NCBI C++ ToolKit
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Search Toolkit Book for StructureObject
#include "structure_set.hpp"
(Private to src/app/cn3d
.)
Public Types | |
typedef std::list< const CoordSet * > | CoordSetList |
typedef std::map< int, const Molecule * > | DomainMap |
typedef std::map< int, int > | DomainIDMap |
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::string > | pdbIDs |
Matrix * | transformToMaster |
const ChemicalGraph * | graph |
CoordSetList | coordSets |
double | minTemperature |
double | maxTemperature |
DomainMap | domainMap |
DomainIDMap | domainID2MMDB |
Public Attributes inherited from StructureBase | |
StructureSet * | parentSet |
Static Public Attributes | |
static const int | NO_MMDB_ID = -1 |
static const double | NO_TEMPERATURE = kMin_Double |
Private Attributes | |
const bool | isMaster |
Definition at line 249 of file structure_set.hpp.
typedef std::list< const CoordSet * > StructureObject::CoordSetList |
Definition at line 269 of file structure_set.hpp.
typedef std::map< int, int > StructureObject::DomainIDMap |
Definition at line 279 of file structure_set.hpp.
typedef std::map< int, const Molecule * > StructureObject::DomainMap |
Definition at line 277 of file structure_set.hpp.
typedef std::map< const Residue *, const Molecule * > StructureObject::ResidueMap |
Definition at line 286 of file structure_set.hpp.
StructureObject::StructureObject | ( | StructureBase * | parent, |
const ncbi::objects::CBiostruc & | biostruc, | ||
bool | isMaster | ||
) |
Definition at line 1148 of file structure_set.cpp.
References coordSets, eModel_type_ncbi_backbone, eModel_type_ncbi_vector, eModel_type_other, CBiostruc_Base::GetChemical_graph(), CBiostruc_Base::GetDescr(), CBiostruc_Base::GetFeatures(), CBiostruc_Base::GetId(), CBiostruc_Base::GetModel(), graph, i, StructureSet::isAlphaOnly, CBiostruc_Base::IsSetDescr(), CBiostruc_Base::IsSetModel(), maxTemperature, minTemperature, mmdbID, StructureSet::objects, StructureBase::parentSet, pdbIDs, and TRACEMSG.
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Definition at line 257 of file structure_set.hpp.
References transformToMaster.
std::string StructureObject::GetPDBID | ( | char | separator = '_' | ) | const |
Definition at line 1208 of file structure_set.cpp.
Referenced by ChemicalGraph::DrawAll(), MoleculeIdentifier::GetIdentifier(), StructureSet::LoadAlignmentsAndStructures(), StructureSet::MatchSequenceToMoleculeInObject(), RealignStructure(), StructureSet::SelectedAtom(), SetTransformToMaster(), and ShowHideObject::ShowHideObject().
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Definition at line 298 of file structure_set.hpp.
References isMaster.
Referenced by StructureSet::SelectedAtom().
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Definition at line 297 of file structure_set.hpp.
References isMaster.
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Definition at line 299 of file structure_set.hpp.
References domainMap.
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.
void StructureObject::SelectByDistance | ( | double | cutoff, |
unsigned int | options, | ||
ResidueMap * | selectedResidues | ||
) | const |
Definition at line 1466 of file structure_set.cpp.
References a, coordSets, StructureSet::eSelectHeterogen, StructureSet::eSelectNucleotide, StructureSet::eSelectOtherMoleculesOnly, StructureSet::eSelectProtein, StructureSet::eSelectSolvent, GlobalMessenger(), graph, Molecule::id, ChemicalGraph::molecules, r(), and AtomCoord::site.
bool StructureObject::SetTransformToMaster | ( | const ncbi::objects::CBiostruc_annot_set & | annot, |
int | masterMMDBID | ||
) |
Definition at line 1221 of file structure_set.cpp.
References ComposeInto(), CBiostruc_feature_Base::eType_alignment, CChem_graph_alignment_Base::GetAlignment(), CChem_graph_alignment_Base::GetBiostruc_ids(), CChem_graph_alignment_Base::GetDimension(), CBiostruc_annot_set_Base::GetFeatures(), GetPDBID(), CRot_matrix_Base::GetRot_11(), CRot_matrix_Base::GetRot_12(), CRot_matrix_Base::GetRot_13(), CRot_matrix_Base::GetRot_21(), CRot_matrix_Base::GetRot_22(), CRot_matrix_Base::GetRot_23(), CRot_matrix_Base::GetRot_31(), CRot_matrix_Base::GetRot_32(), CRot_matrix_Base::GetRot_33(), CRot_matrix_Base::GetScale_factor(), CTrans_matrix_Base::GetScale_factor(), CTrans_matrix_Base::GetTran_1(), CTrans_matrix_Base::GetTran_2(), CTrans_matrix_Base::GetTran_3(), CChem_graph_alignment_Base::GetTransform(), CChem_graph_alignment_Base::IsSetTransform(), Matrix< T >::m, mmdbID, StructureBase::parentSet, SetTranslationMatrix(), TRACEMSG, transformToMaster, StructureSet::usedFeatures, and WARNINGMSG.
CoordSetList StructureObject::coordSets |
Definition at line 270 of file structure_set.hpp.
Referenced by StructureSet::CenterViewOnAlignedResidues(), ChemicalGraph::ChemicalGraph(), Molecule::GetAlphaCoords(), MakeBond(), Residue::Residue(), SelectByDistance(), StructureSet::SelectedAtom(), and StructureObject().
DomainIDMap StructureObject::domainID2MMDB |
Definition at line 280 of file structure_set.hpp.
Referenced by AddDomain().
DomainMap StructureObject::domainMap |
Definition at line 278 of file structure_set.hpp.
Referenced by NDomains(), and ChemicalGraph::UnpackDomainFeatures().
const ChemicalGraph* StructureObject::graph |
Definition at line 268 of file structure_set.hpp.
Referenced by StyleManager::GetBondStyle(), Sequence::GetDescription(), StructureSet::MatchSequenceToMoleculeInObject(), PostRedrawEntity(), Messenger::ProcessRedraws(), SelectByDistance(), CDDAnnotateDialog::ShowEvidence(), and StructureObject().
int StructureObject::id |
Definition at line 262 of file structure_set.hpp.
Referenced by StyleManager::GetAtomStyle(), StyleManager::GetObjectColor(), and StyleManager::GetObjectStyle().
Definition at line 252 of file structure_set.hpp.
Referenced by IsDependent(), and IsMaster().
double StructureObject::maxTemperature |
Definition at line 274 of file structure_set.hpp.
Referenced by AtomSet::AtomSet(), and StructureObject().
double StructureObject::minTemperature |
Definition at line 274 of file structure_set.hpp.
Referenced by AtomSet::AtomSet(), StyleManager::GetAtomStyle(), and StructureObject().
int StructureObject::mmdbID |
Definition at line 262 of file structure_set.hpp.
Referenced by MoleculeIdentifier::GetIdentifier(), Sequence::GetOrSetMMDBLink(), RealignStructure(), SetTransformToMaster(), CDDAnnotateDialog::ShowEvidence(), and StructureObject().
Definition at line 261 of file structure_set.hpp.
Referenced by MoleculeIdentifier::GetIdentifier().
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Definition at line 273 of file structure_set.hpp.
Referenced by AtomSet::AtomSet().
std::vector< std::string > StructureObject::pdbIDs |
Definition at line 263 of file structure_set.hpp.
Referenced by GetPDBID(), and StructureObject().
Matrix* StructureObject::transformToMaster |
Definition at line 264 of file structure_set.hpp.
Referenced by RealignStructure(), StructureSet::SelectedAtom(), SetTransformToMaster(), and ~StructureObject().