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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:
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Public Member Functions

 ReferencePose ()
 Constructor. 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::Sizeresidue_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.

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.

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
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().


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