Rosetta Utilities  2014.35
Functions | Variables
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")
 
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")
 
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
 
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
 

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"  )
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"  )
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().

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

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")
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")

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