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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")
 

Function Documentation

BooleanOptionKey const motifs::aromatic_motifs ( "motifs:aromatic_motifs"  )
StringOptionKey const motifs::BPData ( "motifs:BPData"  )
StringOptionKey const motifs::build_residue_file ( "motifs:build_residue_file"  )
BooleanOptionKey const motifs::clear_bprots ( "motifs:clear_bprots"  )
RealOptionKey const motifs::close_enough ( "motifs:close_enough"  )
StringOptionKey const motifs::data_file ( "motifs:data_file"  )
RealOptionKey const motifs::dtest ( "motifs:dtest"  )
BooleanOptionKey const motifs::dump_motifs ( "motifs:dump_motifs"  )
RealOptionKey const motifs::duplicate_angle_cutoff ( "motifs:duplicate_angle_cutoff"  )

Referenced by process_for_motifs().

RealOptionKey const motifs::duplicate_dist_cutoff ( "motifs:duplicate_dist_cutoff"  )

Referenced by process_for_motifs().

RealOptionKey const motifs::duplicate_motif_cutoff ( "motifs:duplicate_motif_cutoff"  )
RealOptionKey const motifs::elec_max_threshold ( "motifs:elec_max_threshold"  )

Referenced by process_for_motifs().

RealOptionKey const motifs::elec_min_threshold ( "motifs:elec_min_threshold"  )

Referenced by process_for_motifs().

BooleanOptionKey const motifs::eliminate_weak_motifs ( "motifs:eliminate_weak_motifs"  )
BooleanOptionKey const motifs::expand_motifs ( "motifs:expand_motifs"  )
StringOptionKey const motifs::file_prefix ( "motifs:file_prefix"  )
BooleanOptionKey const motifs::flex_sugar ( "motifs:flex_sugar"  )
RealOptionKey const motifs::hb_score_cutoff ( "motifs:hb_score_cutoff"  )
RealOptionKey const motifs::hbond_max_threshold ( "motifs:hbond_max_threshold"  )

Referenced by process_for_motifs().

RealOptionKey const motifs::hbond_min_threshold ( "motifs:hbond_min_threshold"  )

Referenced by process_for_motifs().

BooleanOptionKey const motifs::keep_motif_xtal_location ( "motifs:keep_motif_xtal_location"  )
RealOptionKey const motifs::ligand_motif_sphere ( "motifs:ligand_motif_sphere"  )
FileVectorOptionKey const motifs::list_dnaconformers ( "motifs:list_dnaconformers"  )
FileVectorOptionKey const motifs::list_motifs ( "motifs:list_motifs"  )
IntegerOptionKey const motifs::max_depth ( "motifs:max_depth"  )
BooleanOptionKey const motifs::minimize ( "motifs:minimize"  )
BooleanOptionKey const motifs::minimize_dna ( "motifs:minimize_dna"  )
StringVectorOptionKey const motifs::motif_build_defs ( "motifs:motif_build_defs"  )
IntegerVectorOptionKey const motifs::motif_build_positions ( "motifs:motif_build_positions"  )
StringOptionKey const motifs::motif_filename ( "motifs:motif_filename"  )

Referenced by find_close_motifs().

StringOptionKey const motifs::motif_flexible_loop_file ( "motifs:motif_flexible_loop_file"  )
StringOptionKey const motifs::motif_output_directory ( "motifs:motif_output_directory"  )
BooleanOptionKey const motifs::motifs ( "motifs"  )
BooleanOptionKey const motifs::no_rotamer_bump ( "motifs:no_rotamer_bump"  )
IntegerOptionKey const motifs::num_repacks ( "motifs:num_repacks"  )
StringOptionKey const motifs::output_file ( "motifs:output_file"  )
RealOptionKey const motifs::pack_max_threshold ( "motifs:pack_max_threshold"  )

Referenced by process_for_motifs().

RealOptionKey const motifs::pack_min_threshold ( "motifs:pack_min_threshold"  )

Referenced by process_for_motifs().

RealOptionKey const motifs::pack_score_cutoff ( "motifs:pack_score_cutoff"  )
BooleanOptionKey const motifs::place_adduct_waters ( "motifs:place_adduct_waters"  )
BooleanOptionKey const motifs::preminimize_motif_pdbs ( "motifs:preminimize_motif_pdbs"  )
BooleanOptionKey const motifs::preminimize_motif_pdbs_sconly ( "motifs:preminimize_motif_pdbs_sconly"  )
BooleanOptionKey const motifs::quick_and_dirty ( "motifs:quick_and_dirty"  )
RealOptionKey const motifs::r1 ( "motifs:r1"  )
RealOptionKey const motifs::r2 ( "motifs:r2"  )
BooleanOptionKey const motifs::rerun_motifsearch ( "motifs:rerun_motifsearch"  )
StringOptionKey const motifs::residue_trim_file ( "motifs:residue_trim_file"  )
BooleanOptionKey const motifs::restrict_to_wt ( "motifs:restrict_to_wt"  )
IntegerOptionKey const motifs::rotlevel ( "motifs:rotlevel"  )
IntegerOptionKey const motifs::rots2add ( "motifs:rots2add"  )
BooleanOptionKey const motifs::run_motifs ( "motifs:run_motifs"  )
RealOptionKey const motifs::special_rotweight ( "motifs:special_rotweight"  )
StringOptionKey const motifs::target_aa ( "motifs:target_aa"  )

Referenced by main().

StringVectorOptionKey const motifs::target_dna_defs ( "motifs:target_dna_defs"  )
RealOptionKey const motifs::water_score_cutoff ( "motifs:water_score_cutoff"  )
RealOptionKey const motifs::z1 ( "motifs:z1"  )
RealOptionKey const motifs::z2 ( "motifs:z2"  )