A class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits. More...

#include <SecondaryMatcherToUpstreamResidue.hh>

Inheritance diagram for protocols::match::downstream::SecondaryMatcherToUpstreamResidue:

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Collaboration diagram for protocols::match::downstream::SecondaryMatcherToUpstreamResidue:

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Public Types
typedef DownstreamAlgorithm	parent

typedef utility::fixedsizearray1< Size, 2 >	Size2

typedef utility::OrderedTuple < Size2 >	Size2Tuple

typedef std::pair < SecMatchResiduePairEvaluatorCOP, Size >	Evaluator_MCFI_ID_Pair

typedef std::list < Evaluator_MCFI_ID_Pair >	EvaluatorSet

Public Types inherited from protocols::match::downstream::DownstreamAlgorithm
typedef core::Size	Size

typedef core::Vector	Vector

Public Member Functions
	SecondaryMatcherToUpstreamResidue (Size geom_cst_id)

virtual	~SecondaryMatcherToUpstreamResidue ()

virtual DownstreamAlgorithmOP	clone () const

virtual std::list< Hit >	build_hits_at_all_positions (Matcher &matcher)
	Main driver function for hit generation. This DownstreamAlgorithm structures it's iteration over the hits from previous rounds as follows: for i = 1:n_build_positions recover_rotamer_coordinates_from_previous_round( hits_for_build_point_i ); initialize rotcoord data for all downstream algorithms with the same geom_cst_id #omp parallel for /// All class access below this point is const and parallelizable for j = 1:n_build_positions /// call this function to start k loop: matcher.upstream_builder[ geom_cst_id() ]->build( j ) for k = 1:n_rotamers_j /// call to start l loop: downstream_algorithm->build( j, k, rotamer_k ) ) for l = 1:n_rotamers_from_build_point_i if ( respair_evaluator_->evaluate_residues( rotamer_k, rotamer_l ) hit_list.append( Hit( j, k, ... )); return hit_list There are two important consequences to this hit-generation layout. More...

virtual void	respond_to_primary_hitlist_change (Matcher &matcher, Size round_just_completed)
	Prune hits away from the target_geomcst's hit list following a change to the hits for my geom_cst_id(). Pruning hits from the target_geomcst's hit list will trigger a round of peripheral-hitlist-change responses. More...

virtual void	respond_to_peripheral_hitlist_change (Matcher &matcher)
	Remove my hits if my target_geomcst's hit list has been shortened. This will not trigger a round of peripheral-hitlist-change responses. 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 hits from a particular upstream build point i that were generated in a previous round, and see if the geometry of the input upstream_residue has "satisfactory interactions" with the hits from upstream-build-point i; if so, it appends a Hit to the hitlist returned at the end of the method. (Also, see comments for the build_at_all_positions method.) More...

virtual bool	upstream_only () const
	returns true; this secondary matcher does not describe the location of the downstream partner More...

virtual bool	generates_primary_hits () const
	This method returns 'false' since this matcher does not describe the coordinates of the downstream partner at all. More...

virtual void	prepare_for_match_enumeration (Matcher const &matcher)
	Prepare a map between upstream hits of the target-geomcst and a list of Hit const *'s of this geom_cst_id(). This map will be used in the function hits_to_include_with_partial_match. More...

virtual HitPtrListCOP	hits_to_include_with_partial_match (match_dspos1 const &m) const
	Return the set of hits to be iterated across. More...

virtual Size	n_possible_hits_per_upstream_conformation () const

void	set_target_geomcst_id (Size target_geomcst_id)

void	add_target_restype (core::chemical::ResidueTypeCOP target_restype)

void	add_evaluator_for_target_restype (core::chemical::ResidueTypeCOP target_restype, SecMatchResiduePairEvaluatorCOP evaluator, Size mcfi_id_for_evaluator)

void	process_hit (Hit const &hit, core::conformation::Residue const &upstream_conformation)
	Invoked by SecondaryMatchUpstreamResProcessor; avoids multiple inherritance, while letting the SecondaryMatcherToUpstreamResidue. More...

Public Member Functions inherited from protocols::match::downstream::DownstreamAlgorithm
	DownstreamAlgorithm (Size geom_cst_id)

	DownstreamAlgorithm (DownstreamAlgorithm const &)

DownstreamAlgorithm const &	operator= (DownstreamAlgorithm const &)

virtual	~DownstreamAlgorithm ()

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 Member Functions
void	prepare_for_hit_generation (Matcher &matcher)

bool	prepare_for_hit_generation_at_target_build_point (Matcher &matcher, upstream::ScaffoldBuildPoint const &target_build_point)

void	set_target_rotamer_coords (TargetRotamerCoordsOP target_geomcst_coords)
	Allow another SecondaryMatcherToUpstreamResidue to set my TargetRotamerCoords object so that we can share this data. More...

void	count_rotamer (core::conformation::Residue const &upstream_conformation)

void	store_rotamer_coords (Hit const &hit, core::conformation::Residue const &upstream_conformation)

void	reorder_restypes (upstream::UpstreamBuilder const &builder)

Private Attributes
utility::vector1< core::Size >	smUR_pose_build_resids_

Size	target_geomcst_id_

std::map < core::chemical::ResidueTypeCOP, Size >	target_restype_index_map_

utility::vector1 < core::chemical::ResidueTypeCOP >	target_restypes_

utility::vector1< EvaluatorSet >	respair_evaluators_

bool	count_rotamers_per_target_restype_

core::chemical::ResidueTypeCOP	last_seen_restype_

Size	last_seen_restype_index_

Size	count_rotamer_for_lastseen_restype_

Matcher::HitListConstIterator	target_hits_for_focused_build_point_begin_

Matcher::HitListConstIterator	target_hits_for_focused_build_point_end_

Matcher::HitListConstIterator	target_hits_end_

utility::vector1< Size >	n_rotamers_per_target_restype_

TargetRotamerCoordsOP	target_geomcst_coords_

std::map< Size2Tuple, HitPtrListOP >	my_hits_for_target_hit_map_

Size	n_viable_target_hits_since_last_pruning_

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

A class for an algorithm. Given a conformation of the upstream partner, the algorithm is responsible for producing a set of hits.

Definition at line 60 of file SecondaryMatcherToUpstreamResidue.hh.

Member Typedef Documentation

typedef std::pair< SecMatchResiduePairEvaluatorCOP, Size > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::Evaluator_MCFI_ID_Pair

Definition at line 66 of file SecondaryMatcherToUpstreamResidue.hh.

typedef std::list< Evaluator_MCFI_ID_Pair > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::EvaluatorSet

Definition at line 67 of file SecondaryMatcherToUpstreamResidue.hh.

typedef DownstreamAlgorithm protocols::match::downstream::SecondaryMatcherToUpstreamResidue::parent

Definition at line 63 of file SecondaryMatcherToUpstreamResidue.hh.

typedef utility::fixedsizearray1< Size, 2 > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::Size2

Definition at line 64 of file SecondaryMatcherToUpstreamResidue.hh.

typedef utility::OrderedTuple< Size2 > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::Size2Tuple

Definition at line 65 of file SecondaryMatcherToUpstreamResidue.hh.

Constructor & Destructor Documentation

protocols::match::downstream::SecondaryMatcherToUpstreamResidue::SecondaryMatcherToUpstreamResidue ( Size geom_cst_id)

Definition at line 68 of file SecondaryMatcherToUpstreamResidue.cc.

Referenced by clone().

protocols::match::downstream::SecondaryMatcherToUpstreamResidue::~SecondaryMatcherToUpstreamResidue ( )

virtual

Definition at line 80 of file SecondaryMatcherToUpstreamResidue.cc.

Member Function Documentation

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::add_evaluator_for_target_restype	(	core::chemical::ResidueTypeCOP	target_restype,
		SecMatchResiduePairEvaluatorCOP	evaluator,
		Size	mcfi_id_for_evaluator
	)

Definition at line 422 of file SecondaryMatcherToUpstreamResidue.cc.

References respair_evaluators_, target_restype_index_map_, and target_restypes_.

Referenced by protocols::match::Matcher::add_secondary_upstream_match_geometry_for_constraint().

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::add_target_restype ( core::chemical::ResidueTypeCOP target_restype)

Definition at line 413 of file SecondaryMatcherToUpstreamResidue.cc.

References target_restype_index_map_, and target_restypes_.

Referenced by protocols::match::Matcher::add_secondary_upstream_match_geometry_for_constraint().

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

virtual

Iterate across the hits from a particular upstream build point i that were generated in a previous round, and see if the geometry of the input upstream_residue has "satisfactory interactions" with the hits from upstream-build-point i; if so, it appends a Hit to the hitlist returned at the end of the method. (Also, see comments for the build_at_all_positions method.)

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

Definition at line 281 of file SecondaryMatcherToUpstreamResidue.cc.

References protocols::match::Hit::first(), respair_evaluators_, protocols::match::Hit::second(), smUR_pose_build_resids_, target_geomcst_coords_, and core::conformation::Residue::type().

std::list< Hit > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build_hits_at_all_positions ( Matcher & matcher)

virtual

Main driver function for hit generation. This DownstreamAlgorithm structures it's iteration over the hits from previous rounds as follows: for i = 1:n_build_positions recover_rotamer_coordinates_from_previous_round( hits_for_build_point_i ); initialize rotcoord data for all downstream algorithms with the same geom_cst_id #omp parallel for /// All class access below this point is const and parallelizable for j = 1:n_build_positions /// call this function to start k loop: matcher.upstream_builder[ geom_cst_id() ]->build( j ) for k = 1:n_rotamers_j /// call to start l loop: downstream_algorithm->build( j, k, rotamer_k ) ) for l = 1:n_rotamers_from_build_point_i if ( respair_evaluator_->evaluate_residues( rotamer_k, rotamer_l ) hit_list.append( Hit( j, k, ... )); return hit_list There are two important consequences to this hit-generation layout.

The coordinates for rotamer_k are computed n_build_position times.
Only a single build-position i has it's hit coordinates in memory at any point in time. This is a clear trade-off between performance and memory with a few caveats: A. It is very easy to bound the volume of space where build-point i's rotamers lie, so it should be easy to prune rotamer building, so rotamer k will be build many fewer than n_build_position times. B. By not trying to store all rotamers in memory at once, we do not impose any undue restrictions on the number of rotamers that can be enumerated. This is especially important if we're using backbone flexibility to search a wider region of conformation space.

This DownstreamAlgorithm structures it's iteration over the target hits from previous rounds as follows: for i = 1:n_build_positions recover_rotamer_coordinates_from_previous_round( hits_for_build_point_i ); initialize rotcoord data for all downstream algorithms with the same geom_cst_id #omp parallel for /// All class access below this point is const and parallelizable for j = 1:n_build_positions /// call this function to start k loop: matcher.upstream_builder[ geom_cst_id() ]->build( j ) for k = 1:n_rotamers_j /// call to start l loop: downstream_algorithm->build( j, k, rotamer_k ) ) for l = 1:n_rotamers_from_build_point_i if ( respair_evaluator_->evaluate_residues( rotamer_k, rotamer_l ) hit_list.append( Hit( j, k, ... )); return hit_list There are two important consequences to this hit-generation layout.

The coordinates for rotamer_k are computed n_build_position times.
Only a single build-position i has it's hit coordinates in memory at any point in time. This is a clear trade-off between performance and memory with a few caveats: A. It is very easy to bound the volume of space where build-point i's rotamers lie, so it should be easy to prune rotamer building, so rotamer k will be build many fewer than n_build_position times. B. By not trying to store all rotamers in memory at once, we do not impose any undue restrictions on the number of rotamers that can be enumerated. This is especially important if we're using backbone flexibility to search a wider region of conformation space.

Reimplemented from protocols::match::downstream::DownstreamAlgorithm.

Definition at line 113 of file SecondaryMatcherToUpstreamResidue.cc.

References protocols::fldsgn::topology::compare(), core::sequence::end, protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), protocols::match::Matcher::per_constraint_build_points(), prepare_for_hit_generation(), prepare_for_hit_generation_at_target_build_point(), target_geomcst_id_, protocols::match::downstream::TR(), and protocols::match::Matcher::upstream_builder().

DownstreamAlgorithmOP protocols::match::downstream::SecondaryMatcherToUpstreamResidue::clone ( ) const

virtual

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

Definition at line 83 of file SecondaryMatcherToUpstreamResidue.cc.

References SecondaryMatcherToUpstreamResidue().

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::count_rotamer ( core::conformation::Residue const & upstream_conformation)

private

Definition at line 622 of file SecondaryMatcherToUpstreamResidue.cc.

References last_seen_restype_, last_seen_restype_index_, n_rotamers_per_target_restype_, target_restypes_, and core::conformation::Residue::type().

Referenced by process_hit().

bool protocols::match::downstream::SecondaryMatcherToUpstreamResidue::generates_primary_hits ( ) const

virtual

This method returns 'false' since this matcher does not describe the coordinates of the downstream partner at all.

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

Definition at line 343 of file SecondaryMatcherToUpstreamResidue.cc.

HitPtrListCOP protocols::match::downstream::SecondaryMatcherToUpstreamResidue::hits_to_include_with_partial_match ( match_dspos1 const & m) const

virtual

Return the set of hits to be iterated across.

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

Definition at line 375 of file SecondaryMatcherToUpstreamResidue.cc.

References my_hits_for_target_hit_map_, target_geomcst_id_, and protocols::match::match_dspos1::upstream_hits.

SecondaryMatcherToUpstreamResidue::Size protocols::match::downstream::SecondaryMatcherToUpstreamResidue::n_possible_hits_per_upstream_conformation ( ) const

virtual

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

Definition at line 395 of file SecondaryMatcherToUpstreamResidue.cc.

References target_geomcst_coords_.

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::prepare_for_hit_generation ( Matcher & matcher)

private

Definition at line 450 of file SecondaryMatcherToUpstreamResidue.cc.

References protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), protocols::match::Matcher::get_pose_build_resids(), protocols::match::Matcher::hits(), n_rotamers_per_target_restype_, protocols::match::Matcher::nonconst_downstream_algorithms(), target_geomcst_coords_, target_geomcst_id_, target_hits_end_, target_hits_for_focused_build_point_begin_, target_hits_for_focused_build_point_end_, protocols::match::downstream::TR(), and protocols::match::Matcher::upstream_builder().

Referenced by build_hits_at_all_positions().

bool protocols::match::downstream::SecondaryMatcherToUpstreamResidue::prepare_for_hit_generation_at_target_build_point	(	Matcher &	matcher,
		upstream::ScaffoldBuildPoint const &	target_build_point
	)

private

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::prepare_for_match_enumeration ( Matcher const & matcher)

virtual

Prepare a map between upstream hits of the target-geomcst and a list of Hit const *'s of this geom_cst_id(). This map will be used in the function hits_to_include_with_partial_match.

Reimplemented from protocols::match::downstream::DownstreamAlgorithm.

Definition at line 353 of file SecondaryMatcherToUpstreamResidue.cc.

References protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), protocols::match::Matcher::hits(), and my_hits_for_target_hit_map_.

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::process_hit	(	Hit const &	hit,
		core::conformation::Residue const &	upstream_conformation
	)

Invoked by SecondaryMatchUpstreamResProcessor; avoids multiple inherritance, while letting the SecondaryMatcherToUpstreamResidue.

Definition at line 437 of file SecondaryMatcherToUpstreamResidue.cc.

References count_rotamer(), count_rotamers_per_target_restype_, and store_rotamer_coords().

Referenced by protocols::match::downstream::SecondaryMatchUpstreamResProcessor::process_hit().

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::reorder_restypes ( upstream::UpstreamBuilder const & builder)

private

Definition at line 666 of file SecondaryMatcherToUpstreamResidue.cc.

References protocols::match::upstream::UpstreamBuilder::n_restypes_to_build(), respair_evaluators_, protocols::match::upstream::UpstreamBuilder::restype(), target_restype_index_map_, and target_restypes_.

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respond_to_peripheral_hitlist_change ( Matcher & matcher)

virtual

Remove my hits if my target_geomcst's hit list has been shortened. This will not trigger a round of peripheral-hitlist-change responses.

Reimplemented from protocols::match::downstream::DownstreamAlgorithm.

Definition at line 221 of file SecondaryMatcherToUpstreamResidue.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(), n_viable_target_hits_since_last_pruning_, target_geomcst_id_, and protocols::match::downstream::TR().

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respond_to_primary_hitlist_change	(	Matcher &	matcher,
		Size	round_just_completed
	)

virtual

Prune hits away from the target_geomcst's hit list following a change to the hits for my geom_cst_id(). Pruning hits from the target_geomcst's hit list will trigger a round of peripheral-hitlist-change responses.

Reimplemented from protocols::match::downstream::DownstreamAlgorithm.

Definition at line 169 of file SecondaryMatcherToUpstreamResidue.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(), n_viable_target_hits_since_last_pruning_, target_geomcst_id_, and protocols::match::downstream::TR().

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::set_target_geomcst_id ( Size target_geomcst_id)

Definition at line 407 of file SecondaryMatcherToUpstreamResidue.cc.

References target_geomcst_id_.

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::set_target_rotamer_coords ( TargetRotamerCoordsOP target_geomcst_coords)

private

Allow another SecondaryMatcherToUpstreamResidue to set my TargetRotamerCoords object so that we can share this data.

Definition at line 614 of file SecondaryMatcherToUpstreamResidue.cc.

References target_geomcst_coords_.

void protocols::match::downstream::SecondaryMatcherToUpstreamResidue::store_rotamer_coords	(	Hit const &	hit,
		core::conformation::Residue const &	upstream_conformation
	)

private

Definition at line 640 of file SecondaryMatcherToUpstreamResidue.cc.

References count_rotamer_for_lastseen_restype_, last_seen_restype_, last_seen_restype_index_, n_rotamers_per_target_restype_, target_geomcst_coords_, target_restypes_, and core::conformation::Residue::type().

Referenced by process_hit().

bool protocols::match::downstream::SecondaryMatcherToUpstreamResidue::upstream_only ( ) const

virtual

returns true; this secondary matcher does not describe the location of the downstream partner

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

Definition at line 337 of file SecondaryMatcherToUpstreamResidue.cc.

Member Data Documentation

Size protocols::match::downstream::SecondaryMatcherToUpstreamResidue::count_rotamer_for_lastseen_restype_

private

Definition at line 239 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by prepare_for_hit_generation_at_target_build_point(), and store_rotamer_coords().

bool protocols::match::downstream::SecondaryMatcherToUpstreamResidue::count_rotamers_per_target_restype_

private

Definition at line 236 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by prepare_for_hit_generation_at_target_build_point(), and process_hit().

core::chemical::ResidueTypeCOP protocols::match::downstream::SecondaryMatcherToUpstreamResidue::last_seen_restype_

private

Definition at line 237 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by count_rotamer(), prepare_for_hit_generation_at_target_build_point(), and store_rotamer_coords().

Size protocols::match::downstream::SecondaryMatcherToUpstreamResidue::last_seen_restype_index_

private

Definition at line 238 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by count_rotamer(), prepare_for_hit_generation_at_target_build_point(), and store_rotamer_coords().

std::map< Size2Tuple, HitPtrListOP > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::my_hits_for_target_hit_map_

private

Definition at line 247 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by hits_to_include_with_partial_match(), and prepare_for_match_enumeration().

utility::vector1< Size > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::n_rotamers_per_target_restype_

private

Definition at line 244 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by count_rotamer(), prepare_for_hit_generation(), prepare_for_hit_generation_at_target_build_point(), and store_rotamer_coords().

Size protocols::match::downstream::SecondaryMatcherToUpstreamResidue::n_viable_target_hits_since_last_pruning_

private

Definition at line 249 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by respond_to_peripheral_hitlist_change(), and respond_to_primary_hitlist_change().

utility::vector1< EvaluatorSet > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::respair_evaluators_

private

Definition at line 232 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by add_evaluator_for_target_restype(), build(), and reorder_restypes().

utility::vector1< core::Size > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::smUR_pose_build_resids_

private

Definition at line 223 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by build().

TargetRotamerCoordsOP protocols::match::downstream::SecondaryMatcherToUpstreamResidue::target_geomcst_coords_

private

Definition at line 245 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by build(), n_possible_hits_per_upstream_conformation(), prepare_for_hit_generation(), prepare_for_hit_generation_at_target_build_point(), set_target_rotamer_coords(), and store_rotamer_coords().

Size protocols::match::downstream::SecondaryMatcherToUpstreamResidue::target_geomcst_id_

private

The id for the geom-cst that this SecondaryMatcher is dependent upon; the upstream geometries for residues generated by the target-geometric constraint are examined in the build() method.

Definition at line 228 of file SecondaryMatcherToUpstreamResidue.hh.

Referenced by build_hits_at_all_positions(), hits_to_include_with_partial_match(), prepare_for_hit_generation(), prepare_for_hit_generation_at_target_build_point(), respond_to_peripheral_hitlist_change(), respond_to_primary_hitlist_change(), and set_target_geomcst_id().