NCBI C++ ToolKit
Public Types | Public Member Functions | Public Attributes | Static Public Attributes | List of all members
Molecule Class Reference

Search Toolkit Book for Molecule

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

+ Inheritance diagram for Molecule:
+ Collaboration diagram for Molecule:

Public Types

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 }
 
typedef std::map< int, const Residue * > ResidueMap
 
typedef std::list< const Bond * > BondList
 
typedef std::map< int, intDisulfideMap
 
typedef std::list< unsigned intDisplayListList
 

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::AtomInfoGetAtomInfo (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 Member Functions inherited from StructureBase
 StructureBase (StructureBase *parent)
 
virtual ~StructureBase (void)
 
virtual bool DrawAll (const AtomSet *atomSet=NULL) const
 
virtual bool Draw (const AtomSet *atomSet=NULL) const
 
template<class T >
bool GetParentOfType (const T **ptr, bool warnIfNotFound=true) const
 

Public Attributes

eType type
 
int id
 
std::string name
 
const MoleculeIdentifieridentifier
 
ResidueMap residues
 
BondList interResidueBonds
 
DisulfideMap disulfideMap
 
std::vector< eSecStrucresidueSecondaryStructures
 
std::vector< intresidueDomains
 
int nDomains
 
const Sequencesequence
 
DisplayListList displayLists
 
- Public Attributes inherited from StructureBase
StructureSetparentSet
 

Static Public Attributes

static const int NO_DOMAIN_SET = -1
 

Detailed Description

Definition at line 65 of file molecule.hpp.

Member Typedef Documentation

◆ BondList

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

Definition at line 90 of file molecule.hpp.

◆ DisplayListList

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

Definition at line 111 of file molecule.hpp.

◆ DisulfideMap

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

Definition at line 94 of file molecule.hpp.

◆ ResidueMap

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

Definition at line 88 of file molecule.hpp.

Member Enumeration Documentation

◆ eSecStruc

Enumerator
eHelix 
eStrand 
eCoil 

Definition at line 99 of file molecule.hpp.

◆ eType

Enumerator
eDNA 
eRNA 
eProtein 
eBiopolymer 
eSolvent 
eNonpolymer 
eOther 

Definition at line 74 of file molecule.hpp.

Constructor & Destructor Documentation

◆ Molecule()

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

Member Function Documentation

◆ DrawAllWithTerminiLabels()

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

◆ GetAlphaCoords()

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

◆ GetAtomInfo()

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

Definition at line 122 of file molecule.hpp.

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

◆ GetResidueColor()

Vector Molecule::GetResidueColor ( int  sequenceIndex) const

◆ IsBiopolymer()

bool Molecule::IsBiopolymer ( void  ) const
inline

Definition at line 117 of file molecule.hpp.

References eProtein, and eRNA.

◆ IsHeterogen()

bool Molecule::IsHeterogen ( void  ) const
inline

Definition at line 119 of file molecule.hpp.

Referenced by StructureSet::SelectedAtom().

◆ IsNucleotide()

bool Molecule::IsNucleotide ( void  ) const
inline

Definition at line 116 of file molecule.hpp.

References eRNA.

Referenced by ChemicalGraph::ChemicalGraph(), DrawAllWithTerminiLabels(), and Molecule().

◆ IsProtein()

bool Molecule::IsProtein ( void  ) const
inline

Definition at line 115 of file molecule.hpp.

References eProtein.

Referenced by ChemicalGraph::ChemicalGraph(), DrawAllWithTerminiLabels(), and Molecule().

◆ IsResidueInCoil()

bool Molecule::IsResidueInCoil ( int  residueID) const
inline

Definition at line 144 of file molecule.hpp.

◆ IsResidueInHelix()

bool Molecule::IsResidueInHelix ( int  residueID) const
inline

Definition at line 140 of file molecule.hpp.

Referenced by StyleManager::GetAtomStyle().

◆ IsResidueInStrand()

bool Molecule::IsResidueInStrand ( int  residueID) const
inline

Definition at line 142 of file molecule.hpp.

Referenced by StyleManager::GetAtomStyle().

◆ IsSolvent()

bool Molecule::IsSolvent ( void  ) const
inline

Definition at line 118 of file molecule.hpp.

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

◆ NResidues()

unsigned int Molecule::NResidues ( void  ) const
inline

◆ ResidueDomainID()

int Molecule::ResidueDomainID ( int  residueID) const
inline

Definition at line 148 of file molecule.hpp.

Member Data Documentation

◆ displayLists

DisplayListList Molecule::displayLists

Definition at line 112 of file molecule.hpp.

Referenced by ChemicalGraph::ChemicalGraph().

◆ disulfideMap

DisulfideMap Molecule::disulfideMap

Definition at line 95 of file molecule.hpp.

Referenced by GetVirtualResidue(), and Molecule().

◆ id

int Molecule::id

◆ identifier

const MoleculeIdentifier* Molecule::identifier

◆ interResidueBonds

BondList Molecule::interResidueBonds

Definition at line 91 of file molecule.hpp.

Referenced by Molecule().

◆ name

std::string Molecule::name

Definition at line 85 of file molecule.hpp.

Referenced by Molecule().

◆ nDomains

int Molecule::nDomains

◆ NO_DOMAIN_SET

const int Molecule::NO_DOMAIN_SET = -1
static

◆ residueDomains

std::vector< int > Molecule::residueDomains

◆ residues

ResidueMap Molecule::residues

◆ residueSecondaryStructures

std::vector< eSecStruc > Molecule::residueSecondaryStructures

Definition at line 104 of file molecule.hpp.

Referenced by Molecule(), and ChemicalGraph::UnpackSecondaryStructureFeatures().

◆ sequence

const Sequence* Molecule::sequence

Definition at line 109 of file molecule.hpp.

Referenced by StyleManager::GetAtomStyle().

◆ type

eType Molecule::type

Definition at line 83 of file molecule.hpp.


The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:29:07 2024 by modify_doxy.py rev. 669887