| active_site_grid() const | protocols::match::downstream::DownstreamBuilder | inlineprotected |
| active_site_grid_set() const | protocols::match::downstream::DownstreamBuilder | inlineprotected |
| atom1_atom2_atom3_angle() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| atom1_atom2_distance() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| atom1_belongs_in_active_site() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| atom1_radius() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| atom2_atom3_distance() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| atom2_belongs_in_active_site() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| atom2_radius() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| atom3_belongs_in_active_site() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| atom3_radius() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| atom_radii_ | protocols::match::downstream::LigandConformerBuilder | private |
| atom_required_in_active_site_ | protocols::match::downstream::LigandConformerBuilder | private |
| AtomID typedef | protocols::match::downstream::DownstreamBuilder | |
| atoms_123_ | protocols::match::downstream::LigandConformerBuilder | private |
| ats123_reqd_in_active_site_ | protocols::match::downstream::LigandConformerBuilder | private |
| bbgrid() const | protocols::match::downstream::DownstreamBuilder | inlineprotected |
| bbgrid_set() const | protocols::match::downstream::DownstreamBuilder | inlineprotected |
| build(HTReal const &atom3_frame, Size const scaffold_build_point_id, Size const upstream_conf_id, Size const external_geometry_id, core::conformation::Residue const &upstream_residue) const | protocols::match::downstream::LigandConformerBuilder | virtual |
| build_conformer_group(Size const confgrp_id, HTReal const &atom3_frame, Size const scaffold_build_point_id, Size const upstream_conf_id, Size const external_geometry_id, core::conformation::Residue const &upstream_residue) const | protocols::match::downstream::LigandConformerBuilder | private |
| clone() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| compatible(Hit const &my_hit, DownstreamBuilder const &other, Hit const &other_hit, bool first_dispatch=true) const | protocols::match::downstream::LigandConformerBuilder | virtual |
| compatible(Hit const &my_hit, LigandConformerBuilder const &other, Hit const &other_hit, bool first_dispatch=true) const | protocols::match::downstream::LigandConformerBuilder | virtual |
| protocols::match::downstream::DownstreamBuilder::compatible(Hit const &my_hit, RigidLigandBuilder const &other, Hit const &other_hit, bool first_dispatch=true) const | protocols::match::downstream::DownstreamBuilder | virtual |
| conformer_group_for_conformer_ | protocols::match::downstream::LigandConformerBuilder | private |
| conformer_group_indices_ | protocols::match::downstream::LigandConformerBuilder | private |
| coordinates_from_hit(Hit const &hit, utility::vector1< AtomID > const &atom_indices, utility::vector1< Vector > &atom_coords) const | protocols::match::downstream::LigandConformerBuilder | virtual |
| determine_redundant_conformer_groups(utility::vector1< core::Size > const &relevant_atom_indices) | protocols::match::downstream::LigandConformerBuilder | |
| downstream_pose_from_hit(Hit const &hit) const | protocols::match::downstream::LigandConformerBuilder | virtual |
| downstream_restype_ | protocols::match::downstream::LigandConformerBuilder | private |
| DownstreamBuilder() | protocols::match::downstream::DownstreamBuilder | |
| DownstreamBuilder(DownstreamBuilder const &) | protocols::match::downstream::DownstreamBuilder | |
| get_lig_conformers(core::Size conf_id) const | protocols::match::downstream::LigandConformerBuilder | virtual |
| get_upstream_restype() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| hits_potentially_incompatible() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| HTReal typedef | protocols::match::downstream::DownstreamBuilder | |
| idealize_conformers_ | protocols::match::downstream::LigandConformerBuilder | private |
| ignore_h_collisions(bool setting) | protocols::match::downstream::LigandConformerBuilder | |
| ignore_h_collisions_ | protocols::match::downstream::LigandConformerBuilder | private |
| initialize_conformers(core::conformation::Residue const &residue) | protocols::match::downstream::LigandConformerBuilder | private |
| initialize_from_residue(Size atom1, Size atom2, Size atom3, Size orientation_atom1, Size orientation_atom2, Size orientation_atom3, core::conformation::Residue const &residue) | protocols::match::downstream::LigandConformerBuilder | |
| initialize_upstream_nonbonded_min_separation_d2() | protocols::match::downstream::LigandConformerBuilder | private |
| initialize_upstream_residue(core::chemical::ResidueTypeCOP upstream_res, core::scoring::etable::count_pair::CountPairFunctionCOP count_pair=0) | protocols::match::downstream::LigandConformerBuilder | |
| lig_conformers_ | protocols::match::downstream::LigandConformerBuilder | private |
| LigandConformerBuilder() | protocols::match::downstream::LigandConformerBuilder | |
| LigandConformerBuilder(LigandConformerBuilder const &) | protocols::match::downstream::LigandConformerBuilder | |
| min_sep_d2_from_upstream_atoms_ | protocols::match::downstream::LigandConformerBuilder | private |
| n_possible_hits_per_at3frame() const | protocols::match::downstream::LigandConformerBuilder | virtual |
| non_collision_detection_atoms_reqd_in_active_site_ | protocols::match::downstream::LigandConformerBuilder | private |
| occ_space() const | protocols::match::downstream::DownstreamBuilder | inlineprotected |
| occ_space_set() const | protocols::match::downstream::DownstreamBuilder | inlineprotected |
| orientation_atoms_ | protocols::match::downstream::LigandConformerBuilder | private |
| parent typedef | protocols::match::downstream::LigandConformerBuilder | |
| radii_123_ | protocols::match::downstream::LigandConformerBuilder | private |
| Real typedef | protocols::match::downstream::DownstreamBuilder | |
| require_atom_to_reside_in_active_site(core::id::AtomID const &id) | protocols::match::downstream::LigandConformerBuilder | virtual |
| rmsd_unique_cutoff_ | protocols::match::downstream::LigandConformerBuilder | private |
| set_active_site_grid(ActiveSiteGridCOP active_site_grid) | protocols::match::downstream::DownstreamBuilder | |
| set_bb_grid(BumpGridCOP bbgrid) | protocols::match::downstream::LigandConformerBuilder | virtual |
| set_occupied_space_hash(OccupiedSpaceHashCOP occ_space) | protocols::match::downstream::DownstreamBuilder | |
| upstream_restype_ | protocols::match::downstream::LigandConformerBuilder | private |
| Vector typedef | protocols::match::downstream::DownstreamBuilder | |
| ~DownstreamBuilder() | protocols::match::downstream::DownstreamBuilder | virtual |
| ~LigandConformerBuilder() | protocols::match::downstream::LigandConformerBuilder | virtual |
1.8.4