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>

Inheritance diagram for protocols::match::output::SameSequenceAndDSPositionGrouper:

Collaboration diagram for protocols::match::output::SameSequenceAndDSPositionGrouper:

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

Definition at line 97 of file SameSequenceGrouper.hh.

Member Typedef Documentation

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

Definition at line 102 of file SameSequenceGrouper.hh.

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

Definition at line 100 of file SameSequenceGrouper.hh.

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

Definition at line 101 of file SameSequenceGrouper.hh.

Constructor & Destructor Documentation

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

(

)

Definition at line 95 of file SameSequenceGrouper.cc.

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

(

Size

ncst)

Definition at line 97 of file SameSequenceGrouper.cc.

References dsbuilders_.

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

virtual

Definition at line 103 of file SameSequenceGrouper.cc.

Member Function Documentation

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

private

Definition at line 166 of file SameSequenceGrouper.cc.

References dsbuilders_, protocols::match::full_hit(), protocols::match::match_dspos1::originating_geom_cst_for_dspos, relevant_atom_ids_, representative_dspos_, core::scoring::rms, and rms_group_cutoff_.

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.

Definition at line 120 of file SameSequenceGrouper.cc.

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.

Definition at line 139 of file SameSequenceGrouper.cc.

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
	)

Definition at line 155 of file SameSequenceGrouper.cc.

References dsbuilders_.

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

virtual

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

Definition at line 106 of file SameSequenceGrouper.cc.

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)

Definition at line 147 of file SameSequenceGrouper.cc.

References relevant_atom_ids_.

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

(

Real

cutoff)

Definition at line 113 of file SameSequenceGrouper.cc.

References rms_group_cutoff_.

Member Data Documentation

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

private

Definition at line 157 of file SameSequenceGrouper.hh.

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

Definition at line 155 of file SameSequenceGrouper.hh.

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

Definition at line 154 of file SameSequenceGrouper.hh.

Referenced by assign_downstream_position_group_for_match(), and reset().

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

private

Definition at line 153 of file SameSequenceGrouper.hh.

Referenced by assign_downstream_position_group_for_match(), and set_rms_group_cutoff().

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

private

Definition at line 151 of file SameSequenceGrouper.hh.

Referenced by assign_group_for_match(), and reset().

---

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

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