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

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

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
StringOptionKey const	motif_build_position_chain
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
RealOptionKey const	constraint_max
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

Function Documentation

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

(

"motifs:aromatic_motifs"

)

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

(

"motifs:BPData"

)

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

(

"motifs:build_residue_file"

)

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

(

"motifs:clear_bprots"

)

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

(

"motifs:close_enough"

)

RealOptionKey const basic::options::OptionKeys::motifs::constraint_max

(

"motifs:constraint_max"

)

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

(

"motifs:data_file"

)

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

(

"motifs:dtest"

)

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

(

"motifs:dump_motifs"

)

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

(

"motifs:duplicate_angle_cutoff"

)

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

(

"motifs:duplicate_dist_cutoff"

)

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

(

"motifs:duplicate_motif_cutoff"

)

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

(

"motifs:elec_max_threshold"

)

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

(

"motifs:elec_min_threshold"

)

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

(

"motifs:eliminate_weak_motifs"

)

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

(

"motifs:expand_motifs"

)

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

(

"motifs:file_prefix"

)

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

(

"motifs:flex_sugar"

)

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

(

"motifs:hb_score_cutoff"

)

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

(

"motifs:hbond_max_threshold"

)

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

(

"motifs:hbond_min_threshold"

)

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

(

"motifs:keep_motif_xtal_location"

)

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

(

"motifs:ligand_motif_sphere"

)

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

(

"motifs:list_dnaconformers"

)

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

(

"motifs:list_motifs"

)

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

(

"motifs:max_depth"

)

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

(

"motifs:minimize"

)

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

(

"motifs:minimize_dna"

)

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

(

"motifs:motif_build_defs"

)

StringOptionKey const basic::options::OptionKeys::motifs::motif_build_position_chain

(

"motifs:motif_build_position_chain"

)

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

(

"motifs:motif_build_positions"

)

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

(

"motifs:motif_filename"

)

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

(

"motifs:motif_flexible_loop_file"

)

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

(

"motifs:motif_output_directory"

)

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

(

"motifs"

)

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

(

"motifs:no_rotamer_bump"

)

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

(

"motifs:num_repacks"

)

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

(

"motifs:output_file"

)

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

(

"motifs:pack_max_threshold"

)

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

(

"motifs:pack_min_threshold"

)

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

(

"motifs:pack_score_cutoff"

)

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

(

"motifs:place_adduct_waters"

)

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

(

"motifs:preminimize_motif_pdbs"

)

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

(

"motifs:preminimize_motif_pdbs_sconly"

)

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

(

"motifs:quick_and_dirty"

)

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

(

"motifs:r1"

)

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

(

"motifs:r2"

)

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

(

"motifs:rerun_motifsearch"

)

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

(

"motifs:residue_trim_file"

)

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

(

"motifs:restrict_to_wt"

)

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

(

"motifs:rotlevel"

)

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

(

"motifs:rots2add"

)

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

(

"motifs:run_motifs"

)

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

(

"motifs:special_rotweight"

)

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

(

"motifs:target_aa"

)

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

(

"motifs:target_dna_defs"

)

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

(

"motifs:water_score_cutoff"

)

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

(

"motifs:z1"

)

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

(

"motifs:z2"

)

Variable Documentation

BooleanOptionKey const basic::options::OptionKeys::motifs::aromatic_motifs("motifs:aromatic_motifs")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::BPData("motifs:BPData")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::build_residue_file("motifs:build_residue_file")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::clear_bprots("motifs:clear_bprots")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::close_enough("motifs:close_enough")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::constraint_max("motifs:constraint_max")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::data_file("motifs:data_file")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::dtest("motifs:dtest")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::dump_motifs("motifs:dump_motifs")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::duplicate_angle_cutoff("motifs:duplicate_angle_cutoff")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::duplicate_dist_cutoff("motifs:duplicate_dist_cutoff")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::duplicate_motif_cutoff("motifs:duplicate_motif_cutoff")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::elec_max_threshold("motifs:elec_max_threshold")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::elec_min_threshold("motifs:elec_min_threshold")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::eliminate_weak_motifs("motifs:eliminate_weak_motifs")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::expand_motifs("motifs:expand_motifs")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::file_prefix("motifs:file_prefix")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::flex_sugar("motifs:flex_sugar")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::hb_score_cutoff("motifs:hb_score_cutoff")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::hbond_max_threshold("motifs:hbond_max_threshold")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::hbond_min_threshold("motifs:hbond_min_threshold")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::keep_motif_xtal_location("motifs:keep_motif_xtal_location")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::ligand_motif_sphere("motifs:ligand_motif_sphere")

Referenced by add_rosetta_options_2().

FileVectorOptionKey const basic::options::OptionKeys::motifs::list_dnaconformers("motifs:list_dnaconformers")

Referenced by add_rosetta_options_2().

FileVectorOptionKey const basic::options::OptionKeys::motifs::list_motifs("motifs:list_motifs")

Referenced by add_rosetta_options_2().

IntegerOptionKey const basic::options::OptionKeys::motifs::max_depth("motifs:max_depth")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::minimize("motifs:minimize")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::minimize_dna("motifs:minimize_dna")

Referenced by add_rosetta_options_2().

StringVectorOptionKey const basic::options::OptionKeys::motifs::motif_build_defs("motifs:motif_build_defs")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::motif_build_position_chain("motifs:motif_build_position_chain")

Referenced by add_rosetta_options_2().

IntegerVectorOptionKey const basic::options::OptionKeys::motifs::motif_build_positions("motifs:motif_build_positions")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::motif_filename("motifs:motif_filename")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::motif_flexible_loop_file("motifs:motif_flexible_loop_file")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::motif_output_directory("motifs:motif_output_directory")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::motifs("motifs")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::no_rotamer_bump("motifs:no_rotamer_bump")

Referenced by add_rosetta_options_2().

IntegerOptionKey const basic::options::OptionKeys::motifs::num_repacks("motifs:num_repacks")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::output_file("motifs:output_file")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::pack_max_threshold("motifs:pack_max_threshold")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::pack_min_threshold("motifs:pack_min_threshold")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::pack_score_cutoff("motifs:pack_score_cutoff")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::place_adduct_waters("motifs:place_adduct_waters")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::preminimize_motif_pdbs("motifs:preminimize_motif_pdbs")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::preminimize_motif_pdbs_sconly("motifs:preminimize_motif_pdbs_sconly")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::quick_and_dirty("motifs:quick_and_dirty")

Referenced by add_rosetta_options_2(), and add_rosetta_options_3().

RealOptionKey const basic::options::OptionKeys::motifs::r1("motifs:r1")

Referenced by add_rosetta_options_2(), and Solver_NU::calculate_rho().

RealOptionKey const basic::options::OptionKeys::motifs::r2("motifs:r2")

Referenced by add_rosetta_options_2(), and Solver_NU::calculate_rho().

BooleanOptionKey const basic::options::OptionKeys::motifs::rerun_motifsearch("motifs:rerun_motifsearch")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::residue_trim_file("motifs:residue_trim_file")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::restrict_to_wt("motifs:restrict_to_wt")

Referenced by add_rosetta_options_2().

IntegerOptionKey const basic::options::OptionKeys::motifs::rotlevel("motifs:rotlevel")

Referenced by add_rosetta_options_2().

IntegerOptionKey const basic::options::OptionKeys::motifs::rots2add("motifs:rots2add")

Referenced by add_rosetta_options_2().

BooleanOptionKey const basic::options::OptionKeys::motifs::run_motifs("motifs:run_motifs")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::special_rotweight("motifs:special_rotweight")

Referenced by add_rosetta_options_2().

StringOptionKey const basic::options::OptionKeys::motifs::target_aa("motifs:target_aa")

Referenced by add_rosetta_options_2().

StringVectorOptionKey const basic::options::OptionKeys::motifs::target_dna_defs("motifs:target_dna_defs")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::water_score_cutoff("motifs:water_score_cutoff")

Referenced by add_rosetta_options_2().

RealOptionKey const basic::options::OptionKeys::motifs::z1("motifs:z1")

Referenced by add_rosetta_options_2(), numeric::kinematic_closure::dixon_sturm(), and numeric::linear_algebra::qzvec().

RealOptionKey const basic::options::OptionKeys::motifs::z2("motifs:z2")

Referenced by add_rosetta_options_2(), and numeric::kinematic_closure::dixon_sturm().