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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:
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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
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

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