basic::options::OptionKeys::motifs Namespace Reference

Variables
BooleanOptionKey const	motifs
RealOptionKey const	close_enough
IntegerOptionKey const	max_depth
BooleanOptionKey const	keep_motif_xtal_location
RealOptionKey const	pack_score_cutoff
RealOptionKey const	hb_score_cutoff
RealOptionKey const	water_score_cutoff
RealOptionKey const	pack_min_threshold
RealOptionKey const	pack_max_threshold
RealOptionKey const	hbond_min_threshold
RealOptionKey const	hbond_max_threshold
RealOptionKey const	elec_min_threshold
RealOptionKey const	elec_max_threshold
RealOptionKey const	duplicate_dist_cutoff
RealOptionKey const	duplicate_angle_cutoff
StringOptionKey const	motif_output_directory
BooleanOptionKey const	eliminate_weak_motifs
RealOptionKey const	duplicate_motif_cutoff
BooleanOptionKey const	preminimize_motif_pdbs
BooleanOptionKey const	preminimize_motif_pdbs_sconly
BooleanOptionKey const	place_adduct_waters
FileVectorOptionKey const	list_motifs
StringOptionKey const	motif_filename
StringOptionKey const	file_prefix
StringOptionKey const	build_residue_file
StringOptionKey const	motif_flexible_loop_file
StringOptionKey const	residue_trim_file
StringOptionKey const	BPData
FileVectorOptionKey const	list_dnaconformers
StringVectorOptionKey const	target_dna_defs
StringVectorOptionKey const	motif_build_defs
IntegerVectorOptionKey const	motif_build_positions
RealOptionKey const	r1
RealOptionKey const	r2
RealOptionKey const	z1
RealOptionKey const	z2
RealOptionKey const	dtest
IntegerOptionKey const	rotlevel
IntegerOptionKey const	num_repacks
BooleanOptionKey const	minimize
BooleanOptionKey const	minimize_dna
BooleanOptionKey const	run_motifs
BooleanOptionKey const	expand_motifs
BooleanOptionKey const	aromatic_motifs
BooleanOptionKey const	dump_motifs
BooleanOptionKey const	quick_and_dirty
RealOptionKey const	special_rotweight
StringOptionKey const	output_file
StringOptionKey const	data_file
StringOptionKey const	target_aa
BooleanOptionKey const	flex_sugar
BooleanOptionKey const	clear_bprots
IntegerOptionKey const	rots2add
BooleanOptionKey const	restrict_to_wt
BooleanOptionKey const	rerun_motifsearch
BooleanOptionKey const	no_rotamer_bump
RealOptionKey const	ligand_motif_sphere

Variable Documentation

BooleanOptionKey const basic::options::OptionKeys::motifs::aromatic_motifs

Referenced by add_rosetta_options_10().

StringOptionKey const basic::options::OptionKeys::motifs::BPData

Referenced by add_rosetta_options_10().

StringOptionKey const basic::options::OptionKeys::motifs::build_residue_file

Referenced by add_rosetta_options_10(), and find_close_motifs().

BooleanOptionKey const basic::options::OptionKeys::motifs::clear_bprots

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::close_enough

Referenced by add_rosetta_options_10().

StringOptionKey const basic::options::OptionKeys::motifs::data_file

Referenced by add_rosetta_options_10(), main(), and RNA_ScoreMover::RNA_ScoreMover().

RealOptionKey const basic::options::OptionKeys::motifs::dtest

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::dump_motifs

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::duplicate_angle_cutoff

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::duplicate_dist_cutoff

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::duplicate_motif_cutoff

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::elec_max_threshold

Referenced by add_rosetta_options_10(), and process_for_motifs().

RealOptionKey const basic::options::OptionKeys::motifs::elec_min_threshold

Referenced by add_rosetta_options_10(), and process_for_motifs().

BooleanOptionKey const basic::options::OptionKeys::motifs::eliminate_weak_motifs

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::expand_motifs

Referenced by add_rosetta_options_10().

StringOptionKey const basic::options::OptionKeys::motifs::file_prefix

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::flex_sugar

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::hb_score_cutoff

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::hbond_max_threshold

Referenced by add_rosetta_options_10(), and process_for_motifs().

RealOptionKey const basic::options::OptionKeys::motifs::hbond_min_threshold

Referenced by add_rosetta_options_10(), and process_for_motifs().

BooleanOptionKey const basic::options::OptionKeys::motifs::keep_motif_xtal_location

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::ligand_motif_sphere

Referenced by add_rosetta_options_10().

FileVectorOptionKey const basic::options::OptionKeys::motifs::list_dnaconformers

Referenced by add_rosetta_options_10().

FileVectorOptionKey const basic::options::OptionKeys::motifs::list_motifs

Referenced by add_rosetta_options_10().

IntegerOptionKey const basic::options::OptionKeys::motifs::max_depth

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::minimize

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::minimize_dna

Referenced by add_rosetta_options_10().

StringVectorOptionKey const basic::options::OptionKeys::motifs::motif_build_defs

Referenced by add_rosetta_options_10().

IntegerVectorOptionKey const basic::options::OptionKeys::motifs::motif_build_positions

Referenced by add_rosetta_options_10().

StringOptionKey const basic::options::OptionKeys::motifs::motif_filename

Referenced by add_rosetta_options_10(), and find_close_motifs().

StringOptionKey const basic::options::OptionKeys::motifs::motif_flexible_loop_file

Referenced by add_rosetta_options_10(), and read_in_flexible_regions().

StringOptionKey const basic::options::OptionKeys::motifs::motif_output_directory

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::motifs

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::no_rotamer_bump

Referenced by add_rosetta_options_10().

IntegerOptionKey const basic::options::OptionKeys::motifs::num_repacks

Referenced by add_rosetta_options_10().

StringOptionKey const basic::options::OptionKeys::motifs::output_file

Referenced by add_rosetta_options_10(), and main().

RealOptionKey const basic::options::OptionKeys::motifs::pack_max_threshold

Referenced by add_rosetta_options_10(), and process_for_motifs().

RealOptionKey const basic::options::OptionKeys::motifs::pack_min_threshold

Referenced by add_rosetta_options_10(), and process_for_motifs().

RealOptionKey const basic::options::OptionKeys::motifs::pack_score_cutoff

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::place_adduct_waters

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::preminimize_motif_pdbs

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::preminimize_motif_pdbs_sconly

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::quick_and_dirty

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::r1

Referenced by add_rosetta_options_10(), calc_scores(), Solver_NU::calculate_rho(), correct_dunbrack(), getRotID(), and ScoreFragInfo::ScoreFragInfo().

RealOptionKey const basic::options::OptionKeys::motifs::r2

Referenced by add_rosetta_options_10(), calc_scores(), Solver_NU::calculate_rho(), correct_dunbrack(), getRotID(), and ScoreFragInfo::ScoreFragInfo().

BooleanOptionKey const basic::options::OptionKeys::motifs::rerun_motifsearch

Referenced by add_rosetta_options_10().

StringOptionKey const basic::options::OptionKeys::motifs::residue_trim_file

Referenced by add_rosetta_options_10(), and find_close_motifs().

BooleanOptionKey const basic::options::OptionKeys::motifs::restrict_to_wt

Referenced by add_rosetta_options_10().

IntegerOptionKey const basic::options::OptionKeys::motifs::rotlevel

Referenced by add_rosetta_options_10().

IntegerOptionKey const basic::options::OptionKeys::motifs::rots2add

Referenced by add_rosetta_options_10().

BooleanOptionKey const basic::options::OptionKeys::motifs::run_motifs

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::special_rotweight

Referenced by add_rosetta_options_10().

StringOptionKey const basic::options::OptionKeys::motifs::target_aa

Referenced by add_rosetta_options_10(), main(), and process_for_motifs().

StringVectorOptionKey const basic::options::OptionKeys::motifs::target_dna_defs

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::water_score_cutoff

Referenced by add_rosetta_options_10().

RealOptionKey const basic::options::OptionKeys::motifs::z1

Referenced by add_rosetta_options_10(), numeric::kinematic_closure::dixon_sturm(), numeric::alignment::QCPKernel< Real >::inner_product(), and numeric::linear_algebra::qzvec().

RealOptionKey const basic::options::OptionKeys::motifs::z2

Referenced by add_rosetta_options_10(), numeric::alignment::QCPKernel< Real >::calc_rmsd_Theobald_method(), numeric::kinematic_closure::dixon_sturm(), and numeric::alignment::QCPKernel< Real >::inner_product().