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Residue Class Reference

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#include "residue.hpp"
(Private to src/app/cn3d.)

+ Inheritance diagram for Residue:
+ Collaboration diagram for Residue:

Classes

struct  AtomInfo
 

Public Types

enum  eType { eDNA = ncbi::objects::CResidue_graph::eResidue_type_deoxyribonucleotide , eRNA = ncbi::objects::CResidue_graph::eResidue_type_ribonucleotide , eAminoAcid = ncbi::objects::CResidue_graph::eResidue_type_amino_acid , eOther = ncbi::objects::CResidue_graph::eResidue_type_other }
 
enum  eAtomClassification {
  eSideChainAtom , eAlphaBackboneAtom , ePartialBackboneAtom , eCompleteBackboneAtom ,
  eUnknownAtom
}
 
typedef std::list< const Bond * > BondList
 
typedef std::map< int, const AtomInfo * > AtomInfoMap
 

Public Member Functions

 Residue (StructureBase *parent, const ncbi::objects::CResidue &residue, int moleculeID, const ResidueGraphList &standardDictionary, const ResidueGraphList &localDictionary, int nResidues, int moleculeType)
 
 ~Residue (void)
 
bool HasCode (void) const
 
bool HasName (void) const
 
bool IsNucleotide (void) const
 
bool IsAminoAcid (void) const
 
bool Draw (const AtomSet *atomSet) const
 
int NAtomsInGraph (void) const
 
int NAtomsWithAnyCoords (void) const
 
const AtomInfoMap & GetAtomInfos (void) const
 
const AtomInfo * GetAtomInfo (int aID) const
 
- Public Member Functions inherited from StructureBase
 StructureBase (StructureBase *parent)
 
virtual ~StructureBase (void)
 
virtual bool DrawAll (const AtomSet *atomSet=NULL) const
 
template<class T >
bool GetParentOfType (const T **ptr, bool warnIfNotFound=true) const
 

Public Attributes

int id
 
char code
 
std::string nameGraph
 
std::string namePDB
 
int alphaID
 
eType type
 
BondList bonds
 
- Public Attributes inherited from StructureBase
StructureSet * parentSet
 

Static Public Attributes

static const char NO_CODE = '?'
 
static const int NO_ALPHA_ID = -1
 

Private Attributes

AtomInfoMap atomInfos
 
int nAtomsWithAnyCoords
 

Detailed Description

Definition at line 58 of file residue.hpp.

Member Typedef Documentation

◆ AtomInfoMap

typedef std::map< int , const AtomInfo * > Residue::AtomInfoMap

Definition at line 115 of file residue.hpp.

◆ BondList

typedef std::list< const Bond * > Residue::BondList

Definition at line 105 of file residue.hpp.

Member Enumeration Documentation

◆ eAtomClassification

enum Residue::eAtomClassification
Enumerator
eSideChainAtom 
eAlphaBackboneAtom 
ePartialBackboneAtom 
eCompleteBackboneAtom 
eUnknownAtom 

Definition at line 88 of file residue.hpp.

◆ eType

enum Residue::eType
Enumerator
eDNA 
eRNA 
eAminoAcid 
eOther 

Definition at line 79 of file residue.hpp.

Constructor & Destructor Documentation

◆ Residue()

Residue::Residue ( StructureBase *  parent,
const ncbi::objects::CResidue &  residue,
int  moleculeID,
const ResidueGraphList &  standardDictionary,
const ResidueGraphList &  localDictionary,
int  nResidues,
int  moleculeType 
)

Definition at line 140 of file residue.cpp.

References a, alphaID, atomInfos, b, bonds, ClassifyAtom(), StructureObject::coordSets, StructureSet::CreateName(), eAlphaBackboneAtom, CAtom_Base::eIonizable_proton_true, Molecule::eNonpolymer, Molecule::eOther, ERRORMSG, Molecule::eSolvent, Bond::eUnknown, CAliasBase< TPrim >::Get(), CResidue_graph_Base::GetAtoms(), CBiostruc_residue_graph_set_pntr_Base::GetBiostruc_residue_graph_set_id(), CResidue_graph_Base::GetBonds(), CDbtag_Base::GetDb(), CResidue_graph_Base::GetDescr(), CAtom_Base::GetElement(), CObject_id_Base::GetId(), CAtom_Base::GetId(), CResidue_Base::GetId(), CAtom_Base::GetIonizable_proton(), CAtom_Base::GetIupac_code(), CResidue_graph_Base::GetIupac_code(), CResidue_graph_pntr_Base::GetLocal(), CAtom_Base::GetName(), CResidue_Base::GetName(), CBiostruc_id_Base::GetOther_database(), StructureBase::GetParentOfType(), CResidue_Base::GetResidue_graph(), CBiostruc_residue_graph_set_pntr_Base::GetResidue_graph_id(), CResidue_graph_Base::GetResidue_type(), CResidue_graph_pntr_Base::GetStandard(), CDbtag_Base::GetTag(), i, info, CObject_id_Base::IsId(), CResidue_graph_pntr_Base::IsLocal(), CBiostruc_id_Base::IsOther_database(), CResidue_graph_Base::IsSetDescr(), CAtom_Base::IsSetIonizable_proton(), CAtom_Base::IsSetIupac_code(), CResidue_graph_Base::IsSetIupac_code(), CAtom_Base::IsSetName(), CResidue_Base::IsSetName(), CResidue_graph_Base::IsSetResidue_type(), CResidue_graph_pntr_Base::IsStandard(), MakeBond(), nameGraph, namePDB, nAtomsWithAnyCoords, NULL, StructureBase::parentSet, and standardDictionary.

◆ ~Residue()

Residue::~Residue ( void  )

Definition at line 272 of file residue.cpp.

References a, and atomInfos.

Member Function Documentation

◆ Draw()

bool Residue::Draw ( const AtomSet *  atomSet) const
virtual

Reimplemented from StructureBase.

Definition at line 279 of file residue.cpp.

References a, atomInfos, StyleSettings::backgroundColor, code, AtomStyle::color, OpenGLRenderer::DrawAtom(), OpenGLRenderer::DrawLabel(), Colors::eHighlight, StyleManager::eNotDisplayed, StyleSettings::eOneLetter, StyleSettings::ePDBNumbering, ERRORMSG, StyleSettings::eSequentialNumbering, eSideChainAtom, StyleSettings::eThreeLetter, Colors::Get(), AtomSet::GetAtom(), StyleManager::GetAtomStyle(), StructureBase::GetParentOfType(), StyleManager::GetStyleForResidue(), GlobalColors(), GlobalMessenger(), i, Molecule::id, id, IsAminoAcid(), Messenger::IsHighlighted(), AtomStyle::isHighlighted, Colors::IsLightColor(), IsNucleotide(), nameGraph, namePDB, NO_ALPHA_ID, Vector< T >::normalize(), StyleSettings::nucleotideLabels, NULL, StyleSettings::LabelStyle::numbering, ShowHideManager::OverlayConfEnsembles(), StructureBase::parentSet, StyleSettings::proteinLabels, AtomStyle::radius, StructureSet::renderer, Molecule::residues, Vector< T >::Set(), StructureSet::showHideManager, AtomCoord::site, StyleSettings::LabelStyle::spacing, string, AtomStyle::style, StructureSet::styleManager, tolower(), toupper(), StyleSettings::LabelStyle::type, WARNINGMSG, and StyleSettings::LabelStyle::white.

◆ GetAtomInfo()

const AtomInfo* Residue::GetAtomInfo ( int  aID) const
inline

Definition at line 128 of file residue.hpp.

References ERR_POST, info, NULL, and Warning().

Referenced by StyleManager::GetAtomStyle(), and StructureSet::SelectedAtom().

◆ GetAtomInfos()

const AtomInfoMap& Residue::GetAtomInfos ( void  ) const
inline

Definition at line 127 of file residue.hpp.

Referenced by GetVirtualResidue().

◆ HasCode()

bool Residue::HasCode ( void  ) const
inline

Definition at line 109 of file residue.hpp.

◆ HasName()

bool Residue::HasName ( void  ) const
inline

Definition at line 110 of file residue.hpp.

◆ IsAminoAcid()

bool Residue::IsAminoAcid ( void  ) const
inline

Definition at line 112 of file residue.hpp.

Referenced by ClassifyAtom(), Draw(), StyleManager::GetAtomStyle(), and StyleManager::GetBondStyle().

◆ IsNucleotide()

bool Residue::IsNucleotide ( void  ) const
inline

Definition at line 111 of file residue.hpp.

References eRNA.

Referenced by ClassifyAtom(), Draw(), and StyleManager::GetAtomStyle().

◆ NAtomsInGraph()

int Residue::NAtomsInGraph ( void  ) const
inline

Definition at line 123 of file residue.hpp.

Referenced by StyleManager::GetAtomStyle().

◆ NAtomsWithAnyCoords()

int Residue::NAtomsWithAnyCoords ( void  ) const
inline

Definition at line 125 of file residue.hpp.

Referenced by Molecule::Molecule().

Member Data Documentation

◆ alphaID

int Residue::alphaID

Definition at line 76 of file residue.hpp.

Referenced by Molecule::DrawAllWithTerminiLabels(), Molecule::GetResidueColor(), GetVirtualPeptide(), Molecule::Molecule(), and Residue().

◆ atomInfos

AtomInfoMap Residue::atomInfos
private

Definition at line 118 of file residue.hpp.

Referenced by Draw(), Residue(), and ~Residue().

◆ bonds

BondList Residue::bonds

Definition at line 106 of file residue.hpp.

Referenced by Residue().

◆ code

char Residue::code

Definition at line 71 of file residue.hpp.

Referenced by Draw(), and StyleManager::GetAtomStyle().

◆ id

int Residue::id

Definition at line 69 of file residue.hpp.

Referenced by Draw(), StyleManager::GetAtomStyle(), StyleManager::GetBondStyle(), Molecule::GetResidueColor(), GetVirtualPeptide(), GetVirtualResidue(), Molecule::Molecule(), and StructureSet::SelectedAtom().

◆ nameGraph

std::string Residue::nameGraph

Definition at line 73 of file residue.hpp.

Referenced by Draw(), StyleManager::GetBondStyle(), Residue(), and StructureSet::SelectedAtom().

◆ namePDB

std::string Residue::namePDB

Definition at line 74 of file residue.hpp.

Referenced by Draw(), SequenceDisplay::MouseOver(), Residue(), and StructureSet::SelectedAtom().

◆ nAtomsWithAnyCoords

int Residue::nAtomsWithAnyCoords
private

Definition at line 119 of file residue.hpp.

Referenced by Residue().

◆ NO_ALPHA_ID

const int Residue::NO_ALPHA_ID = -1
static

Definition at line 75 of file residue.hpp.

Referenced by StructureSet::CenterViewOnAlignedResidues(), StructureSet::CenterViewOnStructure(), ChemicalGraph::CheckForDisulfide(), Draw(), Molecule::DrawAllWithTerminiLabels(), Molecule::GetAlphaCoords(), GetMinimumLoopLengths(), Molecule::GetResidueColor(), GetVirtualPeptide(), and Molecule::Molecule().

◆ NO_CODE

const char Residue::NO_CODE = '?'
static

Definition at line 70 of file residue.hpp.

◆ type

eType Residue::type

Definition at line 85 of file residue.hpp.

The documentation for this class was generated from the following files:
Generated by doxygen 1.9.0
Modified on Fri Sep 20 14:57:50 2024 by modify_doxy.py rev. 669887