Molecule Class Reference

Search Toolkit Book for Molecule

#include <molecule.hpp>

Inheritance diagram for Molecule:

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Collaboration diagram for Molecule:

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List of all members.

Detailed Description

Definition at line 65 of file molecule.hpp.

Public Types

typedef std::map< int, const
Residue * > 		ResidueMap
typedef std::list< const Bond * > BondList
typedef std::map< int, int > DisulfideMap
typedef std::list< unsigned
int > 		DisplayListList
enum  eType {
  eDNA = ncbi::objects::CBiomol_descr::eMolecule_type_dna, eRNA = ncbi::objects::CBiomol_descr::eMolecule_type_rna, eProtein = ncbi::objects::CBiomol_descr::eMolecule_type_protein, eBiopolymer = ncbi::objects::CBiomol_descr::eMolecule_type_other_biopolymer,
  eSolvent = ncbi::objects::CBiomol_descr::eMolecule_type_solvent, eNonpolymer = ncbi::objects::CBiomol_descr::eMolecule_type_other_nonpolymer, eOther = ncbi::objects::CBiomol_descr::eMolecule_type_other
}
enum  eSecStruc { eHelix, eStrand, eCoil }

Public Member Functions

 Molecule (ChemicalGraph *parentGraph, const ncbi::objects::CMolecule_graph &graph, const ResidueGraphList &standardDictionary, const ResidueGraphList &localDictionary)
bool IsProtein (void) const
bool IsNucleotide (void) const
bool IsBiopolymer (void) const
bool IsSolvent (void) const
bool IsHeterogen (void) const
unsigned int NResidues (void) const
const Residue::AtomInfo * GetAtomInfo (int rID, int aID) const
Vector GetResidueColor (int sequenceIndex) const
int GetAlphaCoords (int nResidues, const int *seqIndexes, const Vector **coords) const
bool IsResidueInHelix (int residueID) const
bool IsResidueInStrand (int residueID) const
bool IsResidueInCoil (int residueID) const
int ResidueDomainID (int residueID) const
bool DrawAllWithTerminiLabels (const AtomSet *atomSet=NULL) const

Public Attributes

eType type
int id
std::string name
const MoleculeIdentifier * identifier
ResidueMap residues
BondList interResidueBonds
DisulfideMap disulfideMap
std::vector< eSecStruc > residueSecondaryStructures
std::vector< int > residueDomains
int nDomains
const Sequence * sequence
DisplayListList displayLists

Static Public Attributes

static const int NO_DOMAIN_SET = -1

Member Typedef Documentation

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

Definition at line 90 of file molecule.hpp.

typedef std::list< unsigned int > Molecule::DisplayListList
 

Definition at line 111 of file molecule.hpp.

typedef std::map< int, int > Molecule::DisulfideMap
 

Definition at line 94 of file molecule.hpp.

typedef std::map< int, const Residue * > Molecule::ResidueMap
 

Definition at line 88 of file molecule.hpp.

Member Enumeration Documentation

enum Molecule::eSecStruc
 

Enumerator:
eHelix 
eStrand 
eCoil 

Definition at line 99 of file molecule.hpp.

enum Molecule::eType
 

Enumerator:
eDNA 
eRNA 
eProtein 
eBiopolymer 
eSolvent 
eNonpolymer 
eOther 

Definition at line 74 of file molecule.hpp.

Constructor & Destructor Documentation

Molecule::Molecule (  ChemicalGraph *  parentGraph,
const ncbi::objects::CMolecule_graph &  graph,
const ResidueGraphList &  standardDictionary,
const ResidueGraphList &  localDictionary
) 
 

Member Function Documentation

bool Molecule::DrawAllWithTerminiLabels (  const AtomSet *  atomSet = NULL  )  const
 

Definition at line 295 of file molecule.cpp.

References StructureBase::DrawAll(), OpenGLRenderer::DrawLabel(), AtomSet::GetAtom(), StyleManager::GetGlobalStyle(), identifier, Colors::IsLightColor(), IsNucleotide(), IsProtein(), ShowHideManager::IsVisible(), Residue::NO_ALPHA_ID, NResidues(), ShowHideManager::OverlayConfEnsembles(), StructureBase::parentSet, MoleculeIdentifier::pdbChain, StructureSet::renderer, residues, StructureSet::showHideManager, AtomCoord::site, StructureSet::styleManager, MoleculeIdentifier::VALUE_NOT_SET, and WARNINGMSG.

int Molecule::GetAlphaCoords (  int  nResidues,
const int *  seqIndexes,
const Vector **  coords
)  const
 

Definition at line 246 of file molecule.cpp.

References StructureObject::coordSets, ERRORMSG, and StructureBase::GetParentOfType().

Referenced by AlignmentManager::RealignAllDependentStructures().

const Residue::AtomInfo* Molecule::GetAtomInfo (  int  rID,
int  aID
)  const [inline]
 

Definition at line 122 of file molecule.hpp.

References ERR_POST.

Vector Molecule::GetResidueColor (  int  sequenceIndex  )  const
 

Definition at line 218 of file molecule.cpp.

References Residue::alphaID, AtomStyle::color, StructureObject::coordSets, StyleManager::GetAtomStyle(), StructureBase::GetParentOfType(), Residue::id, Residue::NO_ALPHA_ID, ShowHideManager::OverlayConfEnsembles(), StructureBase::parentSet, residues, StructureSet::showHideManager, and StructureSet::styleManager.

Referenced by DisplayRowFromSequence::GetCharacterTraitsAt(), and BlockMultipleAlignment::GetCharacterTraitsAt().

bool Molecule::IsBiopolymer (  void   )  const [inline]
 

Definition at line 117 of file molecule.hpp.

bool Molecule::IsHeterogen (  void   )  const [inline]
 

Definition at line 119 of file molecule.hpp.

Referenced by StructureSet::SelectedAtom().

bool Molecule::IsNucleotide (  void   )  const [inline]
 

Definition at line 116 of file molecule.hpp.

Referenced by DrawAllWithTerminiLabels().

bool Molecule::IsProtein (  void   )  const [inline]
 

Definition at line 115 of file molecule.hpp.

Referenced by DrawAllWithTerminiLabels().

bool Molecule::IsResidueInCoil (  int  residueID  )  const [inline]
 

Definition at line 144 of file molecule.hpp.

bool Molecule::IsResidueInHelix (  int  residueID  )  const [inline]
 

Definition at line 140 of file molecule.hpp.

bool Molecule::IsResidueInStrand (  int  residueID  )  const [inline]
 

Definition at line 142 of file molecule.hpp.

bool Molecule::IsSolvent (  void   )  const [inline]
 

Definition at line 118 of file molecule.hpp.

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

unsigned int Molecule::NResidues (  void   )  const [inline]
 

Definition at line 121 of file molecule.hpp.

Referenced by Messenger::AddHighlights(), DrawAllWithTerminiLabels(), StyleManager::GetAtomStyle(), and ShowHideDomain::IsVisible().

int Molecule::ResidueDomainID (  int  residueID  )  const [inline]
 

Definition at line 148 of file molecule.hpp.

Member Data Documentation

DisplayListList Molecule::displayLists
 

Definition at line 112 of file molecule.hpp.

DisulfideMap Molecule::disulfideMap
 

Definition at line 95 of file molecule.hpp.

int Molecule::id
 

Definition at line 84 of file molecule.hpp.

Referenced by StructureSet::CenterViewOnAlignedResidues(), Residue::Draw(), StyleManager::GetAtomStyle(), GetMinimumLoopLengths(), GetVirtualPeptide(), GetVirtualResidue(), HighlightResidues(), StructureObject::RealignStructure(), and StructureSet::SelectedAtom().

const MoleculeIdentifier* Molecule::identifier
 

Definition at line 86 of file molecule.hpp.

Referenced by Threader::CreateFldMtf(), DrawAllWithTerminiLabels(), StyleManager::GetStyleForResidue(), HighlightResidues(), Messenger::IsHighlighted(), Messenger::IsHighlightedAnywhere(), StructureSet::SelectedAtom(), ShowHideDomain::ShowHideDomain(), ShowHideMolecule::ShowHideMolecule(), and Messenger::ToggleHighlight().

BondList Molecule::interResidueBonds
 

Definition at line 91 of file molecule.hpp.

std::string Molecule::name
 

Definition at line 85 of file molecule.hpp.

int Molecule::nDomains
 

Definition at line 106 of file molecule.hpp.

const int Molecule::NO_DOMAIN_SET = -1 [static]
 

Definition at line 98 of file molecule.hpp.

Referenced by AddDomain(), StyleManager::GetAtomStyle(), StyleManager::GetObjectStyle(), and ShowHideManager::ShowDomainsWithHighlights().

std::vector< int > Molecule::residueDomains
 

Definition at line 105 of file molecule.hpp.

Referenced by AddDomain(), StyleManager::GetAtomStyle(), StyleManager::GetObjectStyle(), and ShowHideDomain::IsVisible().

ResidueMap Molecule::residues
 

Definition at line 89 of file molecule.hpp.

Referenced by StructureSet::CenterViewOnAlignedResidues(), Threader::CreateFldMtf(), DrawAllWithTerminiLabels(), GetMinimumLoopLengths(), StyleManager::GetObjectStyle(), GetResidueColor(), GetVirtualCoordinates(), ShowHideDomain::IsVisible(), and SequenceDisplay::MouseOver().

std::vector< eSecStruc > Molecule::residueSecondaryStructures
 

Definition at line 104 of file molecule.hpp.

const Sequence* Molecule::sequence
 

Definition at line 109 of file molecule.hpp.

Referenced by StyleManager::GetAtomStyle().

eType Molecule::type
 

Definition at line 83 of file molecule.hpp.

The documentation for this class was generated from the following files:
Generated on Wed Dec 9 08:12:54 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Wed Dec 09 08:20:14 2009 by modify_doxy.py rev. 173732