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NCBI C++ ToolKit: CBiostruc_graph_Base Class Reference
A biostruc graph contains the complete chemical graph of the biomolecular assembly. More...
CBiostruc_graph_Base (void) virtual ~CBiostruc_graph_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetDescr (void) const Check if a value has been assigned to Descr data member. More...
bool CanGetDescr (void) const Check if it is safe to call GetDescr method. More...
void ResetDescr (void) Reset Descr data member. More...
const TDescr & GetDescr (void) const Get the Descr member data. More...
TDescr & SetDescr (void) Assign a value to Descr data member. More...
bool IsSetMolecule_graphs (void) const Check if a value has been assigned to Molecule_graphs data member. More...
bool CanGetMolecule_graphs (void) const Check if it is safe to call GetMolecule_graphs method. More...
void ResetMolecule_graphs (void) Reset Molecule_graphs data member. More...
const TMolecule_graphs & GetMolecule_graphs (void) const Get the Molecule_graphs member data. More...
TMolecule_graphs & SetMolecule_graphs (void) Assign a value to Molecule_graphs data member. More...
bool IsSetInter_molecule_bonds (void) const Check if a value has been assigned to Inter_molecule_bonds data member. More...
bool CanGetInter_molecule_bonds (void) const Check if it is safe to call GetInter_molecule_bonds method. More...
void ResetInter_molecule_bonds (void) Reset Inter_molecule_bonds data member. More...
const TInter_molecule_bonds & GetInter_molecule_bonds (void) const Get the Inter_molecule_bonds member data. More...
TInter_molecule_bonds & SetInter_molecule_bonds (void) Assign a value to Inter_molecule_bonds data member. More...
bool IsSetResidue_graphs (void) const Check if a value has been assigned to Residue_graphs data member. More...
bool CanGetResidue_graphs (void) const Check if it is safe to call GetResidue_graphs method. More...
void ResetResidue_graphs (void) Reset Residue_graphs data member. More...
const TResidue_graphs & GetResidue_graphs (void) const Get the Residue_graphs member data. More...
TResidue_graphs & SetResidue_graphs (void) Assign a value to Residue_graphs data member. More...
virtual void Reset (void) Reset the whole object. More...
CSerialObject (void) virtual ~CSerialObject (void) virtual const CTypeInfo * GetThisTypeInfo (void) const =0 virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) Set object to copy of another one. More...
virtual bool Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const Check if both objects contain the same values. More...
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Define method for dumping debug information. More...
void ThrowUnassigned (TMemberIndex index) const void ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const bool HasNamespaceName (void) const Check if object data type has namespace name. More...
const string & GetNamespaceName (void) const Get namespace name. More...
bool HasNamespacePrefix (void) const Check if data type has namespace prefix. More...
const string & GetNamespacePrefix (void) const Get namespace prefix. More...
CObject (void) Constructor. More...
CObject (const CObject &src) Copy constructor. More...
virtual ~CObject (void) Destructor. More...
CObject & operator= (const CObject &src) THROWS_NONE Assignment operator. More...
bool CanBeDeleted (void) const THROWS_NONE Check if object can be deleted. More...
bool IsAllocatedInPool (void) const THROWS_NONE Check if object is allocated in memory pool (not system heap) More...
bool Referenced (void) const THROWS_NONE Check if object is referenced. More...
bool ReferencedOnlyOnce (void) const THROWS_NONE Check if object is referenced only once. More...
void AddReference (void) const Add reference to object. More...
void RemoveReference (void) const Remove reference to object. More...
void ReleaseReference (void) const Remove reference without deleting object. More...
virtual void DoNotDeleteThisObject (void) Mark this object as not allocated in heap – do not delete this object. More...
virtual void DoDeleteThisObject (void) Mark this object as allocated in heap – object can be deleted. More...
void * operator new (size_t size) Define new operator for memory allocation. More...
void * operator new[] (size_t size) Define new[] operator for 'array' memory allocation. More...
void operator delete (void *ptr) Define delete operator for memory deallocation. More...
void operator delete[] (void *ptr) Define delete[] operator for memory deallocation. More...
void * operator new (size_t size, void *place) Define new operator. More...
void operator delete (void *ptr, void *place) Define delete operator. More...
void * operator new (size_t size, CObjectMemoryPool *place) Define new operator using memory pool. More...
void operator delete (void *ptr, CObjectMemoryPool *place) Define delete operator. More...
CDebugDumpable (void) virtual ~CDebugDumpable (void) void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const void DumpToConsole (void) const
A biostruc graph contains the complete chemical graph of the biomolecular assembly.
The assembly graph is defined hierarchically, in terms of subgraphs graphs of component molecules. For PDB-derived biostrucs, the molecules forming the assembly are the individual biopolymer chains and any non-polymer or "heterogen" groups which are present. The PDB-derived "compound name" field appears as the name within the biostruc-graph description. PDB "class" and "source" fields appear as explicit attributes. PDB-derived structures are assigned an assembly type of "other" unless they have been further classified as the "physiological form" or "crystallographic cell" contents. If they have, the source of the type classification appears as a citation within the assembly description. Note that the biostruc-graph also includes as literals the subgraphs of any nonstandard residues present within it. For PDB-derived biostrucs these subgraphs are constructed automatically, with validation as described below.
CBiostruc_graph_Base –
Definition at line 93 of file Biostruc_graph_.hpp.
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