represents a chunk of residues extracted from a vall. More...
#include <VallChunk.hh>
Public Member Functions | |
| ~VallChunk () override | |
| Automatically generated virtual destructor for class deriving directly from VirtualBase. More... | |
| VallChunk (VallProviderAP provider) | |
| VallChunkCOP | get_self_ptr () const |
| VallChunkOP | get_self_ptr () |
| VallChunkCAP | get_self_weak_ptr () const |
| VallChunkAP | get_self_weak_ptr () |
| std::string | get_pdb_id () const |
| returns a PDB id (a string of four letters, e.g. "4mba") More... | |
| char | get_chain_id () const |
| returns protein chain ID More... | |
| core::Size | key () const |
| returns integer key of this chunk, which is the key of this chunk's first residue More... | |
| core::Size | size () const |
| returns the size of this chunk i.e. the number of residues stored in there More... | |
| core::Size | vall_key () const |
| void | vall_key (core::Size key) |
| VallResidueOP | at (core::Size index) const |
| returns i-th residue form this chunk. The first residue has index 1 More... | |
| void | push_back (VallResidueOP what) |
| appends a residue to this chunk More... | |
| std::string & | get_sequence () |
| returns amino acid sequence of this chunk More... | |
| core::sequence::SequenceProfileOP | get_profile () |
| returns amino acid profile of this chunk More... | |
| core::pose::PoseOP | get_pose () |
| returns a pose created for this chunk More... | |
| std::string | get_vall_filename () |
| returns the Vall file used for this chunk More... | |
| VallProviderOP | get_vall_provider () |
| returns the Vall Provider More... | |
| std::string & | chunk_key () |
| returns a string that is unique for each chunk in vall More... | |
Private Member Functions | |
| void | create_key () |
Private Attributes | |
| utility::vector1< VallResidueOP > | residues_ |
| std::string | sequence_ |
| VallProviderAP | my_provider_ |
| std::string | chunk_key_ |
| core::Size | vall_key_ |
| bool | has_key_ |
Detailed Description
represents a chunk of residues extracted from a vall.
VallChunk contains a vector of VallResidue objects and provides a basic ways to access them
Constructor & Destructor Documentation
◆ ~VallChunk()
|
overridedefault |
Automatically generated virtual destructor for class deriving directly from VirtualBase.
Auto-generated virtual destructor
◆ VallChunk()
| protocols::frag_picker::VallChunk::VallChunk | ( | VallProviderAP | provider | ) |
References has_key_, my_provider_, and sequence_.
Member Function Documentation
◆ at()
|
inline |
returns i-th residue form this chunk. The first residue has index 1
References residues_.
Referenced by create_key(), get_chain_id(), get_pdb_id(), and key().
◆ chunk_key()
|
inline |
returns a string that is unique for each chunk in vall
References chunk_key_, create_key(), and has_key_.
◆ create_key()
|
private |
References at(), chunk_key_, get_chain_id(), get_pdb_id(), has_key_, and core::conformation::membrane::out.
Referenced by chunk_key().
◆ get_chain_id()
|
inline |
◆ get_pdb_id()
|
inline |
returns a PDB id (a string of four letters, e.g. "4mba")
References at().
Referenced by create_key().
◆ get_pose()
| core::pose::PoseOP protocols::frag_picker::VallChunk::get_pose | ( | ) |
returns a pose created for this chunk
the pose object is created when this function is called for the first time and then cached within a VallProvider object Every time this method is called for a new chunk, VallProvider caches new data
References get_self_ptr(), and my_provider_.
◆ get_profile()
| core::sequence::SequenceProfileOP protocols::frag_picker::VallChunk::get_profile | ( | ) |
returns amino acid profile of this chunk
the profile object is created when this function is called for the first time and then cached within a VallProvider object. Every time this method is called for a new chunk, VallProvider caches new data
References get_self_ptr(), and my_provider_.
◆ get_self_ptr() [1/2]
|
inline |
◆ get_self_ptr() [2/2]
|
inline |
Referenced by get_pose(), and get_profile().
◆ get_self_weak_ptr() [1/2]
|
inline |
◆ get_self_weak_ptr() [2/2]
|
inline |
◆ get_sequence()
| std::string & protocols::frag_picker::VallChunk::get_sequence | ( | ) |
◆ get_vall_filename()
| std::string protocols::frag_picker::VallChunk::get_vall_filename | ( | ) |
returns the Vall file used for this chunk
References my_provider_, and vall_key_.
◆ get_vall_provider()
| VallProviderOP protocols::frag_picker::VallChunk::get_vall_provider | ( | ) |
returns the Vall Provider
References my_provider_.
◆ key()
|
inline |
returns integer key of this chunk, which is the key of this chunk's first residue
References at().
Referenced by vall_key().
◆ push_back()
|
inline |
appends a residue to this chunk
References residues_.
◆ size()
|
inline |
returns the size of this chunk i.e. the number of residues stored in there
References residues_.
◆ vall_key() [1/2]
|
inline |
References vall_key_.
◆ vall_key() [2/2]
|
inline |
Member Data Documentation
◆ chunk_key_
|
private |
Referenced by chunk_key(), and create_key().
◆ has_key_
|
private |
Referenced by chunk_key(), create_key(), and VallChunk().
◆ my_provider_
|
private |
Referenced by get_pose(), get_profile(), get_vall_filename(), get_vall_provider(), and VallChunk().
◆ residues_
|
private |
Referenced by at(), get_sequence(), push_back(), and size().
◆ sequence_
|
private |
Referenced by get_sequence(), and VallChunk().
◆ vall_key_
|
private |
Referenced by get_vall_filename(), and vall_key().
The documentation for this class was generated from the following files:
- src/protocols/frag_picker/VallChunk.hh
- src/protocols/frag_picker/VallChunk.cc
