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:

[legend]

Public Types
typedef std::map< std::pair < core::Size, core::Size > , core::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< core::Size > >, core::Size >	SequenceMap

Public Types inherited from protocols::match::output::MatchGrouper
typedef core::Real	Real

Public Member Functions
	SameSequenceAndDSPositionGrouper ()

	SameSequenceAndDSPositionGrouper (core::Size ncst)

	~SameSequenceAndDSPositionGrouper () override

core::Size	assign_group_for_match (match_dspos1 const &m) override

void	reset () override

void	set_n_geometric_constraints (core::Size n_csts) override

void	set_rms_group_cutoff (Real cutoff)

void	set_downstream_builder (core::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 (core::Size ncst)

	~SameSequenceGrouper () override

core::Size	assign_group_for_match (match const &m) override

void	set_hit_cacher (UpstreamHitCacherOP cacher)

Public Member Functions inherited from protocols::match::output::MatchGrouper
	MatchGrouper ()

	~MatchGrouper () override

Private Member Functions
core::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< core::Size, core::Size >, core::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 ( core::Size ncst )

References dsbuilders_.

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

overridedefault

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(), 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 )

overridevirtual

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 )

overridevirtual

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	(	core::Size	geomcst_id,
		downstream::DownstreamBuilderCOP	dsbuilder
	)

References dsbuilders_.

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

overridevirtual

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().

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

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation