core::pose::reference_pose::ReferencePoseSet Class Reference

ReferencePoseSet class, used to store sets of ReferencePose data for tracking how a pose changes over the course of a protocol. More...

#include <ReferencePoseSet.hh>

Inheritance diagram for core::pose::reference_pose::ReferencePoseSet:

Public Member Functions
	ReferencePoseSet ()
	Constructor. More...
	ReferencePoseSet (ReferencePoseSet const &src)
	Copy constructor. More...
	~ReferencePoseSet () override
	Destructor. More...
virtual ReferencePoseSetOP	clone () const
	Make a copy of this ReferencePoseSet object (allocate actual memory for it) and return an owning pointer to the copy. More...
ReferencePoseSetCOP	get_self_ptr () const
	Get const owning pointer (e.g. from a reference). More...
ReferencePoseSetOP	get_self_ptr ()
	Get owning pointer (e.g. from a reference). More...
ReferencePoseSetCAP	get_self_weak_ptr () const
	Get const access (weak) pointer (e.g. from a reference). More...
ReferencePoseSetAP	get_self_weak_ptr ()
	Get access (weak) pointer (e.g. from a reference). More...
void	add_and_initialize_reference_pose (std::string const &key_string, core::pose::Pose const &pose, bool override_current=false)
	Given a reference pose, create a new ReferencePose object and initialize it based on the reference pose, then add it to the current map. More...
ReferencePoseOP	reference_pose (std::string const &key_string)
	Get an owning pointer to a reference pose stored in the reference pose map, given a key string. More...
ReferencePoseCOP	reference_pose_cop (std::string const &key_string) const
	Get a const owning pointer to a reference pose stored in the reference pose map, given a key string. More...
core::Size	corresponding_residue_in_current (core::Size const res_index_in_ref, std::string const &ref_pose_key_string) const
	Get the corresponding residue in the current pose to a residue in a reference pose. More...
core::Size	n_reference_pose () const
	Get the number of ReferencePose objects in this ReferencePoseSet. More...
bool	empty () const
	Returns true if and only if there are no ReferencePose objects in this ReferencePoseSet. More...
void	increment_reference_pose_mapping_after_seqpos (core::Size const seqpos)
	Find all mappings to indices in the new pose after seqpos in all ReferencePose objects, and increment them by 1. More...
void	decrement_reference_pose_mapping_after_seqpos (core::Size const seqpos)
	Find all mappings to indices in the new pose after seqpos in all ReferencePose objects, and decrement them by 1. More...
void	zero_reference_pose_mapping_at_seqpos (core::Size const seqpos)
	Find all mappings to indices in the new pose to seqpos in all ReferencePose objects, and set them to point to residue 0 (deletion signal). More...

Private Attributes
std::map< std::string, ReferencePoseOP >	reference_pose_map_
	Owning pointers to the reference poses in this object, indexed by unique name strings. More...

Detailed Description

ReferencePoseSet class, used to store sets of ReferencePose data for tracking how a pose changes over the course of a protocol.

Constructor & Destructor Documentation

core::pose::reference_pose::ReferencePoseSet::ReferencePoseSet

(

)

Constructor.

core::pose::reference_pose::ReferencePoseSet::ReferencePoseSet

(

ReferencePoseSet const &

src

)

Copy constructor.

References reference_pose_map_.

core::pose::reference_pose::ReferencePoseSet::~ReferencePoseSet ( )

overridedefault

Destructor.

Note that Rosetta destructors are generally not called.

Member Function Documentation

void core::pose::reference_pose::ReferencePoseSet::add_and_initialize_reference_pose	(	std::string const &	key_string,
		core::pose::Pose const &	pose,
		bool	override_current = false
	)

Given a reference pose, create a new ReferencePose object and initialize it based on the reference pose, then add it to the current map.

After this operation, the map holds a new ReferencePoseOP pointing to a very uninteresting ReferencePose object that maps a list of residues onto themselves, accessible by the key string. If override_current is set to true, will overrwrite any reference pose with the key_string.

After this operation, the map holds a new ReferencePoseOP pointing to a very uninteresting ReferencePose object that maps a list of residues onto themselves, accessible by the key string.

References reference_pose_map_.

ReferencePoseSetOP core::pose::reference_pose::ReferencePoseSet::clone ( ) const

virtual

Make a copy of this ReferencePoseSet object (allocate actual memory for it) and return an owning pointer to the copy.

core::Size core::pose::reference_pose::ReferencePoseSet::corresponding_residue_in_current	(	core::Size const	res_index_in_ref,
		std::string const &	ref_pose_key_string
	)		const

Get the corresponding residue in the current pose to a residue in a reference pose.

Should return 0 if no corresponding residue exists in the current pose, and throw an error if the residue index provided as a key did not exist in the reference pose.

References reference_pose_map_.

void core::pose::reference_pose::ReferencePoseSet::decrement_reference_pose_mapping_after_seqpos

(

core::Size const

seqpos

)

Find all mappings to indices in the new pose after seqpos in all ReferencePose objects, and decrement them by 1.

If there is no ReferencePose object, do nothing.

References empty(), and reference_pose_map_.

bool core::pose::reference_pose::ReferencePoseSet::empty

(

)

const

Returns true if and only if there are no ReferencePose objects in this ReferencePoseSet.

References reference_pose_map_.

Referenced by decrement_reference_pose_mapping_after_seqpos(), increment_reference_pose_mapping_after_seqpos(), and zero_reference_pose_mapping_at_seqpos().

ReferencePoseSetCOP core::pose::reference_pose::ReferencePoseSet::get_self_ptr ( ) const

inline

Get const owning pointer (e.g. from a reference).

ReferencePoseSetOP core::pose::reference_pose::ReferencePoseSet::get_self_ptr ( )

inline

Get owning pointer (e.g. from a reference).

ReferencePoseSetCAP core::pose::reference_pose::ReferencePoseSet::get_self_weak_ptr ( ) const

inline

Get const access (weak) pointer (e.g. from a reference).

ReferencePoseSetAP core::pose::reference_pose::ReferencePoseSet::get_self_weak_ptr ( )

inline

Get access (weak) pointer (e.g. from a reference).

void core::pose::reference_pose::ReferencePoseSet::increment_reference_pose_mapping_after_seqpos

(

core::Size const

seqpos

)

Find all mappings to indices in the new pose after seqpos in all ReferencePose objects, and increment them by 1.

If there is no ReferencePose object, do nothing.

References empty(), and reference_pose_map_.

core::Size core::pose::reference_pose::ReferencePoseSet::n_reference_pose

(

)

const

Get the number of ReferencePose objects in this ReferencePoseSet.

References reference_pose_map_.

ReferencePoseOP core::pose::reference_pose::ReferencePoseSet::reference_pose ( std::string const &  key_string )

inline

Get an owning pointer to a reference pose stored in the reference pose map, given a key string.

An error is thrown if the key string doesn't associate with anything (i.e. if the reference pose doesn't exist).

References reference_pose_map_.

ReferencePoseCOP core::pose::reference_pose::ReferencePoseSet::reference_pose_cop ( std::string const &  key_string ) const

inline

Get a const owning pointer to a reference pose stored in the reference pose map, given a key string.

An error is thrown if the key string doesn't associate with anything (i.e. if the reference pose doesn't exist).

References reference_pose_map_.

void core::pose::reference_pose::ReferencePoseSet::zero_reference_pose_mapping_at_seqpos

(

core::Size const

seqpos

)

Find all mappings to indices in the new pose to seqpos in all ReferencePose objects, and set them to point to residue 0 (deletion signal).

If there is no ReferencePose object, do nothing.

References empty(), and reference_pose_map_.

Member Data Documentation

std::map< std::string, ReferencePoseOP > core::pose::reference_pose::ReferencePoseSet::reference_pose_map_

private

Owning pointers to the reference poses in this object, indexed by unique name strings.

Referenced by add_and_initialize_reference_pose(), corresponding_residue_in_current(), decrement_reference_pose_mapping_after_seqpos(), empty(), increment_reference_pose_mapping_after_seqpos(), n_reference_pose(), reference_pose(), reference_pose_cop(), ReferencePoseSet(), and zero_reference_pose_mapping_at_seqpos().

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

• src/core/pose/reference_pose/ReferencePoseSet.hh
• src/core/pose/reference_pose/ReferencePoseSet.cc