Search Toolkit Book for StructureObject
#include "structure_set.hpp"
(Private to src/app/cn3d.)
Definition at line 249 of file structure_set.hpp.
◆ CoordSetList ◆ DomainIDMap ◆ DomainMap ◆ ResidueMap ◆ StructureObject() 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.
◆ ~StructureObject() StructureObject::~StructureObject ( void ) inline ◆ GetPDBID() std::string StructureObject::GetPDBID ( char separator ='_' ) const ◆ IsDependent() bool StructureObject::IsDependent ( void ) const inline ◆ IsMaster() bool StructureObject::IsMaster ( void ) const inline ◆ NDomains() int StructureObject::NDomains ( void ) const inline ◆ RealignStructure()
Definition at line 1309 of file structure_set.cpp.
References AddDomain(), StructureSet::AddStructureAlignment(), StructureSet::alignmentManager, b, blocks, ComposeInto(), ComputeRMSD(), CBiostruc_feature_Base::eType_alignment, Block::Range::from, 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, 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, Block::Range::to, MoleculeIdentifier::ToString(), transformToMaster, Vector< T >::x, Vector< T >::y, and Vector< T >::z.
◆ SelectByDistance() void StructureObject::SelectByDistance ( double cutoff, unsigned int options, ResidueMap * selectedResidues ) constDefinition 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.
◆ SetTransformToMaster() 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.
◆ coordSets ◆ domainID2MMDB ◆ domainMap ◆ graph ◆ id ◆ isMaster ◆ maxTemperature double StructureObject::maxTemperature ◆ minTemperature double StructureObject::minTemperature ◆ mmdbID int StructureObject::mmdbID ◆ NO_MMDB_ID const int StructureObject::NO_MMDB_ID = -1 static ◆ NO_TEMPERATURE ◆ pdbIDs ◆ transformToMaster Matrix* StructureObject::transformToMasterThe documentation for this class was generated from the following files:
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