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Rosetta 3.5
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Rosetta 3.5
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Produce hits by hashing building the coordinates of the downstream partner The downstream partner is responsible for building itself from the coordinate frame of three of its atoms. The ExternalGeomSampler describes the ways to orient the downstream partner given the coordinates of the upstream partner. More...
#include <ClassicMatchAlgorithm.hh>
Public Types | |
| typedef DownstreamAlgorithm | parent |
| typedef core::Size | Size |
| typedef core::Real | Real |
| typedef numeric::HomogeneousTransform < Real > | HTReal |
 Public Types inherited from protocols::match::downstream::DownstreamAlgorithm | |
| typedef core::Size | Size |
| typedef core::Vector | Vector |
Public Member Functions | |
| ClassicMatchAlgorithm (Size geom_cst_id) | |
| virtual | ~ClassicMatchAlgorithm () |
| virtual DownstreamAlgorithmOP | clone () const |
| virtual std::list< Hit > | build_hits_at_all_positions (Matcher &matcher) |
| Main driver function for hit generation. The algorithm is responsible for generating hits at all scaffold build points that are valid for this geometric constraint. The base class provides an iterate-across-all-positions-and-splice-together-hit-lists implementation, however, derived classes may overload this function. The base class function is parallelizable with OpenMP. The returned hit list must be in sorted order by 1) hit.scaffold_build_id() and then by 2) hit.upstream_conf_id(). More... | |
| virtual void | respond_to_primary_hitlist_change (Matcher &matcher, Size round_just_completed) |
| Reset the occupied space grid for the matcher so that only those regions which contain hits from this geometric constraint are marked as occupied. More... | |
| virtual void | respond_to_peripheral_hitlist_change (Matcher &matcher) |
| Delete hits for this geometric constraint if they fall into now-empty regions of 6D. This step can be avoided if the occupied-space-grid's revision ID has not changed since the last time this function was invoked. More... | |
| virtual std::list< Hit > | build (Size const scaffold_build_point_id, Size const upstream_conf_id, core::conformation::Residue const &upstream_residue) const |
| Iterate across the external geom samplers that describe the rigid body orientations of the downstream partner from the coordinates of the upstream partner. More... | |
| virtual bool | upstream_only () const |
| This method returns 'false' since the classic match algorithm builds coordinates of the downstream partner and its hits should be hashed in 6D to generate matches. More... | |
| virtual bool | generates_primary_hits () const |
| This method returns 'true' since the classic matcher builds the downstream coordinates from scratch. More... | |
| virtual HitPtrListCOP | hits_to_include_with_partial_match (match_dspos1 const &m) const |
| This method should not be invoked on the ClassicMatchAlgorithm, since it returns "false" in its upstream_only method. More... | |
| virtual Size | n_possible_hits_per_upstream_conformation () const |
| std::list< Hit > | build_from_three_coords (Size const which_external_sampler, Size const scaffold_build_point_id, Size const upstream_conf_id, core::conformation::Residue const &upstream_residue) const |
| This function completes the building of the downstream conformation once the coordinates of the upstream conformation are known (and deemed non-colliding or, generally, pass any filter the upstream builder would use). More... | |
| void | set_residue_type (core::chemical::ResidueTypeCOP restype) |
| void | add_external_geom_sampler (toolbox::match_enzdes_util::ExternalGeomSampler const &sampler, Size const exgeom_id, std::string const &atom1, std::string const &atom2, std::string const &atom3, DownstreamBuilderCOP downstream_builder) |
| void | clear_external_geom_samplers () |
| core::chemical::ResidueType const & | restype () const |
| Accessors. More... | |
| toolbox::match_enzdes_util::ExternalGeomSampler const & | external_sampler (Size external_geom_id) const |
| Size | launch_atom (Size external_geom_id, Size which_point) const |
| Size | n_external_samplers () const |
| Public Member Functions inherited from protocols::match::downstream::DownstreamAlgorithm | |
| DownstreamAlgorithm (Size geom_cst_id) | |
| DownstreamAlgorithm (DownstreamAlgorithm const &) | |
| DownstreamAlgorithm const & | operator= (DownstreamAlgorithm const &) |
| virtual | ~DownstreamAlgorithm () |
| virtual void | prepare_for_match_enumeration (Matcher const &) |
| Called at the conclusion of matching, the Matcher signals to the downstream algorithm that it's time to prepare for match generation; if the downstream algorithm needs to enumerate compatible hits in response to the invokation of its hits_to_include_with_partial_match method, then now is the time to prepare for those calls. Base class has a noop implementation. More... | |
| void | set_bb_grid (BumpGridCOP bbgrid) |
| void | set_active_site_grid (ActiveSiteGridCOP active_site_grid) |
| Size | geom_cst_id () const |
| void | set_dsbuilder (DownstreamBuilderOP dsbuilder) |
| DownstreamBuilderOP | get_dsbuilder () const |
| bool | 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 |
Private Attributes | |
| core::chemical::ResidueTypeCOP | restype_ |
| utility::vector1 < toolbox::match_enzdes_util::ExternalGeomSampler > | external_samplers_ |
| utility::vector1 < utility::fixedsizearray1 < Size, 3 > > | launch_points_ |
| utility::vector1 < DownstreamBuilderCOP > | dsbuilders_ |
| utility::vector1< Size > | exgeom_ids_ |
| Size | occspace_rev_id_at_last_update_ |
Additional Inherited Members | |
| Protected Member Functions inherited from protocols::match::downstream::DownstreamAlgorithm | |
| BumpGrid const & | bbgrid () const |
| bool | active_site_grid_set () const |
| ActiveSiteGrid const & | active_site_grid () const |
| std::list< Hit > | default_build_hits_at_all_positions (Matcher const &matcher) const |
| Non-virtual, const method for generating hits by first iterating across all build points and then invoking upstream_builder->build( build_point_i ) and splicing together the results. This method is invoked by default if the derived class does not override build_hits_at_all_positions. More... | |
Produce hits by hashing building the coordinates of the downstream partner The downstream partner is responsible for building itself from the coordinate frame of three of its atoms. The ExternalGeomSampler describes the ways to orient the downstream partner given the coordinates of the upstream partner.
Definition at line 55 of file ClassicMatchAlgorithm.hh.
| typedef numeric::HomogeneousTransform< Real > protocols::match::downstream::ClassicMatchAlgorithm::HTReal |
Definition at line 61 of file ClassicMatchAlgorithm.hh.
Definition at line 58 of file ClassicMatchAlgorithm.hh.
Definition at line 60 of file ClassicMatchAlgorithm.hh.
Definition at line 59 of file ClassicMatchAlgorithm.hh.
| protocols::match::downstream::ClassicMatchAlgorithm::ClassicMatchAlgorithm | ( | Size | geom_cst_id) |
Definition at line 50 of file ClassicMatchAlgorithm.cc.
Referenced by clone().
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Definition at line 55 of file ClassicMatchAlgorithm.cc.
| void protocols::match::downstream::ClassicMatchAlgorithm::add_external_geom_sampler | ( | toolbox::match_enzdes_util::ExternalGeomSampler const & | sampler, |
| Size const | exgeom_id, | ||
| std::string const & | atom1, | ||
| std::string const & | atom2, | ||
| std::string const & | atom3, | ||
| DownstreamBuilderCOP | dsbuilder | ||
| ) |
Precompute transforms for the external geom sampler as it is added so that the transforms are ready when build() is called.
Definition at line 398 of file ClassicMatchAlgorithm.cc.
References dsbuilders_, exgeom_ids_, external_samplers_, launch_points_, restype(), and protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D1D2().
Referenced by protocols::match::Matcher::add_external_geometry_samples_for_constraint().
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Iterate across the external geom samplers that describe the rigid body orientations of the downstream partner from the coordinates of the upstream partner.
Implements protocols::match::downstream::DownstreamAlgorithm.
Definition at line 178 of file ClassicMatchAlgorithm.cc.
References build_from_three_coords(), external_samplers_, n_external_samplers(), core::conformation::Residue::name(), restype_, and core::conformation::Residue::type().
| std::list< Hit > protocols::match::downstream::ClassicMatchAlgorithm::build_from_three_coords | ( | Size const | which_external_sampler, |
| Size const | scaffold_build_point_id, | ||
| Size const | upstream_conf_id, | ||
| core::conformation::Residue const & | upstream_residue | ||
| ) | const |
This function completes the building of the downstream conformation once the coordinates of the upstream conformation are known (and deemed non-colliding or, generally, pass any filter the upstream builder would use).
Definition at line 259 of file ClassicMatchAlgorithm.cc.
References protocols::match::downstream::DownstreamAlgorithm::active_site_grid(), protocols::match::downstream::DownstreamAlgorithm::active_site_grid_set(), protocols::match::downstream::DownstreamAlgorithm::bbgrid(), dsbuilders_, exgeom_ids_, external_samplers_, protocols::toolbox::match_enzdes_util::HT_ang_U1D2, protocols::toolbox::match_enzdes_util::HT_ang_U2D1, protocols::toolbox::match_enzdes_util::HT_tor_U1D3, protocols::toolbox::match_enzdes_util::HT_tor_U2D2, protocols::toolbox::match_enzdes_util::HT_tor_U3D1, launch_atom(), core::conformation::Residue::xyz(), and protocols::match::ZERO.
Referenced by build().
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Main driver function for hit generation. The algorithm is responsible for generating hits at all scaffold build points that are valid for this geometric constraint. The base class provides an iterate-across-all-positions-and-splice-together-hit-lists implementation, however, derived classes may overload this function. The base class function is parallelizable with OpenMP. The returned hit list must be in sorted order by 1) hit.scaffold_build_id() and then by 2) hit.upstream_conf_id().
By initializing local std::list< Hit > variables inside the loop over all of the build points, and then splicing them into a central vector of hit lists, I can avoid expensive list-copy operations while guaranteeing OpenMP thread saftey.
Reimplemented from protocols::match::downstream::DownstreamAlgorithm.
Definition at line 64 of file ClassicMatchAlgorithm.cc.
References protocols::match::downstream::DownstreamAlgorithm::default_build_hits_at_all_positions(), protocols::match::Matcher::downstream_builders(), protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), and protocols::match::Matcher::occ_space_hash().
| void protocols::match::downstream::ClassicMatchAlgorithm::clear_external_geom_samplers | ( | ) |
Definition at line 441 of file ClassicMatchAlgorithm.cc.
References dsbuilders_, external_samplers_, and launch_points_.
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Implements protocols::match::downstream::DownstreamAlgorithm.
Definition at line 59 of file ClassicMatchAlgorithm.cc.
References ClassicMatchAlgorithm().
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Definition at line 160 of file ClassicMatchAlgorithm.hh.
References external_samplers_.
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This method returns 'true' since the classic matcher builds the downstream coordinates from scratch.
Implements protocols::match::downstream::DownstreamAlgorithm.
Definition at line 217 of file ClassicMatchAlgorithm.cc.
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This method should not be invoked on the ClassicMatchAlgorithm, since it returns "false" in its upstream_only method.
If this function is causing an exit, then there is a bug within the Matcher's match-enumeration logic. There is no meaningful way forward after this function is invoked. It should not be invoked.
Implements protocols::match::downstream::DownstreamAlgorithm.
Definition at line 227 of file ClassicMatchAlgorithm.cc.
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Definition at line 166 of file ClassicMatchAlgorithm.hh.
References launch_points_.
Referenced by build_from_three_coords().
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Definition at line 171 of file ClassicMatchAlgorithm.hh.
References external_samplers_.
Referenced by build(), and n_possible_hits_per_upstream_conformation().
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Implements protocols::match::downstream::DownstreamAlgorithm.
Definition at line 236 of file ClassicMatchAlgorithm.cc.
References dsbuilders_, external_samplers_, protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_ang_U1D2_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_ang_U2D1_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_dis_U1D1_samples(), n_external_samplers(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U1D3_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U2D2_samples(), and protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U3D1_samples().
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Delete hits for this geometric constraint if they fall into now-empty regions of 6D. This step can be avoided if the occupied-space-grid's revision ID has not changed since the last time this function was invoked.
Drop hits that had previously seemed viable after another round completed; during that round, certain previously occupied regions of 6D were not filled with new hits. Any previously-generated hit that falls into a region of 6D which is no longer occupied should be elminated since it could not ever result in a match; it is inviable.
Reimplemented from protocols::match::downstream::DownstreamAlgorithm.
Definition at line 145 of file ClassicMatchAlgorithm.cc.
References protocols::match::Matcher::erase_hit(), protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), protocols::match::Matcher::hit_list_begin(), protocols::match::Matcher::hit_list_end(), protocols::match::Matcher::hits(), protocols::match::Matcher::occ_space_hash(), occspace_rev_id_at_last_update_, and protocols::match::downstream::TR().
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Reset the occupied space grid for the matcher so that only those regions which contain hits from this geometric constraint are marked as occupied.
Reset the occupied space hash that the matcher uses so that it reflects the hits generated this round; this will cause the invalidation of hits generated in previous rounds. These invalidated hits will be deleted in calls to respond_to_peripheral_hitlist_change.
Reimplemented from protocols::match::downstream::DownstreamAlgorithm.
Definition at line 92 of file ClassicMatchAlgorithm.cc.
References protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), protocols::match::Matcher::hits(), protocols::match::Matcher::occ_space_hash(), occspace_rev_id_at_last_update_, and protocols::match::downstream::TR().
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Accessors.
Definition at line 155 of file ClassicMatchAlgorithm.hh.
References restype_.
Referenced by add_external_geom_sampler(), and set_residue_type().
| void protocols::match::downstream::ClassicMatchAlgorithm::set_residue_type | ( | core::chemical::ResidueTypeCOP | restype) |
Definition at line 388 of file ClassicMatchAlgorithm.cc.
References external_samplers_, launch_points_, restype(), and restype_.
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This method returns 'false' since the classic match algorithm builds coordinates of the downstream partner and its hits should be hashed in 6D to generate matches.
Implements protocols::match::downstream::DownstreamAlgorithm.
Definition at line 211 of file ClassicMatchAlgorithm.cc.
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Definition at line 180 of file ClassicMatchAlgorithm.hh.
Referenced by add_external_geom_sampler(), build_from_three_coords(), clear_external_geom_samplers(), and n_possible_hits_per_upstream_conformation().
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Definition at line 181 of file ClassicMatchAlgorithm.hh.
Referenced by add_external_geom_sampler(), and build_from_three_coords().
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Definition at line 178 of file ClassicMatchAlgorithm.hh.
Referenced by add_external_geom_sampler(), build(), build_from_three_coords(), clear_external_geom_samplers(), external_sampler(), n_external_samplers(), n_possible_hits_per_upstream_conformation(), and set_residue_type().
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Definition at line 179 of file ClassicMatchAlgorithm.hh.
Referenced by add_external_geom_sampler(), clear_external_geom_samplers(), launch_atom(), and set_residue_type().
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Definition at line 183 of file ClassicMatchAlgorithm.hh.
Referenced by respond_to_peripheral_hitlist_change(), and respond_to_primary_hitlist_change().
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Definition at line 176 of file ClassicMatchAlgorithm.hh.
Referenced by build(), restype(), and set_residue_type().
1.8.4