| bp_rotamers(Size const seqpos) | protocols::motifs::LigandMotifSearch | |
| bpdata_ | protocols::motifs::LigandMotifSearch | private |
| bpdata_filename_ | protocols::motifs::LigandMotifSearch | private |
| build_positionOPs() const | protocols::motifs::LigandMotifSearch | inline |
| build_positionOPs_ | protocols::motifs::LigandMotifSearch | private |
| BuildPosition_from_Size(Pose const &pose, Size const input_BP) | protocols::motifs::LigandMotifSearch | |
| clear_bprots_ | protocols::motifs::LigandMotifSearch | private |
| data_ | protocols::motifs::LigandMotifSearch | private |
| data_filename_ | protocols::motifs::LigandMotifSearch | private |
| defs2BuildPositions(Pose const &pose, protocols::dna::DnaDesignDefOPs const &defs) | protocols::motifs::LigandMotifSearch | |
| defs2BuildPositions_findts(Pose const &pose, protocols::dna::DnaDesignDefOPs const &defs) | protocols::motifs::LigandMotifSearch | |
| dna_positions() const | protocols::motifs::LigandMotifSearch | inline |
| dna_positions_ | protocols::motifs::LigandMotifSearch | private |
| DnaDesignDefOP typedef | protocols::motifs::LigandMotifSearch | |
| DnaDesignDefOPs typedef | protocols::motifs::LigandMotifSearch | |
| dtest_cutoff() const | protocols::motifs::LigandMotifSearch | inline |
| dtest_cutoff_ | protocols::motifs::LigandMotifSearch | private |
| dump_motifs_ | protocols::motifs::LigandMotifSearch | private |
| get_rotamers() | protocols::motifs::LigandMotifSearch | |
| get_sphere_aa(Pose const &pose, core::Real cut1) | protocols::motifs::LigandMotifSearch | |
| identify_motif_build_positions(Pose const &pose, Sizes &build_positions) | protocols::motifs::LigandMotifSearch | |
| identify_motif_BuildPositions(Pose const &pose) | protocols::motifs::LigandMotifSearch | |
| incorporate_motifs(Pose const &pose) | protocols::motifs::LigandMotifSearch | |
| init_options() | protocols::motifs::LigandMotifSearch | private |
| initialize(Pose const &pose) | protocols::motifs::LigandMotifSearch | |
| initialize(Pose const &pose, utility::vector1< Size > &input_BPs) | protocols::motifs::LigandMotifSearch | |
| LigandMotifSearch() | protocols::motifs::LigandMotifSearch | |
| LigandMotifSearch(LigandMotifSearch const &src) | protocols::motifs::LigandMotifSearch | |
| map2keyvector(std::map< Size, std::set< std::string > > mappositions) | protocols::motifs::LigandMotifSearch | |
| minimize() const | protocols::motifs::LigandMotifSearch | inline |
| minimize_ | protocols::motifs::LigandMotifSearch | private |
| motif_library() const | protocols::motifs::LigandMotifSearch | inline |
| motif_library_ | protocols::motifs::LigandMotifSearch | private |
| operator=(LigandMotifSearch const &src) | protocols::motifs::LigandMotifSearch | |
| output_ | protocols::motifs::LigandMotifSearch | private |
| output_filename_ | protocols::motifs::LigandMotifSearch | private |
| override_option_input(Real const &r1, Real const &z1, Real const &r2, Real const &z2, Real const &d1, Size const &rlevel) | protocols::motifs::LigandMotifSearch | |
| PackerTask typedef | protocols::motifs::LigandMotifSearch | |
| Pose typedef | protocols::motifs::LigandMotifSearch | |
| position_vector_setup(Pose const &pose) | protocols::motifs::LigandMotifSearch | |
| protein_dna_motif() | protocols::motifs::LigandMotifSearch | |
| protein_DNA_motif_build_positions_JA(Pose const &pose, Sizes &build_positions, Sizes &target_positions) | protocols::motifs::LigandMotifSearch | |
| protein_DNA_motif_target_positions_JA(Pose const &pose, Sizes &build_positions, Sizes &target_positions, Sizes &short_tl) | protocols::motifs::LigandMotifSearch | |
| protein_positions() const | protocols::motifs::LigandMotifSearch | inline |
| protein_positions_ | protocols::motifs::LigandMotifSearch | private |
| quick_and_dirty_ | protocols::motifs::LigandMotifSearch | private |
| Real typedef | protocols::motifs::LigandMotifSearch | |
| reset_option_input() | protocols::motifs::LigandMotifSearch | |
| rmsd_cutoff_1() const | protocols::motifs::LigandMotifSearch | inline |
| rmsd_cutoff_1_ | protocols::motifs::LigandMotifSearch | private |
| rmsd_cutoff_2() const | protocols::motifs::LigandMotifSearch | inline |
| rmsd_cutoff_2_ | protocols::motifs::LigandMotifSearch | private |
| rot_level() const | protocols::motifs::LigandMotifSearch | inline |
| rot_level_ | protocols::motifs::LigandMotifSearch | private |
| rots2add_ | protocols::motifs::LigandMotifSearch | private |
| run(Pose const &pose, utility::vector1< Size > &input_BPs) | protocols::motifs::LigandMotifSearch | |
| run(Pose const &pose, PackerTask &task) | protocols::motifs::LigandMotifSearch | |
| run(Pose const &pose, core::Real &ligand_motif_sphere) | protocols::motifs::LigandMotifSearch | |
| set_motif_library(MotifLibrary &motiflibrary) | protocols::motifs::LigandMotifSearch | |
| shorten_target_list(Pose const &pose, Size const bp, Sizes &full_tl) | protocols::motifs::LigandMotifSearch | |
| Size typedef | protocols::motifs::LigandMotifSearch | |
| Sizes typedef | protocols::motifs::LigandMotifSearch | |
| target_conformers_map() const | protocols::motifs::LigandMotifSearch | inline |
| target_conformers_map_ | protocols::motifs::LigandMotifSearch | private |
| target_positions() const | protocols::motifs::LigandMotifSearch | inline |
| target_positions_ | protocols::motifs::LigandMotifSearch | private |
| ztest_cutoff_1() const | protocols::motifs::LigandMotifSearch | inline |
| ztest_cutoff_1_ | protocols::motifs::LigandMotifSearch | private |
| ztest_cutoff_2() const | protocols::motifs::LigandMotifSearch | inline |
| ztest_cutoff_2_ | protocols::motifs::LigandMotifSearch | private |
| ~LigandMotifSearch() | protocols::motifs::LigandMotifSearch | virtual |
1.8.4