clear_pose_cache")
BooleanOptionKey const	explicit_pdb_debug ("abinitio:explicit_pdb_debug")
BooleanOptionKey const	use_filters ("abinitio:use_filters")
RealOptionKey const	increase_cycles ("abinitio:increase_cycles")
IntegerOptionKey const	number_3mer_frags ("abinitio:number_3mer_frags")
IntegerOptionKey const	number_9mer_frags ("abinitio:number_9mer_frags")
RealOptionKey const	temperature ("abinitio:temperature")
RealOptionKey const	rg_reweight ("abinitio:rg_reweight")
RealOptionKey const	rsd_wt_helix ("abinitio:rsd_wt_helix")
RealOptionKey const	rsd_wt_strand ("abinitio:rsd_wt_strand")
RealOptionKey const	rsd_wt_loop ("abinitio:rsd_wt_loop")
BooleanOptionKey const	skip_convergence_check ("abinitio:skip_convergence_check")
FileVectorOptionKey const	stage1_patch ("abinitio:stage1_patch")
FileVectorOptionKey const	stage2_patch ("abinitio:stage2_patch")
FileVectorOptionKey const	stage3a_patch ("abinitio:stage3a_patch")
FileVectorOptionKey const	stage3b_patch ("abinitio:stage3b_patch")
FileVectorOptionKey const	stage4_patch ("abinitio:stage4_patch")
FileVectorOptionKey const	stage5_patch ("abinitio:stage5_patch")
BooleanOptionKey const	steal_3mers ("abinitio:steal_3mers")
BooleanOptionKey const	steal_9mers ("abinitio:steal_9mers")
BooleanOptionKey const	no_write_failures ("abinitio:no_write_failures")
BooleanOptionKey const	relax_failures ("abinitio:relax_failures")
BooleanOptionKey const	relax_with_jumps ("abinitio:relax_with_jumps")
BooleanOptionKey const	process_store ("abinitio:process_store")
IntegerVectorOptionKey const	fix_residues_to_native ("abinitio:fix_residues_to_native")
BooleanOptionKey const	return_full_atom ("abinitio:return_full_atom")
BooleanOptionKey const	detect_disulfide_before_relax ("abinitio:detect_disulfide_before_relax")
BooleanOptionKey const	close_loops ("abinitio:close_loops")
BooleanOptionKey const	bGDT ("abinitio:bGDT")
BooleanOptionKey const	dump_frags ("abinitio:dump_frags")
BooleanOptionKey const	jdist_rerun ("abinitio:jdist_rerun")
RealOptionKey const	perturb ("abinitio:perturb")
BooleanOptionKey const	rerun ("abinitio:rerun")
IntegerVectorOptionKey const	rmsd_residues ("abinitio:rmsd_residues")
BooleanOptionKey const	start_native ("abinitio:start_native")
BooleanOptionKey const	cyclic_peptide ("abinitio:cyclic_peptide")
BooleanOptionKey const	debug_structures ("abinitio:debug_structures")
FileOptionKey const	log_frags ("abinitio:log_frags")
BooleanOptionKey const	only_stage1 ("abinitio:only_stage1")
RealOptionKey const	end_bias ("abinitio:end_bias")
BooleanOptionKey const	apply_end_bias ("abinitio:apply_end_bias")
IntegerOptionKey const	symmetry_residue ("abinitio:symmetry_residue")
RealOptionKey const	vdw_weight_stage1 ("abinitio:vdw_weight_stage1")
BooleanOptionKey const	override_vdw_all_stages ("abinitio:override_vdw_all_stages")
IntegerVectorOptionKey const	recover_low_in_stages ("abinitio:recover_low_in_stages")
IntegerVectorOptionKey const	skip_stages ("abinitio:skip_stages")
BooleanOptionKey const	close_chbrk ("abinitio:close_chbrk")
BooleanOptionKey const	include_stage5 ("abinitio:include_stage5")
BooleanOptionKey const	close_loops_by_idealizing ("abinitio:close_loops_by_idealizing")
BooleanOptionKey const	optimize_cutpoints_using_kic ("abinitio:optimize_cutpoints_using_kic")
IntegerOptionKey const	optimize_cutpoints_margin ("abinitio:optimize_cutpoints_margin")

Function Documentation

BooleanOptionKey const abinitio::abinitio

(

"abinitio"

)

BooleanOptionKey const abinitio::apply_end_bias

(

"abinitio:apply_end_bias"

)

BooleanOptionKey const abinitio::bGDT

(

"abinitio:bGDT"

)

BooleanOptionKey const abinitio::clear_pose_cache

(

"abinitio:clear_pose_cache"

)

BooleanOptionKey const abinitio::close_chbrk

(

"abinitio:close_chbrk"

)

BooleanOptionKey const abinitio::close_loops

(

"abinitio:close_loops"

)

BooleanOptionKey const abinitio::close_loops_by_idealizing

(

"abinitio:close_loops_by_idealizing"

)

BooleanOptionKey const abinitio::cyclic_peptide

(

"abinitio:cyclic_peptide"

)

BooleanOptionKey const abinitio::debug

(

"abinitio:debug"

)

BooleanOptionKey const abinitio::debug_structures

(

"abinitio:debug_structures"

)

BooleanOptionKey const abinitio::detect_disulfide_before_relax

(

"abinitio:detect_disulfide_before_relax"

)

BooleanOptionKey const abinitio::dump_frags

(

"abinitio:dump_frags"

)

RealOptionKey const abinitio::end_bias

(

"abinitio:end_bias"

)

BooleanOptionKey const abinitio::explicit_pdb_debug

(

"abinitio:explicit_pdb_debug"

)

BooleanOptionKey const abinitio::fastrelax

(

"abinitio:fastrelax"

)

BooleanOptionKey const abinitio::final_clean_relax

(

"abinitio:final_clean_relax"

)

IntegerVectorOptionKey const abinitio::fix_residues_to_native

(

"abinitio:fix_residues_to_native"

)

BooleanOptionKey const abinitio::include_stage5

(

"abinitio:include_stage5"

)

RealOptionKey const abinitio::increase_cycles

(

"abinitio:increase_cycles"

)

BooleanOptionKey const abinitio::jdist_rerun

(

"abinitio:jdist_rerun"

)

FileOptionKey const abinitio::kill_hairpins

(

"abinitio:kill_hairpins"

)

RealOptionKey const abinitio::kill_hairpins_frequency

(

"abinitio:kill_hairpins_frequency"

)

FileOptionKey const abinitio::log_frags

(

"abinitio:log_frags"

)

RealOptionKey const abinitio::loophash_filter_acceptance_rate

(

"abinitio:loophash_filter_acceptance_rate"

)

BooleanOptionKey const abinitio::membrane

(

"abinitio:membrane"

)

BooleanOptionKey const abinitio::multifastrelax

(

"abinitio:multifastrelax"

)

BooleanOptionKey const abinitio::no_write_failures

(

"abinitio:no_write_failures"

)

IntegerOptionKey const abinitio::number_3mer_frags

(

"abinitio:number_3mer_frags"

)

IntegerOptionKey const abinitio::number_9mer_frags

(

"abinitio:number_9mer_frags"

)

BooleanOptionKey const abinitio::only_stage1

(

"abinitio:only_stage1"

)

IntegerOptionKey const abinitio::optimize_cutpoints_margin

(

"abinitio:optimize_cutpoints_margin"

)

BooleanOptionKey const abinitio::optimize_cutpoints_using_kic

(

"abinitio:optimize_cutpoints_using_kic"

)

BooleanOptionKey const abinitio::override_vdw_all_stages

(

"abinitio:override_vdw_all_stages"

)

RealOptionKey const abinitio::perturb

(

"abinitio:perturb"

)

BooleanOptionKey const abinitio::process_store

(

"abinitio:process_store"

)

IntegerVectorOptionKey const abinitio::recover_low_in_stages

(

"abinitio:recover_low_in_stages"

)

BooleanOptionKey const abinitio::relax

(

"abinitio:relax"

)

BooleanOptionKey const abinitio::relax_failures

(

"abinitio:relax_failures"

)

BooleanOptionKey const abinitio::relax_with_jumps

(

"abinitio:relax_with_jumps"

)

BooleanOptionKey const abinitio::rerun

(

"abinitio:rerun"

)

BooleanOptionKey const abinitio::return_full_atom

(

"abinitio:return_full_atom"

)

RealOptionKey const abinitio::rg_reweight

(

"abinitio:rg_reweight"

)

IntegerVectorOptionKey const abinitio::rmsd_residues

(

"abinitio:rmsd_residues"

)

RealOptionKey const abinitio::rsd_wt_helix

(

"abinitio:rsd_wt_helix"

)

RealOptionKey const abinitio::rsd_wt_loop

(

"abinitio:rsd_wt_loop"

)

RealOptionKey const abinitio::rsd_wt_strand

(

"abinitio:rsd_wt_strand"

)

BooleanOptionKey const abinitio::skip_convergence_check

(

"abinitio:skip_convergence_check"

)

IntegerVectorOptionKey const abinitio::skip_stages

(

"abinitio:skip_stages"

)

BooleanOptionKey const abinitio::smooth_cycles_only

(

"abinitio:smooth_cycles_only"

)

FileVectorOptionKey const abinitio::stage1_patch

(

"abinitio:stage1_patch"

)

FileVectorOptionKey const abinitio::stage2_patch

(

"abinitio:stage2_patch"

)

FileVectorOptionKey const abinitio::stage3a_patch

(

"abinitio:stage3a_patch"

)

FileVectorOptionKey const abinitio::stage3b_patch

(

"abinitio:stage3b_patch"

)

FileVectorOptionKey const abinitio::stage4_patch

(

"abinitio:stage4_patch"

)

FileVectorOptionKey const abinitio::stage5_patch

(

"abinitio:stage5_patch"

)

BooleanOptionKey const abinitio::start_native

(

"abinitio:start_native"

)

BooleanOptionKey const abinitio::steal_3mers

(

"abinitio:steal_3mers"

)

BooleanOptionKey const abinitio::steal_9mers

(

"abinitio:steal_9mers"

)

IntegerOptionKey const abinitio::symmetry_residue

(

"abinitio:symmetry_residue"

)

RealOptionKey const abinitio::temperature

(

"abinitio:temperature"

)

BooleanOptionKey const abinitio::use_filters

(

"abinitio:use_filters"

)

BooleanOptionKey const abinitio::use_loophash_filter

(

"abinitio:use_loophash_filter"

)

RealOptionKey const abinitio::vdw_weight_stage1

(

"abinitio:vdw_weight_stage1"

)