| add_constraints_to_working_pose(const core::Size trip_atom_1, const core::Size trip_atom_2, const core::Size trip_atom_3, const core::Size working_position, const core::conformation::ResidueOP ligresOP) | LigandDiscoverySearch | private |
| add_ligand_to_pose_residuetypeset(const core::chemical::MutableResidueTypeOP lig_mrt) | LigandDiscoverySearch | private |
| add_working_positions(utility::vector1< core::Size > working_positions) | LigandDiscoverySearch | |
| add_working_positions(core::Size working_positions) | LigandDiscoverySearch | |
| all_residues_ | LigandDiscoverySearch | private |
| atom_trios typedef | LigandDiscoverySearch | |
| clash_pose_grid_ | LigandDiscoverySearch | private |
| ddg_cutoff_ | LigandDiscoverySearch | private |
| derive_adjacent_atoms_of_ligand(const core::conformation::ResidueOP ligresOP, const core::chemical::AtomTypeSetCOP atset) | LigandDiscoverySearch | |
| discover(std::string output_prefix) | LigandDiscoverySearch | |
| fa_atr_cutoff_ | LigandDiscoverySearch | private |
| fa_atr_fxn_ | LigandDiscoverySearch | private |
| fa_atr_rep_cutoff_ | LigandDiscoverySearch | private |
| fa_atr_rep_fxn_ | LigandDiscoverySearch | private |
| fa_rep_cutoff_ | LigandDiscoverySearch | private |
| fa_rep_fxn_ | LigandDiscoverySearch | private |
| get_all_residues() | LigandDiscoverySearch | |
| get_motif_library() | LigandDiscoverySearch | |
| get_motif_sublibrary_by_aa(std::string residue_name) | LigandDiscoverySearch | |
| get_pose_ddg(core::scoring::ScoreFunctionOP score_fxn, core::pose::PoseOP &my_pose) | LigandDiscoverySearch | |
| get_working_pose() | LigandDiscoverySearch | |
| get_working_positions() | LigandDiscoverySearch | |
| LigandDiscoverySearch(core::pose::PoseOP pose_from_PDB, protocols::motifs::MotifCOPs motif_library, utility::vector1< core::conformation::ResidueOP > all_residues, utility::vector1< core::Size > working_position) | LigandDiscoverySearch | |
| LigandDiscoverySearch() | LigandDiscoverySearch | private |
| make_HighResDockOP_for_discovery(const core::scoring::ScoreFunctionOP my_fxn) | LigandDiscoverySearch | private |
| make_minipose(core::pose::PoseOP &minipose, const core::conformation::ResidueOP ligresOP) | LigandDiscoverySearch | private |
| min_motifs_cutoff_ | LigandDiscoverySearch | private |
| min_sig_motifs_cutoff_ | LigandDiscoverySearch | private |
| motif_library_ | LigandDiscoverySearch | private |
| motif_library_for_select_residue_ | LigandDiscoverySearch | private |
| original_pose_ | LigandDiscoverySearch | private |
| real_motif_ratio_cutoff_ | LigandDiscoverySearch | private |
| reset_working_pose() | LigandDiscoverySearch | private |
| run_HighResDock_on_working_pose(const protocols::ligand_docking::HighResDockerOP my_HighResDocker) | LigandDiscoverySearch | private |
| score_minipose(const core::pose::PoseOP &minipose, core::Real &fa_rep, core::Real &fa_atr, core::Real &fa_atr_rep_score_before) | LigandDiscoverySearch | private |
| seed_cutoff_values() | LigandDiscoverySearch | private |
| set_all_residues(utility::vector1< core::conformation::ResidueOP > all_residues) | LigandDiscoverySearch | |
| set_motif_library(protocols::motifs::MotifCOPs motif_library) | LigandDiscoverySearch | |
| set_motif_library(protocols::motifs::MotifLibrary motif_library) | LigandDiscoverySearch | |
| set_working_pose(core::pose::PoseOP pose_from_PDB) | LigandDiscoverySearch | |
| set_working_pose(core::pose::Pose pose_from_PDB) | LigandDiscoverySearch | |
| set_working_positions(utility::vector1< core::Size > working_position) | LigandDiscoverySearch | |
| set_working_positions(core::Size working_position) | LigandDiscoverySearch | |
| setup_score_functions() | LigandDiscoverySearch | private |
| sf_pose_grid_ | LigandDiscoverySearch | private |
| whole_fxn_cutoff_ | LigandDiscoverySearch | private |
| whole_score_fxn_ | LigandDiscoverySearch | private |
| working_fxn_ | LigandDiscoverySearch | private |
| working_pose_ | LigandDiscoverySearch | private |
| working_positions_ | LigandDiscoverySearch | private |
| ~LigandDiscoverySearch() | LigandDiscoverySearch | |
