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protocols::match::output::WriteUpstreamCoordinateKinemage Class Reference

#include <WriteUpstreamCoordinateKineamge.hh>

Inheritance diagram for protocols::match::output::WriteUpstreamCoordinateKinemage:
Inheritance graph
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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< Hitbuild (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< Hitbuild_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< Hitdefault_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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

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)
protocols::match::output::WriteUpstreamCoordinateKinemage::~WriteUpstreamCoordinateKinemage ( )
override

References file_out_.

Member Function Documentation

std::list< Hit > protocols::match::output::WriteUpstreamCoordinateKinemage::build ( core::Size const  scaffold_build_point_id,
core::Size const  upstream_conf_id,
core::conformation::Residue const &  upstream_residue 
) const
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().

downstream::DownstreamAlgorithmOP protocols::match::output::WriteUpstreamCoordinateKinemage::clone ( ) const
overridevirtual
bool protocols::match::output::WriteUpstreamCoordinateKinemage::generates_primary_hits ( ) const
overridevirtual

This method returns 'true' since when it does return hits, it's those generated by the ClassicMatchAlgorithm.

Implements protocols::match::downstream::DownstreamAlgorithm.

HitPtrListCOP protocols::match::output::WriteUpstreamCoordinateKinemage::hits_to_include_with_partial_match ( match_dspos1 const &  m) const
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.

WriteUpstreamCoordinateKinemage::Size protocols::match::output::WriteUpstreamCoordinateKinemage::n_possible_hits_per_upstream_conformation ( ) const
overridevirtual
bool protocols::match::output::WriteUpstreamCoordinateKinemage::return_pseudo_hits ( ) const
inline

References return_pseudo_hits_.

void protocols::match::output::WriteUpstreamCoordinateKinemage::return_pseudo_hits ( bool  setting)
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)
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)
bool protocols::match::output::WriteUpstreamCoordinateKinemage::upstream_only ( ) const
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.

Member Data Documentation

DownstreamCoordinateKinemageWriterCOP protocols::match::output::WriteUpstreamCoordinateKinemage::dswriter_
private

Referenced by build(), and set_downstream_writer().

std::ofstream protocols::match::output::WriteUpstreamCoordinateKinemage::file_out_
private
std::string protocols::match::output::WriteUpstreamCoordinateKinemage::kinemage_file_name_
private
core::Size protocols::match::output::WriteUpstreamCoordinateKinemage::last_scaffold_build_point_
mutableprivate

Referenced by build().

downstream::ClassicMatchAlgorithmCOP protocols::match::output::WriteUpstreamCoordinateKinemage::match_algorithm_
private
core::Size protocols::match::output::WriteUpstreamCoordinateKinemage::n_downstream_to_output_
private
core::Size protocols::match::output::WriteUpstreamCoordinateKinemage::n_output_so_far_
mutableprivate

Referenced by build().

core::Size protocols::match::output::WriteUpstreamCoordinateKinemage::nkins_
mutableprivate

Referenced by build().

std::ostream& protocols::match::output::WriteUpstreamCoordinateKinemage::ostr_
private

Referenced by build().

bool protocols::match::output::WriteUpstreamCoordinateKinemage::return_pseudo_hits_
private

Referenced by build(), and return_pseudo_hits().


The documentation for this class was generated from the following files: