rna::farna Namespace Reference

Namespaces
	db
	erraser
	minimize

Functions
BooleanOptionKey const	farna ("rna:farna")
IntegerOptionKey const	cycles ("rna:farna:cycles")
RealOptionKey const	temperature ("rna:farna:temperature")
BooleanOptionKey const	minimize_rna ("rna:farna:minimize_rna")
StringVectorOptionKey const	sequence ("rna:farna:sequence")
StringOptionKey const	secstruct ("rna:farna:secstruct")
StringOptionKey const	secstruct_general ("rna:farna:secstruct_general")
StringOptionKey const	secstruct_file ("rna:farna:secstruct_file")
StringOptionKey const	secstruct_general_file ("rna:farna:secstruct_general_file")
StringOptionKey const	lores_scorefxn ("rna:farna:lores_scorefxn")
StringOptionKey const	params_file ("rna:farna:params_file")
BooleanOptionKey const	filter_lores_base_pairs ("rna:farna:filter_lores_base_pairs")
BooleanOptionKey const	filter_lores_base_pairs_early ("rna:farna:filter_lores_base_pairs_early")
BooleanOptionKey const	filter_chain_closure ("rna:farna:filter_chain_closure")
BooleanOptionKey const	filter_chain_closure_halfway ("rna:farna:filter_chain_closure_halfway")
RealOptionKey const	filter_chain_closure_distance ("rna:farna:filter_chain_closure_distance")
BooleanOptionKey const	relax_rna ("rna:farna:relax_rna")
BooleanOptionKey const	simple_relax ("rna:farna:simple_relax")
BooleanOptionKey const	ignore_secstruct ("rna:farna:ignore_secstruct")
RealOptionKey const	jump_change_frequency ("rna:farna:jump_change_frequency")
BooleanOptionKey const	close_loops ("rna:farna:close_loops")
BooleanOptionKey const	close_loops_after_each_move ("rna:farna:close_loops_after_each_move")
BooleanOptionKey const	output_lores_silent_file ("rna:farna:output_lores_silent_file")
BooleanOptionKey const	heat ("rna:farna:heat")
BooleanOptionKey const	dump ("rna:farna:dump")
BooleanOptionKey const	staged_constraints ("rna:farna:staged_constraints")
StringOptionKey const	jump_library_file ("rna:farna:jump_library_file")
StringOptionKey const	vall_torsions ("rna:farna:vall_torsions")
BooleanOptionKey const	use_1jj2_torsions ("rna:farna:use_1jj2_torsions")
RealOptionKey const	rna_lores_chainbreak_weight ("rna:farna:rna_lores_chainbreak_weight")
RealOptionKey const	rna_lores_linear_chainbreak_weight ("rna:farna:rna_lores_linear_chainbreak_weight")
BooleanOptionKey const	fixed_stems ("rna:farna:fixed_stems")
BooleanOptionKey const	allow_bulge ("rna:farna:allow_bulge")
IntegerVectorOptionKey const	allowed_bulge_res ("rna:farna:allowed_bulge_res")
BooleanOptionKey const	allow_consecutive_bulges ("rna:farna:allow_consecutive_bulges")
BooleanOptionKey const	binary_output ("rna:farna:binary_output")
BooleanOptionKey const	move_first_rigid_body ("rna:farna:move_first_rigid_body")
BooleanOptionKey const	root_at_first_rigid_body ("rna:farna:root_at_first_rigid_body")
RealOptionKey const	suppress_bp_constraint ("rna:farna:suppress_bp_constraint")
BooleanOptionKey const	output_filters ("rna:farna:output_filters")
BooleanOptionKey const	autofilter ("rna:farna:autofilter")
ResidueChainVectorOptionKey const	output_res_num ("rna:farna:output_res_num")
IntegerOptionKey const	offset ("rna:farna:offset")
ResidueChainVectorOptionKey const	input_silent_res ("rna:farna:input_silent_res")
ResidueChainVectorOptionKey const	virtual_anchor ("rna:farna:virtual_anchor")
ResidueChainVectorOptionKey const	obligate_pair ("rna:farna:obligate_pair")
StringVectorOptionKey const	obligate_pair_explicit ("rna:farna:obligate_pair_explicit")
StringVectorOptionKey const	chain_connection ("rna:farna:chain_connection")
ResidueChainVectorOptionKey const	remove_pair ("rna:farna:remove_pair")
ResidueChainVectorOptionKey const	remove_obligate_pair ("rna:farna:remove_obligate_pair")
StringOptionKey const	refine_silent_file ("rna:farna:refine_silent_file")
BooleanOptionKey const	refine_native ("rna:farna:refine_native")
BooleanOptionKey const	bps_moves ("rna:farna:bps_moves")
BooleanOptionKey const	disallow_bps_at_extra_min_res ("rna:farna:disallow_bps_at_extra_min_res")
BooleanOptionKey const	allow_fragment_moves_in_bps ("rna:farna:allow_fragment_moves_in_bps")
BooleanOptionKey const	VDW_rep_screen_include_sidechains ("rna:farna:VDW_rep_screen_include_sidechains")
BooleanOptionKey const	gradual_constraints ("rna:farna:gradual_constraints")
RealOptionKey const	grid_vdw_weight ("rna:farna:grid_vdw_weight")
StringOptionKey const	tag ("rna:farna:tag")
StringOptionKey const	working_native ("rna:farna:working_native")
BooleanOptionKey const	use_legacy_setup ("rna:farna:use_legacy_setup")
BooleanOptionKey const	cst_gap ("rna:farna:cst_gap")

Function Documentation

BooleanOptionKey const rna::farna::allow_bulge

(

"rna:farna:allow_bulge"

)

Referenced by main().

BooleanOptionKey const rna::farna::allow_consecutive_bulges

(

"rna:farna:allow_consecutive_bulges"

)

Referenced by main().

BooleanOptionKey const rna::farna::allow_fragment_moves_in_bps

(

"rna:farna:allow_fragment_moves_in_bps"

)

IntegerVectorOptionKey const rna::farna::allowed_bulge_res

(

"rna:farna:allowed_bulge_res"

)

Referenced by main().

BooleanOptionKey const rna::farna::autofilter

(

"rna:farna:autofilter"

)

Referenced by main().

BooleanOptionKey const rna::farna::binary_output

(

"rna:farna:binary_output"

)

Referenced by main().

BooleanOptionKey const rna::farna::bps_moves

(

"rna:farna:bps_moves"

)

Referenced by main().

StringVectorOptionKey const rna::farna::chain_connection

(

"rna:farna:chain_connection"

)

BooleanOptionKey const rna::farna::close_loops

(

"rna:farna:close_loops"

)

Referenced by main().

BooleanOptionKey const rna::farna::close_loops_after_each_move

(

"rna:farna:close_loops_after_each_move"

)

Referenced by main().

BooleanOptionKey const rna::farna::cst_gap

(

"rna:farna:cst_gap"

)

IntegerOptionKey const rna::farna::cycles

(

"rna:farna:cycles"

)

Referenced by main().

BooleanOptionKey const rna::farna::disallow_bps_at_extra_min_res

(

"rna:farna:disallow_bps_at_extra_min_res"

)

BooleanOptionKey const rna::farna::dump

(

"rna:farna:dump"

)

Referenced by main().

BooleanOptionKey const rna::farna::farna

(

"rna:farna"

)

BooleanOptionKey const rna::farna::filter_chain_closure

(

"rna:farna:filter_chain_closure"

)

Referenced by main().

RealOptionKey const rna::farna::filter_chain_closure_distance

(

"rna:farna:filter_chain_closure_distance"

)

Referenced by main().

BooleanOptionKey const rna::farna::filter_chain_closure_halfway

(

"rna:farna:filter_chain_closure_halfway"

)

Referenced by main().

BooleanOptionKey const rna::farna::filter_lores_base_pairs

(

"rna:farna:filter_lores_base_pairs"

)

Referenced by main().

BooleanOptionKey const rna::farna::filter_lores_base_pairs_early

(

"rna:farna:filter_lores_base_pairs_early"

)

Referenced by main().

BooleanOptionKey const rna::farna::fixed_stems

(

"rna:farna:fixed_stems"

)

Referenced by main().

BooleanOptionKey const rna::farna::gradual_constraints

(

"rna:farna:gradual_constraints"

)

RealOptionKey const rna::farna::grid_vdw_weight

(

"rna:farna:grid_vdw_weight"

)

BooleanOptionKey const rna::farna::heat

(

"rna:farna:heat"

)

Referenced by main().

BooleanOptionKey const rna::farna::ignore_secstruct

(

"rna:farna:ignore_secstruct"

)

ResidueChainVectorOptionKey const rna::farna::input_silent_res

(

"rna:farna:input_silent_res"

)

RealOptionKey const rna::farna::jump_change_frequency

(

"rna:farna:jump_change_frequency"

)

Referenced by main().

StringOptionKey const rna::farna::jump_library_file

(

"rna:farna:jump_library_file"

)

StringOptionKey const rna::farna::lores_scorefxn

(

"rna:farna:lores_scorefxn"

)

Referenced by main().

BooleanOptionKey const rna::farna::minimize_rna

(

"rna:farna:minimize_rna"

)

Referenced by main().

BooleanOptionKey const rna::farna::move_first_rigid_body

(

"rna:farna:move_first_rigid_body"

)

Referenced by main().

ResidueChainVectorOptionKey const rna::farna::obligate_pair

(

"rna:farna:obligate_pair"

)

Referenced by main().

StringVectorOptionKey const rna::farna::obligate_pair_explicit

(

"rna:farna:obligate_pair_explicit"

)

Referenced by main().

IntegerOptionKey const rna::farna::offset

(

"rna:farna:offset"

)

Referenced by main().

BooleanOptionKey const rna::farna::output_filters

(

"rna:farna:output_filters"

)

Referenced by main().

BooleanOptionKey const rna::farna::output_lores_silent_file

(

"rna:farna:output_lores_silent_file"

)

Referenced by main().

ResidueChainVectorOptionKey const rna::farna::output_res_num

(

"rna:farna:output_res_num"

)

Referenced by main().

StringOptionKey const rna::farna::params_file

(

"rna:farna:params_file"

)

Referenced by main().

BooleanOptionKey const rna::farna::refine_native

(

"rna:farna:refine_native"

)

Referenced by main().

StringOptionKey const rna::farna::refine_silent_file

(

"rna:farna:refine_silent_file"

)

Referenced by main().

BooleanOptionKey const rna::farna::relax_rna

(

"rna:farna:relax_rna"

)

ResidueChainVectorOptionKey const rna::farna::remove_obligate_pair

(

"rna:farna:remove_obligate_pair"

)

ResidueChainVectorOptionKey const rna::farna::remove_pair

(

"rna:farna:remove_pair"

)

RealOptionKey const rna::farna::rna_lores_chainbreak_weight

(

"rna:farna:rna_lores_chainbreak_weight"

)

Referenced by main().

RealOptionKey const rna::farna::rna_lores_linear_chainbreak_weight

(

"rna:farna:rna_lores_linear_chainbreak_weight"

)

Referenced by main().

BooleanOptionKey const rna::farna::root_at_first_rigid_body

(

"rna:farna:root_at_first_rigid_body"

)

Referenced by main().

StringOptionKey const rna::farna::secstruct

(

"rna:farna:secstruct"

)

Referenced by main().

StringOptionKey const rna::farna::secstruct_file

(

"rna:farna:secstruct_file"

)

Referenced by main().

StringOptionKey const rna::farna::secstruct_general

(

"rna:farna:secstruct_general"

)

StringOptionKey const rna::farna::secstruct_general_file

(

"rna:farna:secstruct_general_file"

)

StringVectorOptionKey const rna::farna::sequence

(

"rna:farna:sequence"

)

Referenced by main().

BooleanOptionKey const rna::farna::simple_relax

(

"rna:farna:simple_relax"

)

BooleanOptionKey const rna::farna::staged_constraints

(

"rna:farna:staged_constraints"

)

Referenced by main().

RealOptionKey const rna::farna::suppress_bp_constraint

(

"rna:farna:suppress_bp_constraint"

)

Referenced by main().

StringOptionKey const rna::farna::tag

(

"rna:farna:tag"

)

Referenced by main().

RealOptionKey const rna::farna::temperature

(

"rna:farna:temperature"

)

Referenced by main().

BooleanOptionKey const rna::farna::use_1jj2_torsions

(

"rna:farna:use_1jj2_torsions"

)

Referenced by main().

BooleanOptionKey const rna::farna::use_legacy_setup

(

"rna:farna:use_legacy_setup"

)

StringOptionKey const rna::farna::vall_torsions

(

"rna:farna:vall_torsions"

)

BooleanOptionKey const rna::farna::VDW_rep_screen_include_sidechains

(

"rna:farna:VDW_rep_screen_include_sidechains"

)

ResidueChainVectorOptionKey const rna::farna::virtual_anchor

(

"rna:farna:virtual_anchor"

)

StringOptionKey const rna::farna::working_native

(

"rna:farna:working_native"

)