| advanced_select_points(core::pose::Pose const &pose, core::Size const ligid, core::Real radius, core::Real skeleton_threshold_const, core::Size neighborhood_size, core::Size pool_size) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| apply(LigandConformer &lig) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| assign_neighbors(numeric::xyzVector< core::Real > point, core::Size neighborhood_size=27) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| check_voxel_distance_to_receptor(numeric::xyzVector< core::Real > voxel, core::pose::Pose const &pose, core::Size const ligid) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| chi_step_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| erode_points(utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > selected_points, core::Size neighborhood_size=27) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| estimate_nstruct_sample(core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, core::Size const ntotal) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| faster_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| find_biggest_skeleton(utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > eroded_points) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| find_network(numeric::xyzVector< core::Real > start_point, utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > network, utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > eroded_points, core::Real distance_cutoff=3.1) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| gridStep_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| is_base_blob(utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > network, core::conformation::Residue const lig) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| is_point_in_network(numeric::xyzVector< core::Real > point, utility::vector1< utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > > networks) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| is_point_in_search_group(utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > selected_points, numeric::xyzVector< core::Real > point_to_compare) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| istruct_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| LigandAligner() | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| LigandAligner(bool use_pharmacophore, utility::vector1< core::Size > const &movable_scs, bool faster) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| movable_scs_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| perturb_lig(core::pose::Pose &pose, utility::vector1< core::Size > ligid) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| points_to_search() const | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| points_to_search_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| prealigned_input(bool setting) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| prealigned_input() const | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| prealigned_input_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| print_skeletons_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| randomize_lig(core::pose::Pose &pose, utility::vector1< core::Size > ligid, numeric::xyzVector< core::Real > const &T) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| refine_input(bool setting) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| refine_input_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| rot_step_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| sample_ring_conformers() const | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| sample_ring_conformers_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| score_base_blob(utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > network, core::pose::Pose const &pose, core::conformation::Residue const lig) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| score_satellite_blob(utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > base_blob, utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > satellite_blob, core::pose::Pose const &pose, core::conformation::Residue const lig) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| select_points(core::pose::Pose const &pose, core::Size const ligid, core::Real radius, core::Real skeleton_threshold_const=2.5, core::Size neighborhood_size=27) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| set_chi_step(core::Size chi_step_in) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_constraints(core::pose::Pose &pose, utility::vector1< core::Size > ligids, utility::vector1< std::pair< core::Size, core::Size > > &marked_pairs, core::Real const w_prior=1.0, utility::vector1< core::Size > const &SrcPriorIDs=utility::vector1< core::Size >(), utility::vector1< core::Size > const &TgtPriorIDs=utility::vector1< core::Size >()) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| set_hard_constraint_on_marked(core::pose::Pose &pose, utility::vector1< core::Size > ligid, utility::vector1< std::pair< core::Size, core::Size > > const &marked_pairs) const | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| set_pharmacophore_reference(core::pose::Pose const &pose) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | |
| set_rot_step(core::Size rot_step_in) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_sample_ring_conformers(bool const setting) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_sf(GridScorerOP sf_in) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_target(ConstraintInfo const &tgt_in) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_trans_step(core::Size trans_step_in) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| set_use_pharmacophore(bool setting) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| sf_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| sort_satellite_blobs(utility::vector1< utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > > satellites, utility::vector1< std::pair< numeric::xyzVector< core::Real >, core::Real > > base_blob) | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| target_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| trans_step_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| use_pharmacophore() const | protocols::ligand_docking::ga_ligand_dock::LigandAligner | inline |
| use_pharmacophore_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
| weighted_score_ij_ | protocols::ligand_docking::ga_ligand_dock::LigandAligner | private |
