| active_site_grid() const | protocols::match::downstream::DownstreamAlgorithm | inlineprotected |
| active_site_grid_set() const | protocols::match::downstream::DownstreamAlgorithm | inlineprotected |
| add_evaluator(SecMatchResiduePairEvaluatorCOP evaluator, core::Size mcfi_id) | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | |
| are_colliding(core::conformation::Residue const &us_res, core::conformation::Residue const &ds_res, utility::vector1< core::id::AtomID > const &ds_atoms, utility::vector1< core::Size > const &catalytic_atoms) const | protocols::match::downstream::DownstreamAlgorithm | |
| bbgrid() const | protocols::match::downstream::DownstreamAlgorithm | inlineprotected |
| build(core::Size const scaffold_build_point_id, core::Size const upstream_conf_id, core::conformation::Residue const &upstream_residue) const override | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | virtual |
| build_hits_at_all_positions(Matcher &matcher) override | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | virtual |
| catalytic_atoms_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| clone() const override | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | virtual |
| default_build_hits_at_all_positions(Matcher const &matcher) const | protocols::match::downstream::DownstreamAlgorithm | protected |
| downstream_atom_coordinates_needed_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| downstream_restype_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| DownstreamAlgorithm(core::Size geom_cst_id) | protocols::match::downstream::DownstreamAlgorithm | |
| DownstreamAlgorithm(DownstreamAlgorithm const &) | protocols::match::downstream::DownstreamAlgorithm | |
| ds_atom_present(core::Size index) const | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| Evaluator_MCFI_ID_Pair typedef | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | |
| EvaluatorSet typedef | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | |
| focused_geomcst_id_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| generates_primary_hits() const override | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | virtual |
| geom_cst_id() const | protocols::match::downstream::DownstreamAlgorithm | |
| get_dsbuilder() const | protocols::match::downstream::DownstreamAlgorithm | |
| get_min_sep_d2_from_upstream_atoms() const | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| hits_for_focused_geomcst_and_build_point_begin_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| hits_for_focused_geomcst_and_build_point_end_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| hits_for_focused_geomcst_end_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| hits_to_include_with_partial_match(match_dspos1 const &) const override | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | virtual |
| n_possible_hits_per_upstream_conformation() const override | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | virtual |
| occspace_rev_id_at_last_update_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| operator=(DownstreamAlgorithm const &) | protocols::match::downstream::DownstreamAlgorithm | |
| parent typedef | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | |
| prepare_for_hit_generation(Matcher &matcher) | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| prepare_for_hit_generation_at_target_build_point(Matcher &matcher, core::Size target_geomcst_id, upstream::ScaffoldBuildPoint const &target_build_point) | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| prepare_for_hit_generation_for_geomcst(Matcher &matcher, core::Size target_geomcst_id) | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| prepare_for_match_enumeration(Matcher const &) | protocols::match::downstream::DownstreamAlgorithm | virtual |
| respair_evaluators_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| respond_to_peripheral_hitlist_change(Matcher &matcher) override | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | virtual |
| respond_to_primary_hitlist_change(Matcher &matcher, core::Size round_just_completed) override | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | virtual |
| SecondaryMatcherToDownstreamResidue(core::pose::PoseCOP upstream_pose, core::Size geom_cst_id) | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | |
| set_active_site_grid(ActiveSiteGridCOP active_site_grid) | protocols::match::downstream::DownstreamAlgorithm | |
| set_bb_grid(BumpGridCOP bbgrid) | protocols::match::downstream::DownstreamAlgorithm | |
| set_catalytic_atoms(utility::vector1< core::Size > catalytic_atoms) | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | inline |
| set_downstream_restype(core::chemical::ResidueTypeCOP downstream_restype) | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | |
| set_ds_coords_needed(utility::vector1< core::id::AtomID > ds_coords) | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | inlineprivate |
| set_dsbuilder(DownstreamBuilderOP dsbuilder) | protocols::match::downstream::DownstreamAlgorithm | |
| set_focused_geomcst_id(core::Size focused_geomcst_id) | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | |
| set_target_rotamer_coords(TargetRotamerCoordsOP target_geomcst_coords) | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| Size typedef | protocols::match::downstream::DownstreamAlgorithm | |
| target_downstream_coords_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | mutableprivate |
| upstream_only() const override | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | virtual |
| upstream_pose_ | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | private |
| Vector typedef | protocols::match::downstream::DownstreamAlgorithm | |
| ~DownstreamAlgorithm() override | protocols::match::downstream::DownstreamAlgorithm | |
| ~SecondaryMatcherToDownstreamResidue() override | protocols::match::downstream::SecondaryMatcherToDownstreamResidue | |
1.8.7