protocols::match::output::SameSequenceAndDSPositionGrouper Class Reference

class that groups based on same sequence and proximity of the downstream object (based on rms ) NOTE: right now only the downstream position according to the first geomcst id upstream residue is taken into account More...

#include <SameSequenceGrouper.hh>

Public Types
typedef std::map< std::pair < Size, Size >, Size >	SequenceLigPosMap
typedef core::Vector	Vector
typedef SameSequenceGrouper	parent
Public Types inherited from protocols::match::output::SameSequenceGrouper
typedef core::Real	Real
typedef core::Size	Size
typedef std::map < utility::OrderedTuple < utility::vector1< Size > >, Size >	SequenceMap
Public Types inherited from protocols::match::output::MatchGrouper
typedef core::Real	Real

Public Member Functions
	SameSequenceAndDSPositionGrouper ()
	SameSequenceAndDSPositionGrouper (Size ncst)
virtual	~SameSequenceAndDSPositionGrouper ()
virtual Size	assign_group_for_match (match_dspos1 const &m)
virtual void	reset ()
virtual void	set_n_geometric_constraints (Size n_csts)
void	set_rms_group_cutoff (Real cutoff)
void	set_downstream_builder (Size geomcst_id, downstream::DownstreamBuilderCOP dsbuilder)
void	set_relevant_atom_ids (utility::vector1< core::id::AtomID > const &relevant_atom_ids)
Public Member Functions inherited from protocols::match::output::SameSequenceGrouper
	SameSequenceGrouper ()
	SameSequenceGrouper (Size ncst)
virtual	~SameSequenceGrouper ()
virtual Size	assign_group_for_match (match const &m)
void	set_hit_cacher (UpstreamHitCacherOP cacher)
Public Member Functions inherited from protocols::match::output::MatchGrouper
	MatchGrouper ()
virtual	~MatchGrouper ()

Private Member Functions
Size	assign_downstream_position_group_for_match (match_dspos1 const &m)

Private Attributes
SequenceLigPosMap	sequence_pos_map_
Real	rms_group_cutoff_
utility::vector1 < utility::vector1< Vector > >	representative_dspos_
utility::vector1 < core::id::AtomID >	relevant_atom_ids_
utility::vector1 < downstream::DownstreamBuilderCOP >	dsbuilders_

Detailed Description

class that groups based on same sequence and proximity of the downstream object (based on rms ) NOTE: right now only the downstream position according to the first geomcst id upstream residue is taken into account

Member Typedef Documentation

typedef SameSequenceGrouper protocols::match::output::SameSequenceAndDSPositionGrouper::parent

typedef std::map< std::pair< Size, Size >, Size > protocols::match::output::SameSequenceAndDSPositionGrouper::SequenceLigPosMap

typedef core::Vector protocols::match::output::SameSequenceAndDSPositionGrouper::Vector

Constructor & Destructor Documentation

protocols::match::output::SameSequenceAndDSPositionGrouper::SameSequenceAndDSPositionGrouper

(

)

protocols::match::output::SameSequenceAndDSPositionGrouper::SameSequenceAndDSPositionGrouper

(

Size

ncst

)

References dsbuilders_.

protocols::match::output::SameSequenceAndDSPositionGrouper::~SameSequenceAndDSPositionGrouper ( )

virtual

Member Function Documentation

SameSequenceGrouper::Size protocols::match::output::SameSequenceAndDSPositionGrouper::assign_downstream_position_group_for_match ( match_dspos1 const &  m )

private

References dsbuilders_, protocols::match::full_hit(), numeric::xyzVector< class >::length_squared(), protocols::match::match_dspos1::originating_geom_cst_for_dspos, relevant_atom_ids_, representative_dspos_, rms, rms_group_cutoff_, and runtime_assert.

Referenced by assign_group_for_match().

SameSequenceGrouper::Size protocols::match::output::SameSequenceAndDSPositionGrouper::assign_group_for_match ( match_dspos1 const &  m )

virtual

Reimplemented from protocols::match::output::SameSequenceGrouper.

References assign_downstream_position_group_for_match(), protocols::match::output::SameSequenceGrouper::assign_group_for_match(), and sequence_pos_map_.

void protocols::match::output::SameSequenceAndDSPositionGrouper::reset ( void  )

virtual

Reimplemented from protocols::match::output::SameSequenceGrouper.

References representative_dspos_, protocols::match::output::SameSequenceGrouper::reset(), and sequence_pos_map_.

void protocols::match::output::SameSequenceAndDSPositionGrouper::set_downstream_builder	(	Size	geomcst_id,
		downstream::DownstreamBuilderCOP	dsbuilder
	)

References dsbuilders_, and runtime_assert.

void protocols::match::output::SameSequenceAndDSPositionGrouper::set_n_geometric_constraints ( Size  n_csts )

virtual

Reimplemented from protocols::match::output::SameSequenceGrouper.

References dsbuilders_, and protocols::match::output::SameSequenceGrouper::set_n_geometric_constraints().

void protocols::match::output::SameSequenceAndDSPositionGrouper::set_relevant_atom_ids

(

utility::vector1< core::id::AtomID > const &

relevant_atom_ids

)

References relevant_atom_ids_.

void protocols::match::output::SameSequenceAndDSPositionGrouper::set_rms_group_cutoff

(

Real

cutoff

)

References rms_group_cutoff_.

Member Data Documentation

utility::vector1< downstream::DownstreamBuilderCOP > protocols::match::output::SameSequenceAndDSPositionGrouper::dsbuilders_

private

Referenced by assign_downstream_position_group_for_match(), SameSequenceAndDSPositionGrouper(), set_downstream_builder(), and set_n_geometric_constraints().

utility::vector1< core::id::AtomID > protocols::match::output::SameSequenceAndDSPositionGrouper::relevant_atom_ids_

private

Referenced by assign_downstream_position_group_for_match(), and set_relevant_atom_ids().

utility::vector1< utility::vector1< Vector> > protocols::match::output::SameSequenceAndDSPositionGrouper::representative_dspos_

private

Referenced by assign_downstream_position_group_for_match(), and reset().

Real protocols::match::output::SameSequenceAndDSPositionGrouper::rms_group_cutoff_

private

Referenced by assign_downstream_position_group_for_match(), and set_rms_group_cutoff().

SequenceLigPosMap protocols::match::output::SameSequenceAndDSPositionGrouper::sequence_pos_map_

private

Referenced by assign_group_for_match(), and reset().

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

• src/protocols/match/output/SameSequenceGrouper.hh
• src/protocols/match/output/SameSequenceGrouper.cc