basic::options::OptionKeys::rna::denovo Namespace Reference

Namespaces
	db
	minimize
	out

Variables
BooleanOptionKey const	denovo
IntegerOptionKey const	cycles
RealOptionKey const	rna_protein_docking_freq
IntegerOptionKey const	rounds
RealOptionKey const	temperature
BooleanOptionKey const	minimize_rna
StringVectorOptionKey const	sequence
StringOptionKey const	secstruct
StringOptionKey const	secstruct_general
StringOptionKey const	secstruct_file
StringOptionKey const	secstruct_general_file
StringOptionKey const	secstruct_legacy
StringOptionKey const	lores_scorefxn
StringVectorOptionKey const	set_lores_weights
IntegerOptionKey const	symm_hack_arity
IntegerOptionKey const	exhaustive_fragment_insertion
BooleanOptionKey const	filter_lores_base_pairs
BooleanOptionKey const	filter_lores_base_pairs_early
BooleanOptionKey const	filter_chain_closure
BooleanOptionKey const	filter_chain_closure_halfway
RealOptionKey const	filter_chain_closure_distance
BooleanOptionKey const	relax_rna
BooleanOptionKey const	simple_relax
BooleanOptionKey const	ignore_secstruct
RealOptionKey const	jump_change_frequency
BooleanOptionKey const	close_loops
BooleanOptionKey const	close_loops_after_each_move
BooleanOptionKey const	heat
BooleanOptionKey const	staged_constraints
StringOptionKey const	jump_library_file
StringOptionKey const	vall_torsions
BooleanOptionKey const	use_1jj2_torsions
RealOptionKey const	fuzz_fragments
RealOptionKey const	rna_lores_chainbreak_weight
RealOptionKey const	rna_lores_linear_chainbreak_weight
BooleanOptionKey const	fixed_stems
BooleanOptionKey const	allow_bulge
IntegerVectorOptionKey const	allowed_bulge_res
BooleanOptionKey const	allow_consecutive_bulges
BooleanOptionKey const	move_first_rigid_body
BooleanOptionKey const	root_at_first_rigid_body
BooleanOptionKey const	dock_each_chunk
BooleanOptionKey const	dock_each_chunk_per_chain
FileVectorOptionKey const	dock_chunks
BooleanOptionKey const	center_jumps_in_single_stranded
FileVectorOptionKey const	initial_structures
BooleanOptionKey const	ft_close_chains
FileVectorOptionKey const	helical_substructs
RealOptionKey const	suppress_bp_constraint
BooleanOptionKey const	output_filters
BooleanOptionKey const	autofilter
BooleanOptionKey const	no_filters
ResidueChainVectorOptionKey const	output_res_num
IntegerOptionKey const	offset
ResidueChainVectorOptionKey const	input_silent_res
ResidueChainVectorOptionKey const	virtual_anchor
ResidueChainVectorOptionKey const	obligate_pair
StringVectorOptionKey const	obligate_pair_explicit
StringVectorOptionKey const	chain_connection
ResidueChainVectorOptionKey const	remove_pair
ResidueChainVectorOptionKey const	remove_obligate_pair
StringOptionKey const	refine_silent_file
StringVectorOptionKey const	refine_silent_tags
IntegerOptionKey const	refine_silent_number_of_poses
StringOptionKey const	get_fold_tree_from_silent_file
StringVectorOptionKey const	fold_tree_from_silent_file_tag
BooleanOptionKey const	refine_native_get_good_FT
BooleanOptionKey const	refine_native
BooleanOptionKey const	override_refine_pose_rounds
BooleanOptionKey const	bps_moves
BooleanOptionKey const	disallow_bps_at_extra_min_res
BooleanOptionKey const	allow_fragment_moves_in_bps
IntegerOptionKey const	frag_size
BooleanOptionKey const	VDW_rep_screen_include_sidechains
BooleanOptionKey const	gradual_constraints
BooleanOptionKey const	ramp_rnp_vdw
RealOptionKey const	grid_vdw_weight
StringOptionKey const	tag
StringOptionKey const	working_native
BooleanOptionKey const	use_legacy_setup
BooleanOptionKey const	cst_gap
BooleanOptionKey const	convert_protein_CEN
BooleanOptionKey const	rna_protein_docking
BooleanOptionKey const	small_docking_moves
RealOptionKey const	docking_move_size
BooleanOptionKey const	rna_protein_docking_legacy
BooleanOptionKey const	rnp_high_res_relax
IntegerOptionKey const	rnp_high_res_cycles
BooleanOptionKey const	rnp_pack_first
BooleanOptionKey const	rnp_min_first
BooleanOptionKey const	rnp_ramp_rep
BooleanOptionKey const	new_fold_tree_initializer
BooleanOptionKey const	randomize_init_rnp
BooleanOptionKey const	dock_into_density
BooleanOptionKey const	dock_into_density_legacy
IntegerVectorOptionKey const	exclude_fragments
StringOptionKey const	exclusion_match_type
RealOptionKey const	fragment_homology_rmsd
BooleanOptionKey const	exclude_native_fragments
StringVectorOptionKey const	exclude_fragment_files
BooleanOptionKey const	dump_stems

Variable Documentation

allow_bulge

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::allow_bulge

extern

allow_consecutive_bulges

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::allow_consecutive_bulges

extern

allow_fragment_moves_in_bps

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::allow_fragment_moves_in_bps

extern

allowed_bulge_res

IntegerVectorOptionKey const basic::options::OptionKeys::rna::denovo::allowed_bulge_res

extern

autofilter

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::autofilter

extern

bps_moves

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::bps_moves

extern

center_jumps_in_single_stranded

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::center_jumps_in_single_stranded

extern

chain_connection

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::chain_connection

extern

close_loops

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::close_loops

extern

close_loops_after_each_move

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::close_loops_after_each_move

extern

convert_protein_CEN

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::convert_protein_CEN

extern

cst_gap

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::cst_gap

extern

cycles

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::cycles

extern

denovo

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::denovo

extern

Referenced by align_pdbs(), align_pdbs_function(), build_helix_test(), build_next_nucleotide_test(), calc_rmsd_test(), calculate_pairwise_RMSD(), coarse_rb_test(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), color_by_lj_test(), convert_to_coarse_test(), create_base_pair_step_database_test(), create_bp_jump_database_test(), dinucleotide_test(), env_sugar_test(), files_for_openMM_test(), general_initialize(), get_icoor(), get_pose_and_numbering(), graft_pdb(), mismatch_test(), modeler_map_test(), mutate_residues_wrapper(), pdb_little_motif_test(), prepare_threaded_model(), print_hbonds_test(), protein_helix_test(), rna_assemble_all_combinations_test(), rna_assemble_test(), rna_build_helix_test_OLD(), rna_build_helix_test_precompute(), rna_denovo_legacy(), rna_design_test(), rna_features_from_pose(), rna_fullatom_minimize_test(), rna_helix_pdbstats_from_pose(), rna_stack_pdbstats_from_pose(), rna_stats_test(), rna_suitename(), rotamerize_rna_test(), sasa_test(), stepwise_lores_test(), sugar_frag_RNA_test(), sugar_geometry_RNA_test(), and tar_motif_test().

disallow_bps_at_extra_min_res

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::disallow_bps_at_extra_min_res

extern

dock_chunks

FileVectorOptionKey const basic::options::OptionKeys::rna::denovo::dock_chunks

extern

Referenced by rna_denovo().

dock_each_chunk

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::dock_each_chunk

extern

dock_each_chunk_per_chain

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::dock_each_chunk_per_chain

extern

dock_into_density

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::dock_into_density

extern

dock_into_density_legacy

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::dock_into_density_legacy

extern

docking_move_size

RealOptionKey const basic::options::OptionKeys::rna::denovo::docking_move_size

extern

dump_stems

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::dump_stems

extern

exclude_fragment_files

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::exclude_fragment_files

extern

exclude_fragments

IntegerVectorOptionKey const basic::options::OptionKeys::rna::denovo::exclude_fragments

extern

exclude_native_fragments

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::exclude_native_fragments

extern

exclusion_match_type

StringOptionKey const basic::options::OptionKeys::rna::denovo::exclusion_match_type

extern

Referenced by get_min_frag_rmsd().

exhaustive_fragment_insertion

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::exhaustive_fragment_insertion

extern

filter_chain_closure

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::filter_chain_closure

extern

filter_chain_closure_distance

RealOptionKey const basic::options::OptionKeys::rna::denovo::filter_chain_closure_distance

extern

filter_chain_closure_halfway

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::filter_chain_closure_halfway

extern

filter_lores_base_pairs

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs

extern

Referenced by main().

filter_lores_base_pairs_early

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs_early

extern

fixed_stems

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::fixed_stems

extern

fold_tree_from_silent_file_tag

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::fold_tree_from_silent_file_tag

extern

frag_size

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::frag_size

extern

fragment_homology_rmsd

RealOptionKey const basic::options::OptionKeys::rna::denovo::fragment_homology_rmsd

extern

Referenced by main().

ft_close_chains

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::ft_close_chains

extern

fuzz_fragments

RealOptionKey const basic::options::OptionKeys::rna::denovo::fuzz_fragments

extern

get_fold_tree_from_silent_file

StringOptionKey const basic::options::OptionKeys::rna::denovo::get_fold_tree_from_silent_file

extern

gradual_constraints

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::gradual_constraints

extern

grid_vdw_weight

RealOptionKey const basic::options::OptionKeys::rna::denovo::grid_vdw_weight

extern

heat

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::heat

extern

Referenced by main().

helical_substructs

FileVectorOptionKey const basic::options::OptionKeys::rna::denovo::helical_substructs

extern

Referenced by rna_denovo().

ignore_secstruct

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::ignore_secstruct

extern

Referenced by main().

initial_structures

FileVectorOptionKey const basic::options::OptionKeys::rna::denovo::initial_structures

extern

Referenced by rna_denovo().

input_silent_res

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::input_silent_res

extern

jump_change_frequency

RealOptionKey const basic::options::OptionKeys::rna::denovo::jump_change_frequency

extern

Referenced by main().

jump_library_file

StringOptionKey const basic::options::OptionKeys::rna::denovo::jump_library_file

extern

Referenced by main(), rna_assemble_all_combinations_test(), and rna_assemble_test().

lores_scorefxn

StringOptionKey const basic::options::OptionKeys::rna::denovo::lores_scorefxn

extern

Referenced by create_bp_jump_database_test(), rna_close_chainbreaks_test(), rna_fullatom_minimize_silent_test(), rna_torsion_check_test(), and score_and_minimize().

minimize_rna

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::minimize_rna

extern

Referenced by get_stepwise_score_function(), main(), rna_denovo(), and StepWiseJobQueen::StepWiseJobQueen().

move_first_rigid_body

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::move_first_rigid_body

extern

new_fold_tree_initializer

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::new_fold_tree_initializer

extern

no_filters

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::no_filters

extern

obligate_pair

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::obligate_pair

extern

obligate_pair_explicit

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::obligate_pair_explicit

extern

offset

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::offset

extern

output_filters

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::output_filters

extern

output_res_num

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::output_res_num

extern

override_refine_pose_rounds

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::override_refine_pose_rounds

extern

ramp_rnp_vdw

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::ramp_rnp_vdw

extern

randomize_init_rnp

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::randomize_init_rnp

extern

refine_native

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::refine_native

extern

refine_native_get_good_FT

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::refine_native_get_good_FT

extern

refine_silent_file

StringOptionKey const basic::options::OptionKeys::rna::denovo::refine_silent_file

extern

refine_silent_number_of_poses

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::refine_silent_number_of_poses

extern

refine_silent_tags

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::refine_silent_tags

extern

relax_rna

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::relax_rna

extern

Referenced by main().

remove_obligate_pair

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::remove_obligate_pair

extern

remove_pair

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::remove_pair

extern

rna_lores_chainbreak_weight

RealOptionKey const basic::options::OptionKeys::rna::denovo::rna_lores_chainbreak_weight

extern

rna_lores_linear_chainbreak_weight

RealOptionKey const basic::options::OptionKeys::rna::denovo::rna_lores_linear_chainbreak_weight

extern

rna_protein_docking

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rna_protein_docking

extern

rna_protein_docking_freq

RealOptionKey const basic::options::OptionKeys::rna::denovo::rna_protein_docking_freq

extern

rna_protein_docking_legacy

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rna_protein_docking_legacy

extern

rnp_high_res_cycles

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::rnp_high_res_cycles

extern

rnp_high_res_relax

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rnp_high_res_relax

extern

rnp_min_first

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rnp_min_first

extern

rnp_pack_first

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rnp_pack_first

extern

rnp_ramp_rep

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::rnp_ramp_rep

extern

root_at_first_rigid_body

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::root_at_first_rigid_body

extern

rounds

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::rounds

extern

secstruct

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct

extern

secstruct_file

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct_file

extern

Referenced by main(), and rna_fullatom_minimize_test().

secstruct_general

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct_general

extern

secstruct_general_file

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct_general_file

extern

secstruct_legacy

StringOptionKey const basic::options::OptionKeys::rna::denovo::secstruct_legacy

extern

sequence

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::sequence

extern

set_lores_weights

StringVectorOptionKey const basic::options::OptionKeys::rna::denovo::set_lores_weights

extern

simple_relax

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::simple_relax

extern

small_docking_moves

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::small_docking_moves

extern

staged_constraints

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::staged_constraints

extern

Referenced by coarse_rna_denovo_test(), and main().

suppress_bp_constraint

RealOptionKey const basic::options::OptionKeys::rna::denovo::suppress_bp_constraint

extern

symm_hack_arity

IntegerOptionKey const basic::options::OptionKeys::rna::denovo::symm_hack_arity

extern

tag

StringOptionKey const basic::options::OptionKeys::rna::denovo::tag

extern

temperature

RealOptionKey const basic::options::OptionKeys::rna::denovo::temperature

extern

use_1jj2_torsions

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::use_1jj2_torsions

extern

use_legacy_setup

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::use_legacy_setup

extern

vall_torsions

StringOptionKey const basic::options::OptionKeys::rna::denovo::vall_torsions

extern

Referenced by create_rna_vall_torsions_test(), main(), my_main(), and rna_backbone_rebuild_test().

VDW_rep_screen_include_sidechains

BooleanOptionKey const basic::options::OptionKeys::rna::denovo::VDW_rep_screen_include_sidechains

extern

virtual_anchor

ResidueChainVectorOptionKey const basic::options::OptionKeys::rna::denovo::virtual_anchor

extern

working_native

StringOptionKey const basic::options::OptionKeys::rna::denovo::working_native

extern