protocols::pack_daemon::EntityCorrespondence Class Reference

#include <EntityCorrespondence.hh>

Inheritance diagram for protocols::pack_daemon::EntityCorrespondence:

Collaboration diagram for protocols::pack_daemon::EntityCorrespondence:

Public Types
typedef core::Size	Size
typedef std::list< Size >	ResIDList
typedef ResIDList::const_iterator	ResIDListConstIter
typedef utility::pointer::ReferenceCount	parent

Public Member Functions
	EntityCorrespondence ()
virtual	~EntityCorrespondence ()
	EntityCorrespondence (EntityCorrespondence const &)
EntityCorrespondence const &	operator= (EntityCorrespondence const &)
void	set_pose (core::pose::PoseCOP pose)
void	set_num_entities (Size num_entities)
void	initialize_from_correspondence_file (std::istream &)
void	add_resid_to_entity_list (Size EntityID, Size ResID)
Size	num_entities () const
Size	num_residues () const
Size	entity_for_residue (Size resid) const
Size	n_residues_for_entity (Size entity_id) const
ResIDListConstIter	residues_for_entity_begin (Size entity_id) const
ResIDListConstIter	residues_for_entity_end (Size entity_id) const

Private Member Functions
void	bounds_check_entity (std::string const &funcname, Size entity_id) const
void	bounds_check_residue (std::string const &funcname, Size resid) const

Private Attributes
core::pose::PoseCOP	pose_
core::pose::PDBPoseMapCOP	pdb_pose_map_
utility::vector1< ResIDList >	entity_id_2_resids_
utility::vector1< Size >	resid_2_entity_id_
utility::vector1< std::string >	funcnames_

Detailed Description

Definition at line 37 of file EntityCorrespondence.hh.

Member Typedef Documentation

typedef utility::pointer::ReferenceCount protocols::pack_daemon::EntityCorrespondence::parent

Definition at line 42 of file EntityCorrespondence.hh.

typedef std::list< Size > protocols::pack_daemon::EntityCorrespondence::ResIDList

Definition at line 40 of file EntityCorrespondence.hh.

typedef ResIDList::const_iterator protocols::pack_daemon::EntityCorrespondence::ResIDListConstIter

Definition at line 41 of file EntityCorrespondence.hh.

typedef core::Size protocols::pack_daemon::EntityCorrespondence::Size

Definition at line 39 of file EntityCorrespondence.hh.

Constructor & Destructor Documentation

protocols::pack_daemon::EntityCorrespondence::EntityCorrespondence

(

)

Definition at line 44 of file EntityCorrespondence.cc.

References protocols::pack_daemon::func_add_resid_to_entity_list, protocols::pack_daemon::func_entity_for_residue, protocols::pack_daemon::func_n_residues_for_entity, protocols::pack_daemon::func_residues_for_entity_begin, protocols::pack_daemon::func_residues_for_entity_end, and funcnames_.

protocols::pack_daemon::EntityCorrespondence::~EntityCorrespondence ( )

virtual

Definition at line 54 of file EntityCorrespondence.cc.

protocols::pack_daemon::EntityCorrespondence::EntityCorrespondence

(

EntityCorrespondence const &

src)

Definition at line 56 of file EntityCorrespondence.cc.

Member Function Documentation

void protocols::pack_daemon::EntityCorrespondence::add_resid_to_entity_list	(	Size	EntityID,
		Size	ResID
	)

Definition at line 194 of file EntityCorrespondence.cc.

References bounds_check_entity(), bounds_check_residue(), entity_id_2_resids_, protocols::pack_daemon::func_add_resid_to_entity_list, funcnames_, and resid_2_entity_id_.

Referenced by initialize_from_correspondence_file().

void protocols::pack_daemon::EntityCorrespondence::bounds_check_entity ( std::string const &  funcname, Size  entity_id  ) const

private

Definition at line 253 of file EntityCorrespondence.cc.

References num_entities().

Referenced by add_resid_to_entity_list(), n_residues_for_entity(), residues_for_entity_begin(), and residues_for_entity_end().

void protocols::pack_daemon::EntityCorrespondence::bounds_check_residue ( std::string const &  funcname, Size  resid  ) const

private

Definition at line 265 of file EntityCorrespondence.cc.

References num_residues(), and pose_.

Referenced by add_resid_to_entity_list(), and entity_for_residue().

EntityCorrespondence::Size protocols::pack_daemon::EntityCorrespondence::entity_for_residue

(

Size

resid)

const

Definition at line 224 of file EntityCorrespondence.cc.

References bounds_check_residue(), protocols::pack_daemon::func_entity_for_residue, funcnames_, and resid_2_entity_id_.

void protocols::pack_daemon::EntityCorrespondence::initialize_from_correspondence_file

(

std::istream &

instream)

File format for entity correspondence: Column 1: entity id. Columns 2 and 3 PDB id (resid+[optional insertion code] chain)

Definition at line 105 of file EntityCorrespondence.cc.

References add_resid_to_entity_list(), num_entities(), num_residues(), and pdb_pose_map_.

EntityCorrespondence::Size protocols::pack_daemon::EntityCorrespondence::n_residues_for_entity

(

Size

entity_id)

const

Definition at line 231 of file EntityCorrespondence.cc.

References bounds_check_entity(), entity_id_2_resids_, protocols::pack_daemon::func_n_residues_for_entity, and funcnames_.

EntityCorrespondence::Size protocols::pack_daemon::EntityCorrespondence::num_entities

(

)

const

Definition at line 211 of file EntityCorrespondence.cc.

References entity_id_2_resids_.

Referenced by bounds_check_entity(), and initialize_from_correspondence_file().

EntityCorrespondence::Size protocols::pack_daemon::EntityCorrespondence::num_residues

(

)

const

Definition at line 218 of file EntityCorrespondence.cc.

References pose_.

Referenced by bounds_check_residue(), initialize_from_correspondence_file(), and protocols::pack_daemon::PackDaemon::set_entity_correspondence().

EntityCorrespondence const & protocols::pack_daemon::EntityCorrespondence::operator=

(

EntityCorrespondence const &

other)

Definition at line 66 of file EntityCorrespondence.cc.

References entity_id_2_resids_, funcnames_, pdb_pose_map_, pose_, and resid_2_entity_id_.

EntityCorrespondence::ResIDListConstIter protocols::pack_daemon::EntityCorrespondence::residues_for_entity_begin

(

Size

entity_id)

const

Definition at line 238 of file EntityCorrespondence.cc.

References bounds_check_entity(), entity_id_2_resids_, protocols::pack_daemon::func_residues_for_entity_begin, and funcnames_.

EntityCorrespondence::ResIDListConstIter protocols::pack_daemon::EntityCorrespondence::residues_for_entity_end

(

Size

entity_id)

const

Definition at line 246 of file EntityCorrespondence.cc.

References bounds_check_entity(), entity_id_2_resids_, protocols::pack_daemon::func_residues_for_entity_end, and funcnames_.

void protocols::pack_daemon::EntityCorrespondence::set_num_entities

(

Size

num_entities)

Definition at line 96 of file EntityCorrespondence.cc.

References entity_id_2_resids_, and resid_2_entity_id_.

void protocols::pack_daemon::EntityCorrespondence::set_pose

(

core::pose::PoseCOP

pose)

Definition at line 79 of file EntityCorrespondence.cc.

References pdb_pose_map_, pose_, and resid_2_entity_id_.

Referenced by protocols::pack_daemon::DaemonSet::add_pack_daemon().

Member Data Documentation

utility::vector1< ResIDList > protocols::pack_daemon::EntityCorrespondence::entity_id_2_resids_

private

Definition at line 69 of file EntityCorrespondence.hh.

Referenced by add_resid_to_entity_list(), n_residues_for_entity(), num_entities(), operator=(), residues_for_entity_begin(), residues_for_entity_end(), and set_num_entities().

utility::vector1< std::string > protocols::pack_daemon::EntityCorrespondence::funcnames_

private

Definition at line 72 of file EntityCorrespondence.hh.

Referenced by add_resid_to_entity_list(), entity_for_residue(), EntityCorrespondence(), n_residues_for_entity(), operator=(), residues_for_entity_begin(), and residues_for_entity_end().

core::pose::PDBPoseMapCOP protocols::pack_daemon::EntityCorrespondence::pdb_pose_map_

private

Definition at line 68 of file EntityCorrespondence.hh.

Referenced by initialize_from_correspondence_file(), operator=(), and set_pose().

core::pose::PoseCOP protocols::pack_daemon::EntityCorrespondence::pose_

private

Definition at line 67 of file EntityCorrespondence.hh.

Referenced by bounds_check_residue(), num_residues(), operator=(), and set_pose().

utility::vector1< Size > protocols::pack_daemon::EntityCorrespondence::resid_2_entity_id_

private

Definition at line 70 of file EntityCorrespondence.hh.

Referenced by add_resid_to_entity_list(), entity_for_residue(), operator=(), set_num_entities(), and set_pose().

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

• src/protocols/pack_daemon/EntityCorrespondence.hh
• src/protocols/pack_daemon/EntityCorrespondence.cc