Rosetta Protocols  2014.35
protocols::match::Matcher Member List

This is the complete list of members for protocols::match::Matcher, including all inherited members.

active_site_grid_protocols::match::Matcherprivate
add_external_geometry_samples_for_constraint(Size cst_id, core::chemical::ResidueTypeCOP restype, utility::vector1< std::string > const &upstream_launch_atoms, utility::vector1< core::id::AtomID > const &downstream_3atoms, toolbox::match_enzdes_util::ExternalGeomSampler const &exgeom, Size const exgeom_id, bool enumerate_ligand_rotamers=false, bool catalytic_bond=false, bool build_round1_hits_twice=false)protocols::match::Matcher
add_secondary_downstream_match_geometry_for_constraint(Size geom_cst_id, core::chemical::ResidueTypeCOP candidate_restype, core::chemical::ResidueTypeCOP downstream_restype, utility::vector1< Size > const &candidate_atids, utility::vector1< Size > const &target_atids, toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi, std::string SecMatchStr, core::pose::Pose const &upstream_pose, bool catalytic_bond)protocols::match::Matcher
add_secondary_upstream_match_geometry_for_constraint(Size geom_cst_id, Size target_geom_cst_id, core::chemical::ResidueTypeCOP candidate_restype, core::chemical::ResidueTypeCOP target_restype, utility::vector1< Size > const &candidate_atids, utility::vector1< Size > const &target_atids, toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi, std::string SecMatchStr, core::pose::Pose const &upstream_pose)protocols::match::Matcher
add_upstream_restype_for_constraint(Size cst_id, core::chemical::ResidueTypeCOP restype)protocols::match::Matcher
all_build_points_protocols::match::Matcherprivate
all_downstream_algorithms_protocols::match::Matcherprivate
all_downstream_builders_protocols::match::Matcherprivate
bb_grid_protocols::match::Matcherprivate
BoundingBox typedefprotocols::match::Matcher
build_point(Size index) const protocols::match::Matcher
build_point(Size index)protocols::match::Matcher
build_round1_hits_twice_protocols::match::Matcherprivate
build_set_id_for_restype_protocols::match::Matcherprivate
check_downstream_hit_incompatibility(match const &m, utility::LexicographicalIterator &lex) const protocols::match::Matcherprivate
check_non_upstream_only_hit_incompatibility(match_dspos1 const &m1, utility::LexicographicalIterator &lex, output::MatchProcessor const &processor) const protocols::match::Matcherprivate
check_potential_dsbuilder_incompatibility_protocols::match::Matchermutableprivate
create_ds_builder(Size const cst_id, core::chemical::ResidueTypeCOP restype, utility::vector1< std::string > const &upstream_launch_atoms, utility::vector1< core::id::AtomID > const &downstream_3atoms, bool enumerate_ligand_rotamers, bool catalytic_bond)protocols::match::Matcherprivate
desymmeterize_upstream_restype_for_constraint(Size cst_id)protocols::match::Matcher
downstream_algorithms(Size cst_id) const protocols::match::Matcher
downstream_algorithms_protocols::match::Matcherprivate
downstream_atoms_required_inside_active_site_protocols::match::Matcherprivate
downstream_builder(Size cst_id) const protocols::match::Matcher
downstream_builder(Size)protocols::match::Matcher
downstream_builders(Size cst_id) const protocols::match::Matcher
downstream_builders_protocols::match::Matcherprivate
downstream_orientation_atoms_protocols::match::Matcherprivate
downstream_pose() const protocols::match::Matcher
downstream_pose_protocols::match::Matcherprivate
dynamic_grid_refinement_protocols::match::Matcherprivate
erase_hit(downstream::DownstreamAlgorithm const &dsalg, Size geom_cst_id_for_hit, HitListIterator const &iter)protocols::match::Matcher
euclidean_bin_widths_protocols::match::Matcherprivate
euler_bin_widths_protocols::match::Matcherprivate
find_hits()protocols::match::Matcher
finish_hit_generation_for_constraint(Size cst_id)protocols::match::Matcherprivate
generate_hits()protocols::match::Matcherprivate
generate_hits_for_constraint(Size cst_id)protocols::match::Matcherprivate
geom_cst_has_primary_modification_protocols::match::Matcherprivate
geom_csts_with_primary_hitlist_modificiations_protocols::match::Matcherprivate
geomcst_is_upstream_only_protocols::match::Matcherprivate
get_pose_build_resids() const protocols::match::Matcher
gridlig_fname_protocols::match::Matcherprivate
has_upstream_only_geomcsts() const protocols::match::Matcher
hit_list_begin(Size geom_cst_id)protocols::match::Matcher
hit_list_end(Size geom_cst_id)protocols::match::Matcher
HitList typedefprotocols::match::Matcher
HitListConstIterator typedefprotocols::match::Matcher
HitListIterator typedefprotocols::match::Matcher
hits(Size cst_id) const protocols::match::Matcher
hits_protocols::match::Matcherprivate
increment_upstream_only_hit_combination(utility::vector1< HitPtrListCOP > const &upstream_only_hits, Size starting_point, utility::vector1< std::list< Hit const * >::const_iterator > &upstream_only_hit_iterators, Size &last_upstream_only_geomcst_advanced) const protocols::match::Matcherprivate
initialize_active_site_grid()protocols::match::Matcherprivate
initialize_bump_grids()protocols::match::Matcherprivate
initialize_downstream_algorithms()protocols::match::Matcherprivate
initialize_from_file(toolbox::match_enzdes_util::EnzConstraintIO const &enz_data, MatcherTask const &task)protocols::match::Matcher
initialize_from_task(MatcherTask const &task)protocols::match::Matcher
initialize_occupied_space_hash()protocols::match::Matcherprivate
initialize_scaffold_build_points()protocols::match::Matcherprivate
Matcher()protocols::match::Matcher
Matcher(Matcher const &)protocols::match::Matcherprivate
n_geometric_constraints() const protocols::match::Matcherinline
n_geometric_constraints_protocols::match::Matcherprivate
nonconst_downstream_algorithms(Size cst_id)protocols::match::Matcher
note_primary_change_to_geom_csts_hitlist(Size geom_cst_id)protocols::match::Matcherprivate
occ_space_bounding_box_protocols::match::Matcherprivate
occ_space_hash() const protocols::match::Matcher
occ_space_hash()protocols::match::Matcher
occ_space_hash_protocols::match::Matcherprivate
operator=(Matcher const &rhs)protocols::match::Matcherprivate
original_scaffold_residue_bump_grids_protocols::match::Matcherprivate
output_match_dspos1_for_geomcst_protocols::match::Matcherprivate
output_matches_as_singular_downstream_positioning_protocols::match::Matcherprivate
per_constraint_build_points(Size cst_id) const protocols::match::Matcher
per_constraint_build_points_protocols::match::Matcherprivate
per_cst_build_resids_protocols::match::Matcherprivate
pose_build_resids_protocols::match::Matcherprivate
predict_n_matches_for_hit_subsets(Vector const &euclidean_bin_widths, Vector const &euler_bin_widths, utility::vector1< std::list< Hit const * > > const &neighbor_hits, Size accuracy_threshold) const protocols::match::Matcherprivate
prepare_for_hit_generation_for_constraint(Size cst_id)protocols::match::Matcherprivate
process_matches(output::MatchProcessor &processor) const protocols::match::Matcher
process_matches_all_hit_combos_for_hit_subsets(output::MatchProcessor &processor, HitHasher &hit_hasher, utility::vector1< std::list< Hit const * > > const &neighbor_hits) const protocols::match::Matcherprivate
process_matches_main_loop_enumerating_all_hit_combos(output::MatchProcessor &processor) const protocols::match::Matcherprivate
process_matches_where_one_geomcst_defines_downstream_location(output::MatchProcessor &processor) const protocols::match::Matcherprivate
read_gridlig_file_protocols::match::Matcherprivate
Real typedefprotocols::match::Matcher
refine_grid_and_subsample_for_hit_subsets(Vector &good_euclidean_bin_widths, Vector &good_euler_bin_widths, utility::vector1< std::list< Hit const * > > const &neighbor_hits) const protocols::match::Matcherprivate
regenerate_round1_hits()protocols::match::Matcherprivate
relevant_downstream_atoms_protocols::match::Matcherprivate
representative_downstream_algorithm(Size cst_id) const protocols::match::Matcher
representative_downstream_algorithm_protocols::match::Matcherprivate
same_build_resids_for_all_csts_protocols::match::Matcherprivate
select_hit_representatives(utility::vector1< utility::vector1< Hit const * > > const &hit_vectors, utility::vector1< Size > &n_hits_per_geomcst, utility::vector1< utility::vector1< Size > > &reps) const protocols::match::Matcherprivate
set_bump_tolerance(Real permitted_overlap)protocols::match::Matcher
set_downstream_pose(core::pose::Pose const &pose, utility::vector1< core::id::AtomID > orientation_atoms)protocols::match::Matcher
set_fa_dun_cutoff_for_constraint(Size cst_id, core::chemical::ResidueTypeCOP restype, core::Real fa_dun_cutoff)protocols::match::Matcher
set_hash_euclidean_bin_width(Real width)protocols::match::Matcher
set_hash_euclidean_bin_widths(Vector widths)protocols::match::Matcher
set_hash_euler_bin_width(Real width)protocols::match::Matcher
set_hash_euler_bin_widths(Vector widths)protocols::match::Matcher
set_n_geometric_constraints(Size n_constraints)protocols::match::Matcher
set_occupied_space_bounding_box(BoundingBox const &bb)protocols::match::Matcher
set_original_scaffold_build_points(utility::vector1< Size > const &resids)protocols::match::Matcher
set_original_scaffold_build_points_for_constraint(Size cst_id, utility::vector1< Size > const &resids)protocols::match::Matcher
set_sample_startegy_for_constraint(Size cst_id, core::chemical::ResidueTypeCOP restype, Size chi, upstream::SampleStrategyData const &strat)protocols::match::Matcher
set_upstream_pose(core::pose::Pose const &pose)protocols::match::Matcher
Size typedefprotocols::match::Matcher
subsample_hits(Vector const &euclidean_bin_widths, Vector const &euler_bin_widths, utility::vector1< std::list< Hit const * > > const &neighbor_hits) const protocols::match::Matcherprivate
test_upstream_only_hit_incompatibility(match const &m, utility::vector1< HitPtrListCOP > const &upstream_only_hits, utility::vector1< std::list< Hit const * >::const_iterator > &upstream_only_hit_iterators, Size &last_upstream_only_geomcst_advanced, output::MatchProcessor const &processor) const protocols::match::Matcherprivate
test_upstream_only_hit_incompatibility(match_dspos1 const &m1, utility::vector1< HitPtrListCOP > const &upstream_only_hits, utility::vector1< std::list< Hit const * >::const_iterator > &upstream_only_hit_iterators, Size &last_upstream_only_geomcst_advanced, output::MatchProcessor const &processor) const protocols::match::Matcherprivate
upstream_builder(Size cst_id) const protocols::match::Matcher
upstream_builder(Size cst_id)protocols::match::Matcher
upstream_builders_protocols::match::Matcherprivate
upstream_pose() const protocols::match::Matcher
upstream_pose_protocols::match::Matcherprivate
upstream_resids_and_radii_defining_active_site_protocols::match::Matcherprivate
use_input_sc_protocols::match::Matcherprivate
Vector typedefprotocols::match::Matcher
~Matcher()protocols::match::Matchervirtual