Produce hits by hashing building the coordinates of the downstream partner The downstream partner is responsible for building itself from the coordinate frame of three of its atoms. The ExternalGeomSampler describes the ways to orient the downstream partner given the coordinates of the upstream partner. More...

#include <ClassicMatchAlgorithm.hh>

Public Types
typedef DownstreamAlgorithm	parent

typedef core::Size	Size

typedef core::Real	Real

typedef numeric::HomogeneousTransform < Real >	HTReal

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

typedef core::Vector	Vector

Public Member Functions
	ClassicMatchAlgorithm (Size geom_cst_id)

virtual	~ClassicMatchAlgorithm ()

virtual DownstreamAlgorithmOP	clone () const

void	set_build_round1_hits_twice ()
	Enable a strategy where the first round hits are discarded after they are generated and then, after the second round completes, they are regenerated but respecting the occ-space hash, thereby decreasing the memory use dramatically. That is, the hits for the first geometric constraint (round 1 hits) are discarded, but their presence in the occupied space hash is recorded. Then the hits for the second round are collected, but only the ones that fall into the regions of 6D where the hits from the first round fell. At the end of round 2, the occ-space hash is updated to reflect the regions of 6D where both rounds produced hits. Then the round 1 hits are generated a second time, and this time saved. More...

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...

std::list< Hit >	build_and_discard_first_round_hits_at_all_positions (Matcher &matcher)

virtual void	respond_to_primary_hitlist_change (Matcher &matcher, Size round_just_completed)
	Reset the occupied space grid for the matcher so that only those regions which contain hits from this geometric constraint are marked as occupied. More...

virtual void	respond_to_peripheral_hitlist_change (Matcher &matcher)
	Delete hits for this geometric constraint if they fall into now-empty regions of 6D. This step can be avoided if the occupied-space-grid's revision ID has not changed since the last time this function was invoked. 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 external geom samplers that describe the rigid body orientations of the downstream partner from the coordinates of the upstream partner. More...

virtual bool	upstream_only () const
	This method returns 'false' since the classic match algorithm builds coordinates of the downstream partner and its hits should be hashed in 6D to generate matches. More...

virtual bool	generates_primary_hits () const
	This method returns 'true' since the classic matcher builds the downstream coordinates from scratch. More...

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

virtual Size	n_possible_hits_per_upstream_conformation () const

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

void	set_residue_type (core::chemical::ResidueTypeCOP restype)

void	add_external_geom_sampler (toolbox::match_enzdes_util::ExternalGeomSampler const &sampler, Size const exgeom_id, std::string const &atom1, std::string const &atom2, std::string const &atom3, DownstreamBuilderCOP downstream_builder)

void	clear_external_geom_samplers ()

core::chemical::ResidueType const &	restype () const
	Accessors. More...

toolbox::match_enzdes_util::ExternalGeomSampler const &	external_sampler (Size external_geom_id) const

Size	launch_atom (Size external_geom_id, Size which_point) const

Size	n_external_samplers () const

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 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
core::chemical::ResidueTypeCOP	restype_

utility::vector1 < toolbox::match_enzdes_util::ExternalGeomSampler >	external_samplers_

utility::vector1 < utility::fixedsizearray1 < Size, 3 > >	launch_points_

utility::vector1 < DownstreamBuilderCOP >	dsbuilders_

utility::vector1< Size >	exgeom_ids_

Size	occspace_rev_id_at_last_update_

bool	build_round1_hits_twice_
	control whether this algorithm expects to rebuild round 1 hits after round 2 completes. Only used if the geom_cst_id() for this instance is 1. More...

bool	completed_first_round1_hit_building_

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

Produce hits by hashing building the coordinates of the downstream partner The downstream partner is responsible for building itself from the coordinate frame of three of its atoms. The ExternalGeomSampler describes the ways to orient the downstream partner given the coordinates of the upstream partner.

Member Typedef Documentation

typedef numeric::HomogeneousTransform< Real > protocols::match::downstream::ClassicMatchAlgorithm::HTReal

typedef DownstreamAlgorithm protocols::match::downstream::ClassicMatchAlgorithm::parent

typedef core::Real protocols::match::downstream::ClassicMatchAlgorithm::Real

typedef core::Size protocols::match::downstream::ClassicMatchAlgorithm::Size

Constructor & Destructor Documentation

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

Referenced by clone().

protocols::match::downstream::ClassicMatchAlgorithm::~ClassicMatchAlgorithm ( )

virtual

Member Function Documentation

void protocols::match::downstream::ClassicMatchAlgorithm::add_external_geom_sampler	(	toolbox::match_enzdes_util::ExternalGeomSampler const &	sampler,
		Size const	exgeom_id,
		std::string const &	atom1,
		std::string const &	atom2,
		std::string const &	atom3,
		DownstreamBuilderCOP	dsbuilder
	)

Precompute transforms for the external geom sampler as it is added so that the transforms are ready when build() is called.

References dsbuilders_, exgeom_ids_, external_samplers_, has, launch_points_, restype(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D1D2(), and utility_exit_with_message.

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

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

virtual

Iterate across the external geom samplers that describe the rigid body orientations of the downstream partner from the coordinates of the upstream partner.

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

References build_from_three_coords(), external_samplers_, utility::pointer::owning_ptr< T >::get(), n_external_samplers(), core::conformation::Residue::name(), restype_, core::conformation::Residue::type(), and utility_exit_with_message.

std::list< Hit > protocols::match::downstream::ClassicMatchAlgorithm::build_and_discard_first_round_hits_at_all_positions ( Matcher & matcher )

References protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), protocols::match::Matcher::occ_space_hash(), protocols::match::Matcher::per_constraint_build_points(), and protocols::match::Matcher::upstream_builder().

Referenced by build_hits_at_all_positions().

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

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).

References protocols::match::downstream::DownstreamAlgorithm::active_site_grid(), protocols::match::downstream::DownstreamAlgorithm::active_site_grid_set(), protocols::match::downstream::DownstreamAlgorithm::bbgrid(), dsbuilders_, exgeom_ids_, external_samplers_, protocols::toolbox::match_enzdes_util::HT_ang_U1D2, protocols::toolbox::match_enzdes_util::HT_ang_U2D1, protocols::toolbox::match_enzdes_util::HT_tor_U1D3, protocols::toolbox::match_enzdes_util::HT_tor_U2D2, protocols::toolbox::match_enzdes_util::HT_tor_U3D1, launch_atom(), nn, numeric::HomogeneousTransform< T >::point(), numeric::HomogeneousTransform< T >::walk_along_z(), core::conformation::Residue::xyz(), and protocols::match::ZERO.

Referenced by build().

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

virtual

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().

By initializing local std::list< Hit > variables inside the loop over all of the build points, and then splicing them into a central vector of hit lists, I can avoid expensive list-copy operations while guaranteeing OpenMP thread saftey.

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

References build_and_discard_first_round_hits_at_all_positions(), build_round1_hits_twice_, completed_first_round1_hit_building_, protocols::match::downstream::DownstreamAlgorithm::default_build_hits_at_all_positions(), protocols::match::Matcher::downstream_builders(), protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), and protocols::match::Matcher::occ_space_hash().

void protocols::match::downstream::ClassicMatchAlgorithm::clear_external_geom_samplers ( )

References dsbuilders_, external_samplers_, and launch_points_.

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

virtual

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

References ClassicMatchAlgorithm().

toolbox::match_enzdes_util::ExternalGeomSampler const& protocols::match::downstream::ClassicMatchAlgorithm::external_sampler ( Size external_geom_id ) const

inline

References external_samplers_.

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

virtual

This method returns 'true' since the classic matcher builds the downstream coordinates from scratch.

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

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

virtual

This method should not be invoked on the ClassicMatchAlgorithm, since it returns "false" 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.

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

References empty, and utility_exit_with_message.

Size protocols::match::downstream::ClassicMatchAlgorithm::launch_atom	(	Size	external_geom_id,
		Size	which_point
	)		const

inline

References launch_points_.

Referenced by build_from_three_coords().

Size protocols::match::downstream::ClassicMatchAlgorithm::n_external_samplers ( ) const

inline

References external_samplers_.

Referenced by build(), and n_possible_hits_per_upstream_conformation().

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

virtual

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

References dsbuilders_, external_samplers_, protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_ang_U1D2_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_ang_U2D1_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_dis_U1D1_samples(), n_external_samplers(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U1D3_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U2D2_samples(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::n_tor_U3D1_samples(), and protocols::analysis::total.

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

virtual

Delete hits for this geometric constraint if they fall into now-empty regions of 6D. This step can be avoided if the occupied-space-grid's revision ID has not changed since the last time this function was invoked.

Drop hits that had previously seemed viable after another round completed; during that round, certain previously occupied regions of 6D were not filled with new hits. Any previously-generated hit that falls into a region of 6D which is no longer occupied should be elminated since it could not ever result in a match; it is inviable.

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(), protocols::match::Matcher::occ_space_hash(), occspace_rev_id_at_last_update_, and protocols::match::downstream::TR.

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

virtual

Reset the occupied space grid for the matcher so that only those regions which contain hits from this geometric constraint are marked as occupied.

Reset the occupied space hash that the matcher uses so that it reflects the hits generated this round; this will cause the invalidation of hits generated in previous rounds. These invalidated hits will be deleted in calls to respond_to_peripheral_hitlist_change.

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

References build_round1_hits_twice_, protocols::match::downstream::DownstreamAlgorithm::geom_cst_id(), protocols::match::Matcher::hits(), protocols::match::Matcher::occ_space_hash(), occspace_rev_id_at_last_update_, and protocols::match::downstream::TR.

core::chemical::ResidueType const& protocols::match::downstream::ClassicMatchAlgorithm::restype ( ) const

inline

Accessors.

References restype_.

Referenced by add_external_geom_sampler(), and set_residue_type().

void protocols::match::downstream::ClassicMatchAlgorithm::set_build_round1_hits_twice ( )

Enable a strategy where the first round hits are discarded after they are generated and then, after the second round completes, they are regenerated but respecting the occ-space hash, thereby decreasing the memory use dramatically. That is, the hits for the first geometric constraint (round 1 hits) are discarded, but their presence in the occupied space hash is recorded. Then the hits for the second round are collected, but only the ones that fall into the regions of 6D where the hits from the first round fell. At the end of round 2, the occ-space hash is updated to reflect the regions of 6D where both rounds produced hits. Then the round 1 hits are generated a second time, and this time saved.

References build_round1_hits_twice_, and protocols::match::downstream::DownstreamAlgorithm::geom_cst_id().

void protocols::match::downstream::ClassicMatchAlgorithm::set_residue_type ( core::chemical::ResidueTypeCOP restype )

References external_samplers_, launch_points_, restype(), and restype_.

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

virtual

This method returns 'false' since the classic match algorithm builds coordinates of the downstream partner and its hits should be hashed in 6D to generate matches.

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

Member Data Documentation

bool protocols::match::downstream::ClassicMatchAlgorithm::build_round1_hits_twice_

private

control whether this algorithm expects to rebuild round 1 hits after round 2 completes. Only used if the geom_cst_id() for this instance is 1.

Referenced by build_hits_at_all_positions(), respond_to_primary_hitlist_change(), and set_build_round1_hits_twice().

bool protocols::match::downstream::ClassicMatchAlgorithm::completed_first_round1_hit_building_

private

Referenced by build_hits_at_all_positions().

utility::vector1< DownstreamBuilderCOP > protocols::match::downstream::ClassicMatchAlgorithm::dsbuilders_

private

Referenced by add_external_geom_sampler(), build_from_three_coords(), clear_external_geom_samplers(), and n_possible_hits_per_upstream_conformation().

utility::vector1< Size > protocols::match::downstream::ClassicMatchAlgorithm::exgeom_ids_

private

Referenced by add_external_geom_sampler(), and build_from_three_coords().

utility::vector1< toolbox::match_enzdes_util::ExternalGeomSampler > protocols::match::downstream::ClassicMatchAlgorithm::external_samplers_

private

Referenced by add_external_geom_sampler(), build(), build_from_three_coords(), clear_external_geom_samplers(), external_sampler(), n_external_samplers(), n_possible_hits_per_upstream_conformation(), and set_residue_type().

utility::vector1< utility::fixedsizearray1< Size, 3 > > protocols::match::downstream::ClassicMatchAlgorithm::launch_points_

private

Referenced by add_external_geom_sampler(), clear_external_geom_samplers(), launch_atom(), and set_residue_type().

Size protocols::match::downstream::ClassicMatchAlgorithm::occspace_rev_id_at_last_update_

private

Referenced by respond_to_peripheral_hitlist_change(), and respond_to_primary_hitlist_change().

core::chemical::ResidueTypeCOP protocols::match::downstream::ClassicMatchAlgorithm::restype_

private

Referenced by build(), restype(), and set_residue_type().

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

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

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation