#include <WriteUpstreamCoordinateKineamge.hh>

Inheritance diagram for protocols::match::output::WriteUpstreamCoordinateKinemage:

Collaboration diagram for protocols::match::output::WriteUpstreamCoordinateKinemage:

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)

virtual	~WriteUpstreamCoordinateKinemage ()

virtual downstream::DownstreamAlgorithmOP	clone () const

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

virtual bool	upstream_only () const
	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...

virtual bool	generates_primary_hits () const
	This method returns 'true' since when it does return hits, it's those generated by the ClassicMatchAlgorithm. More...

virtual HitPtrListCOP	hits_to_include_with_partial_match (match_dspos1 const &m) const
	This method should not be invoked on this class, since it returns "true" in its upstream_only method. More...

virtual Size	n_possible_hits_per_upstream_conformation () const

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 (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 (Size geom_cst_id)

	DownstreamAlgorithm (DownstreamAlgorithm const &)

DownstreamAlgorithm const &	operator= (DownstreamAlgorithm const &)

virtual	~DownstreamAlgorithm ()

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 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)

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_

Size	last_scaffold_build_point_

Size	nkins_

downstream::ClassicMatchAlgorithmCOP	match_algorithm_

DownstreamCoordinateKinemageWriterCOP	dswriter_

Size	n_downstream_to_output_

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...

Detailed Description

Definition at line 82 of file WriteUpstreamCoordinateKineamge.hh.

Member Typedef Documentation

typedef core::Size protocols::match::output::WriteUpstreamCoordinateKinemage::Size

Definition at line 85 of file WriteUpstreamCoordinateKineamge.hh.

typedef core::Vector protocols::match::output::WriteUpstreamCoordinateKinemage::Vector

Definition at line 86 of file WriteUpstreamCoordinateKineamge.hh.

Constructor & Destructor Documentation

protocols::match::output::WriteUpstreamCoordinateKinemage::WriteUpstreamCoordinateKinemage ( )

Definition at line 177 of file WriteUpstreamCoordinateKineamge.cc.

Referenced by clone().

protocols::match::output::WriteUpstreamCoordinateKinemage::WriteUpstreamCoordinateKinemage ( std::string const & fname)

Definition at line 191 of file WriteUpstreamCoordinateKineamge.cc.

References file_out_, and kinemage_file_name_.

protocols::match::output::WriteUpstreamCoordinateKinemage::WriteUpstreamCoordinateKinemage ( std::ostream & ostr)

Definition at line 207 of file WriteUpstreamCoordinateKineamge.cc.

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

virtual

Definition at line 221 of file WriteUpstreamCoordinateKineamge.cc.

References file_out_.

Member Function Documentation

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

virtual

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.

Definition at line 237 of file WriteUpstreamCoordinateKineamge.cc.

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

virtual

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

Definition at line 227 of file WriteUpstreamCoordinateKineamge.cc.

References WriteUpstreamCoordinateKinemage().

bool protocols::match::output::WriteUpstreamCoordinateKinemage::generates_primary_hits ( ) const

virtual

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

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

Definition at line 315 of file WriteUpstreamCoordinateKineamge.cc.

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

virtual

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.

Definition at line 325 of file WriteUpstreamCoordinateKineamge.cc.

WriteUpstreamCoordinateKinemage::Size protocols::match::output::WriteUpstreamCoordinateKinemage::n_possible_hits_per_upstream_conformation ( ) const

virtual

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

Definition at line 333 of file WriteUpstreamCoordinateKineamge.cc.

References match_algorithm_.

bool protocols::match::output::WriteUpstreamCoordinateKinemage::return_pseudo_hits ( ) const

inline

Definition at line 144 of file WriteUpstreamCoordinateKineamge.hh.

References return_pseudo_hits_.

void protocols::match::output::WriteUpstreamCoordinateKinemage::return_pseudo_hits ( bool setting)

inline

Definition at line 149 of file WriteUpstreamCoordinateKineamge.hh.

References return_pseudo_hits_.

void protocols::match::output::WriteUpstreamCoordinateKinemage::set_downstream_writer ( DownstreamCoordinateKinemageWriterCOP dswriter)

Definition at line 362 of file WriteUpstreamCoordinateKineamge.cc.

References dswriter_.

void protocols::match::output::WriteUpstreamCoordinateKinemage::set_kinemage_file_name ( std::string const & filename)

Definition at line 344 of file WriteUpstreamCoordinateKineamge.cc.

References file_out_, protocols::abinitio::filename(), and kinemage_file_name_.

void protocols::match::output::WriteUpstreamCoordinateKinemage::set_match_algorithm ( downstream::ClassicMatchAlgorithmCOP algorithm)

Definition at line 356 of file WriteUpstreamCoordinateKineamge.cc.

References match_algorithm_.

void protocols::match::output::WriteUpstreamCoordinateKinemage::set_n_downstream_to_output ( Size n_downstream_to_output)

Definition at line 368 of file WriteUpstreamCoordinateKineamge.cc.

References n_downstream_to_output_.

bool protocols::match::output::WriteUpstreamCoordinateKinemage::upstream_only ( ) const

virtual

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.

Definition at line 309 of file WriteUpstreamCoordinateKineamge.cc.