core::pose::reference_pose::ReferencePose Class Reference

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

#include <ReferencePose.hh>

Inheritance diagram for core::pose::reference_pose::ReferencePose:

Public Member Functions
	ReferencePose ()
	Constructor. More...
	ReferencePose (ReferencePose const &src)
	Copy constructor. More...
	~ReferencePose ()
	Destructor. More...
virtual ReferencePoseOP	clone () const
	Make a copy of this ReferencePose object (allocate actual memory for it) and return an owning pointer to the copy. More...
ReferencePoseCOP	get_self_ptr () const
	Get const owning pointer (e.g. from a reference). More...
ReferencePoseOP	get_self_ptr ()
	Get owning pointer (e.g. from a reference). More...
ReferencePoseCAP	get_self_weak_ptr () const
	Get const access (weak) pointer (e.g. from a reference). More...
ReferencePoseAP	get_self_weak_ptr ()
	Get access (weak) pointer (e.g. from a reference). More...
bool	stores_residue_map () const
	Returns true if this ReferencePose object stores a map of (old residue indices->new residue indices), false otherwise. More...
void	initialize_residue_map_from_pose (core::pose::Pose const &pose)
	Initializes the residue_map_ based on an input reference pose. More...
void	increment_reference_pose_mapping_after_seqpos (core::Size const seqpos)
	Find all mappings to indices in the new pose after seqpos, 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, 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, and set them to point to residue 0 (deletion signal). More...
core::Size	corresponding_residue_in_current (core::Size const res_in_ref) const
	Get the residue in the current pose corresponding to a particular residue in the reference pose. More...

Private Attributes
bool	stores_residue_map_
	Does this ReferencePose store a residue map of (old residue indices -> new residue indices)? More...
std::map< core::Size, core::Size >	residue_map_
	Mapping of reference pose residue indices (key) onto new pose residue indices (mapped values). More...

Detailed Description

ReferencePose 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::ReferencePose::ReferencePose

(

)

Constructor.

Referenced by clone().

core::pose::reference_pose::ReferencePose::ReferencePose

(

ReferencePose const &

src

)

Copy constructor.

core::pose::reference_pose::ReferencePose::~ReferencePose

(

)

Destructor.

Note that Rosetta destructors are generally not called.

Member Function Documentation

ReferencePoseOP core::pose::reference_pose::ReferencePose::clone ( ) const

virtual

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

References ReferencePose().

core::Size core::pose::reference_pose::ReferencePose::corresponding_residue_in_current ( core::Size const  res_in_ref ) const

inline

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

Should return 0 if there is no corresponding residue in the current pose (e.g. if the residue was deleted.) Throws an error if there was no residue with the given index in the reference pose.

References residue_map_.

void core::pose::reference_pose::ReferencePose::decrement_reference_pose_mapping_after_seqpos

(

core::Size const

seqpos

)

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

If there is no ReferencePose object, do nothing.

References residue_map_.

ReferencePoseCOP core::pose::reference_pose::ReferencePose::get_self_ptr ( ) const

inline

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

ReferencePoseOP core::pose::reference_pose::ReferencePose::get_self_ptr ( )

inline

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

ReferencePoseCAP core::pose::reference_pose::ReferencePose::get_self_weak_ptr ( ) const

inline

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

ReferencePoseAP core::pose::reference_pose::ReferencePose::get_self_weak_ptr ( )

inline

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

void core::pose::reference_pose::ReferencePose::increment_reference_pose_mapping_after_seqpos

(

core::Size const

seqpos

)

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

If there is no ReferencePose object, do nothing.

References residue_map_.

void core::pose::reference_pose::ReferencePose::initialize_residue_map_from_pose

(

core::pose::Pose const &

pose

)

Initializes the residue_map_ based on an input reference pose.

After this operation, the residue_map_ is a very uninteresting map that maps every residue index in the pose onto itself. This also sets the stores_residue_map_ bit to true.

References residue_map_, core::pose::Pose::size(), and stores_residue_map_.

bool core::pose::reference_pose::ReferencePose::stores_residue_map ( ) const

inline

Returns true if this ReferencePose object stores a map of (old residue indices->new residue indices), false otherwise.

References stores_residue_map_.

void core::pose::reference_pose::ReferencePose::zero_reference_pose_mapping_at_seqpos

(

core::Size const

seqpos

)

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

If there is no ReferencePose object, do nothing.

References residue_map_.

Member Data Documentation

std::map<core::Size, core::Size> core::pose::reference_pose::ReferencePose::residue_map_

private

Mapping of reference pose residue indices (key) onto new pose residue indices (mapped values).

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

bool core::pose::reference_pose::ReferencePose::stores_residue_map_

private

Does this ReferencePose store a residue map of (old residue indices -> new residue indices)?

Default false.

Referenced by initialize_residue_map_from_pose(), and stores_residue_map().

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

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