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:

[legend]

Public Types
typedef DownstreamAlgorithm	parent

typedef utility::fixedsizearray1 < core::Size, 2 >	Size2

typedef utility::OrderedTuple < Size2 >	Size2Tuple

typedef std::pair < SecMatchResiduePairEvaluatorCOP, core::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 (core::Size geom_cst_id)

	~SecondaryMatcherToUpstreamResidue () override

DownstreamAlgorithmOP	clone () const override

std::list< Hit >	build_hits_at_all_positions (Matcher &matcher) override
	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...

void	respond_to_primary_hitlist_change (Matcher &matcher, core::Size round_just_completed) override
	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...

void	respond_to_peripheral_hitlist_change (Matcher &matcher) override
	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...

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
	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...

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

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

void	prepare_for_match_enumeration (Matcher const &matcher) override
	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...

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

core::Size	n_possible_hits_per_upstream_conformation () const override

void	set_target_geomcst_id (core::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, core::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 (core::Size geom_cst_id)

	DownstreamAlgorithm (DownstreamAlgorithm const &)

DownstreamAlgorithm const &	operator= (DownstreamAlgorithm const &)

	~DownstreamAlgorithm () override

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 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_

core::Size	target_geomcst_id_

std::map < core::chemical::ResidueTypeCOP, core::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_

core::Size	last_seen_restype_index_

core::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< core::Size >	n_rotamers_per_target_restype_

TargetRotamerCoordsOP	target_geomcst_coords_

std::map< Size2Tuple, HitPtrListOP >	my_hits_for_target_hit_map_

core::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.

Member Typedef Documentation

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

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

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

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

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

Constructor & Destructor Documentation

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

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

overridedefault

Member Function Documentation

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

References respair_evaluators_, target_restype_index_map_, and target_restypes_.

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

References target_restype_index_map_, and target_restypes_.

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

overridevirtual

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.

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

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

overridevirtual

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.

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

overridevirtual

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

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

private

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

Referenced by process_hit().

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

overridevirtual

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

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

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

overridevirtual

Return the set of hits to be iterated across.

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

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

overridevirtual

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

References target_geomcst_coords_.

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

private

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

References count_rotamer_for_lastseen_restype_, count_rotamers_per_target_restype_, protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), protocols::match::upstream::ScaffoldBuildPoint::index(), last_seen_restype_, last_seen_restype_index_, n_rotamers_per_target_restype_, protocols::match::Matcher::nonconst_downstream_algorithms(), protocols::match::upstream::ScaffoldBuildPoint::original_insertion_point(), target_geomcst_coords_, target_geomcst_id_, target_hits_end_, target_hits_for_focused_build_point_begin_, target_hits_for_focused_build_point_end_, target_restypes_, protocols::match::downstream::TR(), and protocols::match::Matcher::upstream_builder().

Referenced by build_hits_at_all_positions().

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

overridevirtual

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.

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.

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

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 )

overridevirtual

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.

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,
		core::Size	round_just_completed
	)

overridevirtual

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.

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 ( core::Size target_geomcst_id )

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.

References target_geomcst_coords_.

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

private

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

Referenced by process_hit().

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

overridevirtual

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

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

Member Data Documentation

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

private

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

Referenced by prepare_for_hit_generation_at_target_build_point(), and process_hit().

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

private

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

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

private

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

Referenced by hits_to_include_with_partial_match(), and prepare_for_match_enumeration().

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

private

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

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

private

Referenced by respond_to_peripheral_hitlist_change(), and respond_to_primary_hitlist_change().

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

private

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

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

private

Referenced by build().

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

private

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().

core::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.

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().

Matcher::HitListConstIterator protocols::match::downstream::SecondaryMatcherToUpstreamResidue::target_hits_end_

private

Referenced by prepare_for_hit_generation(), and prepare_for_hit_generation_at_target_build_point().

Matcher::HitListConstIterator protocols::match::downstream::SecondaryMatcherToUpstreamResidue::target_hits_for_focused_build_point_begin_

private

Referenced by prepare_for_hit_generation(), and prepare_for_hit_generation_at_target_build_point().

Matcher::HitListConstIterator protocols::match::downstream::SecondaryMatcherToUpstreamResidue::target_hits_for_focused_build_point_end_

private

Referenced by prepare_for_hit_generation(), and prepare_for_hit_generation_at_target_build_point().

std::map< core::chemical::ResidueTypeCOP, core::Size > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::target_restype_index_map_

private

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

utility::vector1< core::chemical::ResidueTypeCOP > protocols::match::downstream::SecondaryMatcherToUpstreamResidue::target_restypes_

private

Referenced by add_evaluator_for_target_restype(), add_target_restype(), count_rotamer(), prepare_for_hit_generation_at_target_build_point(), reorder_restypes(), and store_rotamer_coords().

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

src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.hh
src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation