NCBI C++ ToolKit
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StructureObject Class Reference

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

+ Inheritance diagram for StructureObject:
+ Collaboration diagram for StructureObject:

Public Types

typedef std::list< const CoordSet * > CoordSetList
 
typedef std::map< int, const Molecule * > DomainMap
 
typedef std::map< int, intDomainIDMap
 
typedef std::map< const Residue *, const Molecule * > ResidueMap
 

Public Member Functions

 StructureObject (StructureBase *parent, const ncbi::objects::CBiostruc &biostruc, bool isMaster)
 
 ~StructureObject (void)
 
std::string GetPDBID (char separator='_') const
 
void SelectByDistance (double cutoff, unsigned int options, ResidueMap *selectedResidues) const
 
bool SetTransformToMaster (const ncbi::objects::CBiostruc_annot_set &annot, int masterMMDBID)
 
void RealignStructure (int nCoords, const Vector *const *masterCoords, const Vector *const *dependentCoords, const double *weights, int dependentRow)
 
bool IsMaster (void) const
 
bool IsDependent (void) const
 
int NDomains (void) 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

int id
 
int mmdbID
 
std::vector< std::stringpdbIDs
 
MatrixtransformToMaster
 
const ChemicalGraphgraph
 
CoordSetList coordSets
 
double minTemperature
 
double maxTemperature
 
DomainMap domainMap
 
DomainIDMap domainID2MMDB
 
- Public Attributes inherited from StructureBase
StructureSetparentSet
 

Static Public Attributes

static const int NO_MMDB_ID = -1
 
static const double NO_TEMPERATURE = kMin_Double
 

Private Attributes

const bool isMaster
 

Detailed Description

Definition at line 249 of file structure_set.hpp.

Member Typedef Documentation

◆ CoordSetList

Definition at line 269 of file structure_set.hpp.

◆ DomainIDMap

typedef std::map< int, int > StructureObject::DomainIDMap

Definition at line 279 of file structure_set.hpp.

◆ DomainMap

typedef std::map< int, const Molecule * > StructureObject::DomainMap

Definition at line 277 of file structure_set.hpp.

◆ ResidueMap

Definition at line 286 of file structure_set.hpp.

Constructor & Destructor Documentation

◆ StructureObject()

StructureObject::StructureObject ( StructureBase parent,
const ncbi::objects::CBiostruc &  biostruc,
bool  isMaster 
)

◆ ~StructureObject()

StructureObject::~StructureObject ( void  )
inline

Definition at line 257 of file structure_set.hpp.

References transformToMaster.

Member Function Documentation

◆ GetPDBID()

std::string StructureObject::GetPDBID ( char  separator = '_') const

◆ IsDependent()

bool StructureObject::IsDependent ( void  ) const
inline

Definition at line 298 of file structure_set.hpp.

References isMaster.

Referenced by StructureSet::SelectedAtom().

◆ IsMaster()

bool StructureObject::IsMaster ( void  ) const
inline

Definition at line 297 of file structure_set.hpp.

References isMaster.

◆ NDomains()

int StructureObject::NDomains ( void  ) const
inline

Definition at line 299 of file structure_set.hpp.

References domainMap.

◆ RealignStructure()

void StructureObject::RealignStructure ( int  nCoords,
const Vector *const masterCoords,
const Vector *const dependentCoords,
const double *  weights,
int  dependentRow 
)

Definition at line 1309 of file structure_set.cpp.

References AddDomain(), StructureSet::AddStructureAlignment(), StructureSet::alignmentManager, b, blocks, ComposeInto(), ComputeRMSD(), CBiostruc_feature_Base::eType_alignment, AlignmentManager::GetCurrentMultipleAlignment(), StructureBase::GetParentOfType(), GetPDBID(), BlockMultipleAlignment::GetSequenceOfRow(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), i, Molecule::id, Molecule::identifier, Sequence::identifier, INFOMSG, location, mmdbID, Sequence::molecule, NO_DOMAIN, StructureSet::objects, StructureBase::parentSet, MoleculeIdentifier::pdbChain, MoleculeIdentifier::pdbID, compile_time_bits::range(), RigidBodyFit(), CChem_graph_alignment_Base::SetAlignment(), CChem_graph_alignment_Base::SetBiostruc_ids(), CChem_graph_alignment_Base::SetDimension(), CResidue_interval_pntr_Base::SetFrom(), CTransform_Base::SetId(), CResidue_pntrs_Base::SetInterval(), CBiostruc_feature_Base::SetLocation(), CBiostruc_id_Base::SetMmdb_id(), CResidue_interval_pntr_Base::SetMolecule_id(), CTransform_Base::SetMoves(), CBiostruc_feature_Base::SetName(), CChem_graph_pntrs_Base::SetResidues(), CRot_matrix_Base::SetRot_11(), CRot_matrix_Base::SetRot_12(), CRot_matrix_Base::SetRot_13(), CRot_matrix_Base::SetRot_21(), CRot_matrix_Base::SetRot_22(), CRot_matrix_Base::SetRot_23(), CRot_matrix_Base::SetRot_31(), CRot_matrix_Base::SetRot_32(), CRot_matrix_Base::SetRot_33(), CMove_Base::SetRotate(), CRot_matrix_Base::SetScale_factor(), CTrans_matrix_Base::SetScale_factor(), CResidue_interval_pntr_Base::SetTo(), CTrans_matrix_Base::SetTran_1(), CTrans_matrix_Base::SetTran_2(), CTrans_matrix_Base::SetTran_3(), CChem_graph_alignment_Base::SetTransform(), CMove_Base::SetTranslate(), SetTranslationMatrix(), CBiostruc_feature_Base::SetType(), si, MoleculeIdentifier::ToString(), transformToMaster, Vector< T >::x, Vector< T >::y, and Vector< T >::z.

◆ SelectByDistance()

void StructureObject::SelectByDistance ( double  cutoff,
unsigned int  options,
ResidueMap selectedResidues 
) const

◆ SetTransformToMaster()

bool StructureObject::SetTransformToMaster ( const ncbi::objects::CBiostruc_annot_set &  annot,
int  masterMMDBID 
)

Member Data Documentation

◆ coordSets

CoordSetList StructureObject::coordSets

◆ domainID2MMDB

DomainIDMap StructureObject::domainID2MMDB

Definition at line 280 of file structure_set.hpp.

Referenced by AddDomain().

◆ domainMap

DomainMap StructureObject::domainMap

Definition at line 278 of file structure_set.hpp.

Referenced by NDomains(), and ChemicalGraph::UnpackDomainFeatures().

◆ graph

const ChemicalGraph* StructureObject::graph

◆ id

int StructureObject::id

◆ isMaster

const bool StructureObject::isMaster
private

Definition at line 252 of file structure_set.hpp.

Referenced by IsDependent(), and IsMaster().

◆ maxTemperature

double StructureObject::maxTemperature

Definition at line 274 of file structure_set.hpp.

Referenced by AtomSet::AtomSet(), and StructureObject().

◆ minTemperature

double StructureObject::minTemperature

◆ mmdbID

int StructureObject::mmdbID

◆ NO_MMDB_ID

const int StructureObject::NO_MMDB_ID = -1
static

Definition at line 261 of file structure_set.hpp.

Referenced by MoleculeIdentifier::GetIdentifier().

◆ NO_TEMPERATURE

const double StructureObject::NO_TEMPERATURE = kMin_Double
static

Definition at line 273 of file structure_set.hpp.

Referenced by AtomSet::AtomSet().

◆ pdbIDs

std::vector< std::string > StructureObject::pdbIDs

Definition at line 263 of file structure_set.hpp.

Referenced by GetPDBID(), and StructureObject().

◆ transformToMaster

Matrix* StructureObject::transformToMaster

The documentation for this class was generated from the following files:
Modified on Tue Jun 18 13:38:08 2024 by modify_doxy.py rev. 669887