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Rosetta
2021.16
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Rosetta
2021.16
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#include <WriteUpstreamCoordinateKineamge.hh>
Public Types | |
| typedef core::Size | Size |
| typedef core::Vector | Vector |
 Public Types inherited from protocols::match::downstream::DownstreamAlgorithm | |
| typedef core::Size | Size |
| typedef core::Vector | Vector |
Public Member Functions | |
| WriteUpstreamCoordinateKinemage () | |
| WriteUpstreamCoordinateKinemage (std::string const &fname) | |
| WriteUpstreamCoordinateKinemage (std::ostream &ostr) | |
| ~WriteUpstreamCoordinateKinemage () override | |
| downstream::DownstreamAlgorithmOP | clone () const override |
| std::list< Hit > | build (core::Size const scaffold_build_point_id, core::Size const upstream_conf_id, core::conformation::Residue const &upstream_residue) const override |
| To be invoked by derived classes, 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... | |
| bool | upstream_only () const override |
| This method returns 'true' whether or not it's ClassicMatchAlgorithm is set as it should not have its hits_to_include_with_partial_match method invoked. More... | |
| bool | generates_primary_hits () const override |
| This method returns 'true' since when it does return hits, it's those generated by the ClassicMatchAlgorithm. More... | |
| HitPtrListCOP | hits_to_include_with_partial_match (match_dspos1 const &m) const override |
| This method should not be invoked on this class, since it returns "true" in its upstream_only method. More... | |
| core::Size | n_possible_hits_per_upstream_conformation () const override |
| void | set_kinemage_file_name (std::string const &filename) |
| void | set_match_algorithm (downstream::ClassicMatchAlgorithmCOP algorithm) |
| void | set_downstream_writer (DownstreamCoordinateKinemageWriterCOP dswriter) |
| void | set_n_downstream_to_output (core::Size n_downstream_to_output) |
| bool | return_pseudo_hits () const |
| void | return_pseudo_hits (bool setting) |
| Public Member Functions inherited from protocols::match::downstream::DownstreamAlgorithm | |
| DownstreamAlgorithm (core::Size geom_cst_id) | |
| DownstreamAlgorithm (DownstreamAlgorithm const &) | |
| DownstreamAlgorithm const & | operator= (DownstreamAlgorithm const &) |
| ~DownstreamAlgorithm () override | |
| 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, core::Size round_just_completed) |
| Reset appropriate Matcher data to spawn the deletion of hits from other rounds following either hit generation by this geometric constraint, or following hit generation by another geometric constraint which caused the deletion of hits from this geometric constraint. The classic match algorithm, for example, resets the occupied-space hash so that other classic-match algorithms can delete their non-viable hits in subsequent calls to respond_to_peripheral_hitlist_change. More... | |
| virtual void | respond_to_peripheral_hitlist_change (Matcher &matcher) |
| Following the change in the number of hits of some other round – either from the conclusion of that round in which a new set of hits has been generated, or from the cascading change to the hits from round A which were deleted after the conclusion of round B. More... | |
| 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) |
| core::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 | |
| std::string | kinemage_file_name_ |
| std::ofstream | file_out_ |
| std::ostream & | ostr_ |
| core::Size | last_scaffold_build_point_ |
| core::Size | nkins_ |
| downstream::ClassicMatchAlgorithmCOP | match_algorithm_ |
| DownstreamCoordinateKinemageWriterCOP | dswriter_ |
| core::Size | n_downstream_to_output_ |
| core::Size | n_output_so_far_ |
| bool | return_pseudo_hits_ |
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... | |
| protocols::match::output::WriteUpstreamCoordinateKinemage::WriteUpstreamCoordinateKinemage | ( | ) |
| protocols::match::output::WriteUpstreamCoordinateKinemage::WriteUpstreamCoordinateKinemage | ( | std::string const & | fname | ) |
References file_out_, and kinemage_file_name_.
| protocols::match::output::WriteUpstreamCoordinateKinemage::WriteUpstreamCoordinateKinemage | ( | std::ostream & | ostr | ) |
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override |
References file_out_.
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overridevirtual |
To be invoked by derived classes, 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).
Implements protocols::match::downstream::DownstreamAlgorithm.
References dswriter_, protocols::match::Hit::first(), core::conformation::Residue::has(), last_scaffold_build_point_, protocols::match::output::ResidueKinemageWriter::master(), match_algorithm_, n_downstream_to_output_, n_output_so_far_, nkins_, ostr_, return_pseudo_hits_, protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::Residue::xyz().
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overridevirtual |
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overridevirtual |
This method returns 'true' since when it does return hits, it's those generated by the ClassicMatchAlgorithm.
Implements protocols::match::downstream::DownstreamAlgorithm.
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overridevirtual |
This method should not be invoked on this class, since it returns "true" 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. Truely, this class should not be used in match enumeration.
Implements protocols::match::downstream::DownstreamAlgorithm.
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overridevirtual |
Implements protocols::match::downstream::DownstreamAlgorithm.
References match_algorithm_.
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inline |
References return_pseudo_hits_.
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inline |
References return_pseudo_hits_.
| void protocols::match::output::WriteUpstreamCoordinateKinemage::set_downstream_writer | ( | DownstreamCoordinateKinemageWriterCOP | dswriter | ) |
References dswriter_.
| void protocols::match::output::WriteUpstreamCoordinateKinemage::set_kinemage_file_name | ( | std::string const & | filename | ) |
References file_out_, protocols::abinitio::filename(), and kinemage_file_name_.
| void protocols::match::output::WriteUpstreamCoordinateKinemage::set_match_algorithm | ( | downstream::ClassicMatchAlgorithmCOP | algorithm | ) |
References match_algorithm_.
| void protocols::match::output::WriteUpstreamCoordinateKinemage::set_n_downstream_to_output | ( | core::Size | n_downstream_to_output | ) |
References n_downstream_to_output_.
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overridevirtual |
This method returns 'true' whether or not it's ClassicMatchAlgorithm is set as it should not have its hits_to_include_with_partial_match method invoked.
This is an acceptalbe return value for this debugging-purposed class.
Implements protocols::match::downstream::DownstreamAlgorithm.
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private |
Referenced by build(), and set_downstream_writer().
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private |
Referenced by set_kinemage_file_name(), WriteUpstreamCoordinateKinemage(), and ~WriteUpstreamCoordinateKinemage().
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private |
Referenced by set_kinemage_file_name(), and WriteUpstreamCoordinateKinemage().
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mutableprivate |
Referenced by build().
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private |
Referenced by build(), n_possible_hits_per_upstream_conformation(), and set_match_algorithm().
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private |
Referenced by build(), and set_n_downstream_to_output().
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mutableprivate |
Referenced by build().
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mutableprivate |
Referenced by build().
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private |
Referenced by build().
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private |
Referenced by build(), and return_pseudo_hits().
1.8.7