NCBI C++ ToolKit
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ChemicalGraph Class Reference

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

+ Inheritance diagram for ChemicalGraph:
+ Collaboration diagram for ChemicalGraph:

Public Types

typedef std::map< int, const Molecule * > MoleculeMap
 
typedef std::list< const Bond * > BondList
 

Public Member Functions

 ChemicalGraph (StructureBase *parent, const ncbi::objects::CBiostruc_graph &graph, const FeatureList &features)
 
void RedrawMolecule (int moleculeID) const
 
bool DrawAll (const AtomSet *atomSet=NULL) const
 
const Residue::AtomInfo * GetAtomInfo (const AtomPntr &atom) const
 
bool CheckForDisulfide (const Molecule *molecule, const ncbi::objects::CAtom_pntr &atomPtr1, const ncbi::objects::CAtom_pntr &atomPtr2, std::list< const Bond * > *bondList, Bond *bond, StructureBase *parent)
 
- Public Member Functions inherited from StructureBase
 StructureBase (StructureBase *parent)
 
virtual ~StructureBase (void)
 
virtual bool Draw (const AtomSet *atomSet=NULL) const
 
template<class T >
bool GetParentOfType (const T **ptr, bool warnIfNotFound=true) const
 

Public Attributes

std::string name
 
MoleculeMap molecules
 
BondList interMoleculeBonds
 
- Public Attributes inherited from StructureBase
StructureSet * parentSet
 

Private Types

typedef std::list< std::pair< AtomSet *, const std::string * > > AtomSetList
 

Private Member Functions

void UnpackDomainFeatures (const ncbi::objects::CBiostruc_feature_set &featureSet)
 
void UnpackSecondaryStructureFeatures (const ncbi::objects::CBiostruc_feature_set &featureSet)
 

Private Attributes

AtomSetList atomSetList
 
unsigned int displayListOtherStart
 

Detailed Description

Definition at line 69 of file chemical_graph.hpp.

Member Typedef Documentation

◆ AtomSetList

typedef std::list< std::pair < AtomSet *, const std::string * > > ChemicalGraph::AtomSetList
private

Definition at line 104 of file chemical_graph.hpp.

◆ BondList

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

Definition at line 79 of file chemical_graph.hpp.

◆ MoleculeMap

typedef std::map< int, const Molecule * > ChemicalGraph::MoleculeMap

Definition at line 77 of file chemical_graph.hpp.

Constructor & Destructor Documentation

◆ ChemicalGraph()

ChemicalGraph::ChemicalGraph ( StructureBase *  parent,
const ncbi::objects::CBiostruc_graph &  graph,
const FeatureList &  features 
)

Definition at line 101 of file chemical_graph.cpp.

References atomSetList, CheckForDisulfide(), StructureObject::coordSets, displayListOtherStart, Molecule::displayLists, AtomSet::ensembles, Bond::eRealDisulfide, ERRORMSG, Bond::eUnknown, FATALMSG, StructureSet::frameMap, CBiostruc_graph_Base::GetDescr(), CBiostruc_graph_Base::GetInter_molecule_bonds(), CBiostruc_graph_Base::GetMolecule_graphs(), StructureBase::GetParentOfType(), CBiostruc_graph_Base::GetResidue_graphs(), CBiostruc_residue_graph_set_Base::GetResidue_graphs(), i, Molecule::id, interMoleculeBonds, StructureSet::IsMultiStructure(), Molecule::IsNucleotide(), Molecule::IsProtein(), CBiostruc_graph_Base::IsSetDescr(), CBiostruc_graph_Base::IsSetInter_molecule_bonds(), StructureSet::lastDisplayList, le(), MakeBond(), molecules, n, name, Molecule::nDomains, Molecule::NO_DOMAIN_SET, OpenGLRenderer::NO_LIST, NULL, Bond::order, StructureBase::parentSet, r(), Molecule::residueDomains, Molecule::residues, standardDictionary, TRACEMSG, StructureSet::transformMap, UnpackDomainFeatures(), UnpackSecondaryStructureFeatures(), and WARNINGMSG.

Member Function Documentation

◆ CheckForDisulfide()

bool ChemicalGraph::CheckForDisulfide ( const Molecule *  molecule,
const ncbi::objects::CAtom_pntr &  atomPtr1,
const ncbi::objects::CAtom_pntr &  atomPtr2,
std::list< const Bond * > *  bondList,
Bond *  bond,
StructureBase *  parent 
)

Definition at line 471 of file chemical_graph.cpp.

References Residue::AtomInfo::atomicNumber, Residue::eAminoAcid, Bond::eRealDisulfide, ERRORMSG, Bond::eVirtualDisulfide, CAliasBase< TPrim >::Get(), CAtom_pntr_Base::GetAtom_id(), CAtom_pntr_Base::GetMolecule_id(), CAtom_pntr_Base::GetResidue_id(), MakeBond(), molecules, Residue::NO_ALPHA_ID, Bond::order, Molecule::residues, and TRACEMSG.

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

◆ DrawAll()

bool ChemicalGraph::DrawAll ( const AtomSet *  atomSet = NULL) const
virtual

Reimplemented from StructureBase.

Definition at line 382 of file chemical_graph.cpp.

References a, atomSetList, b, displayListOtherStart, OpenGLRenderer::EndDisplayList(), StructureBase::GetParentOfType(), StructureObject::GetPDBID(), interMoleculeBonds, molecules, moleculeToRedraw, n, OpenGLRenderer::NO_LIST, CoordSet::objectMap, StructureBase::parentSet, StructureSet::renderer, OpenGLRenderer::StartDisplayList(), and TRACEMSG.

Referenced by RedrawMolecule().

◆ GetAtomInfo()

const Residue::AtomInfo* ChemicalGraph::GetAtomInfo ( const AtomPntr &  atom) const
inline

Definition at line 86 of file chemical_graph.hpp.

References AtomPntr::aID, ERR_POST, info, AtomPntr::mID, molecules, NULL, AtomPntr::rID, and Warning().

Referenced by StyleManager::GetBondStyle().

◆ RedrawMolecule()

void ChemicalGraph::RedrawMolecule ( int  moleculeID) const

Definition at line 374 of file chemical_graph.cpp.

References DrawAll(), moleculeToRedraw, and NULL.

Referenced by Messenger::ProcessRedraws().

◆ UnpackDomainFeatures()

void ChemicalGraph::UnpackDomainFeatures ( const ncbi::objects::CBiostruc_feature_set &  featureSet)
private

Definition at line 274 of file chemical_graph.cpp.

References StructureObject::domainMap, ERRORMSG, CBiostruc_feature_Base::eType_subgraph, f(), ctll::front(), CBiostruc_feature_set_Base::GetFeatures(), StructureBase::GetParentOfType(), i, Molecule::id, molecules, Molecule::nDomains, Molecule::NO_DOMAIN_SET, NULL, StructureBase::parentSet, r(), Molecule::residueDomains, Molecule::residues, TRACEMSG, and WARNINGMSG.

Referenced by ChemicalGraph().

◆ UnpackSecondaryStructureFeatures()

void ChemicalGraph::UnpackSecondaryStructureFeatures ( const ncbi::objects::CBiostruc_feature_set &  featureSet)
private

Definition at line 329 of file chemical_graph.cpp.

References Molecule::eCoil, Molecule::eHelix, ERRORMSG, Molecule::eStrand, CBiostruc_feature_Base::eType_helix, CBiostruc_feature_Base::eType_strand, f(), CAliasBase< TPrim >::Get(), CBiostruc_feature_set_Base::GetFeatures(), CResidue_interval_pntr_Base::GetFrom(), CResidue_interval_pntr_Base::GetMolecule_id(), CResidue_interval_pntr_Base::GetTo(), Molecule::id, molecules, r(), Molecule::residues, Molecule::residueSecondaryStructures, TRACEMSG, and WARNINGMSG.

Referenced by ChemicalGraph().

Member Data Documentation

◆ atomSetList

AtomSetList ChemicalGraph::atomSetList
private

Definition at line 105 of file chemical_graph.hpp.

Referenced by ChemicalGraph(), and DrawAll().

◆ displayListOtherStart

unsigned int ChemicalGraph::displayListOtherStart
private

Definition at line 106 of file chemical_graph.hpp.

Referenced by ChemicalGraph(), and DrawAll().

◆ interMoleculeBonds

BondList ChemicalGraph::interMoleculeBonds

Definition at line 80 of file chemical_graph.hpp.

Referenced by ChemicalGraph(), and DrawAll().

◆ molecules

MoleculeMap ChemicalGraph::molecules

Definition at line 78 of file chemical_graph.hpp.

Referenced by CheckForDisulfide(), ChemicalGraph(), DrawAll(), GetAtomInfo(), StructureSet::MatchSequenceToMoleculeInObject(), PostRedrawEntity(), StructureObject::SelectByDistance(), CDDAnnotateDialog::ShowEvidence(), UnpackDomainFeatures(), and UnpackSecondaryStructureFeatures().

◆ name

std::string ChemicalGraph::name

Definition at line 76 of file chemical_graph.hpp.

Referenced by ChemicalGraph(), and Sequence::GetDescription().

The documentation for this class was generated from the following files:
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Modified on Wed May 15 15:06:58 2024 by modify_doxy.py rev. 669887