NCBI C++ ToolKit
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Search Toolkit Book for CResidue_graph_Base
Residue graphs define atomic formulae, connectivity, chirality, and names. More...
#include <objects/mmdb1/Residue_graph_.hpp>
Public Member Functions | |
CResidue_graph_Base (void) | |
virtual | ~CResidue_graph_Base (void) |
DECLARE_INTERNAL_TYPE_INFO () | |
bool | IsSetId (void) const |
Check if a value has been assigned to Id data member. More... | |
bool | CanGetId (void) const |
Check if it is safe to call GetId method. More... | |
void | ResetId (void) |
Reset Id data member. More... | |
const TId & | GetId (void) const |
Get the Id member data. More... | |
void | SetId (const TId &value) |
Assign a value to Id data member. More... | |
TId & | SetId (void) |
Assign a value to Id data member. More... | |
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 | IsSetResidue_type (void) const |
Check if a value has been assigned to Residue_type data member. More... | |
bool | CanGetResidue_type (void) const |
Check if it is safe to call GetResidue_type method. More... | |
void | ResetResidue_type (void) |
Reset Residue_type data member. More... | |
TResidue_type | GetResidue_type (void) const |
Get the Residue_type member data. More... | |
void | SetResidue_type (TResidue_type value) |
Assign a value to Residue_type data member. More... | |
TResidue_type & | SetResidue_type (void) |
Assign a value to Residue_type data member. More... | |
bool | IsSetIupac_code (void) const |
Check if a value has been assigned to Iupac_code data member. More... | |
bool | CanGetIupac_code (void) const |
Check if it is safe to call GetIupac_code method. More... | |
void | ResetIupac_code (void) |
Reset Iupac_code data member. More... | |
const TIupac_code & | GetIupac_code (void) const |
Get the Iupac_code member data. More... | |
TIupac_code & | SetIupac_code (void) |
Assign a value to Iupac_code data member. More... | |
bool | IsSetAtoms (void) const |
Check if a value has been assigned to Atoms data member. More... | |
bool | CanGetAtoms (void) const |
Check if it is safe to call GetAtoms method. More... | |
void | ResetAtoms (void) |
Reset Atoms data member. More... | |
const TAtoms & | GetAtoms (void) const |
Get the Atoms member data. More... | |
TAtoms & | SetAtoms (void) |
Assign a value to Atoms data member. More... | |
bool | IsSetBonds (void) const |
Check if a value has been assigned to Bonds data member. More... | |
bool | CanGetBonds (void) const |
Check if it is safe to call GetBonds method. More... | |
void | ResetBonds (void) |
Reset Bonds data member. More... | |
const TBonds & | GetBonds (void) const |
Get the Bonds member data. More... | |
TBonds & | SetBonds (void) |
Assign a value to Bonds data member. More... | |
bool | IsSetChiral_centers (void) const |
Check if a value has been assigned to Chiral_centers data member. More... | |
bool | CanGetChiral_centers (void) const |
Check if it is safe to call GetChiral_centers method. More... | |
void | ResetChiral_centers (void) |
Reset Chiral_centers data member. More... | |
const TChiral_centers & | GetChiral_centers (void) const |
Get the Chiral_centers member data. More... | |
TChiral_centers & | SetChiral_centers (void) |
Assign a value to Chiral_centers data member. More... | |
virtual void | Reset (void) |
Reset the whole object. More... | |
Public Member Functions inherited from CSerialObject | |
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... | |
Public Member Functions inherited from CObject | |
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... | |
Public Member Functions inherited from CDebugDumpable | |
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 |
Static Public Member Functions | |
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EResidue_type (void) |
Access to EResidue_type's attributes (values, names) as defined in spec. More... | |
Static Public Member Functions inherited from CSerialObject | |
static void | SetVerifyDataThread (ESerialVerifyData verify) |
static void | SetVerifyDataGlobal (ESerialVerifyData verify) |
static string | UnassignedString (void) |
static CStringUTF8 | UnassignedStringUTF8 (void) |
static char | UnassignedByte (void) |
Static Public Member Functions inherited from CObject | |
static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
Define method to throw null pointer exception. More... | |
static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
static EAllocFillMode | GetAllocFillMode (void) |
static void | SetAllocFillMode (EAllocFillMode mode) |
static void | SetAllocFillMode (const string &value) |
Set mode from configuration parameter value. More... | |
Static Public Member Functions inherited from CDebugDumpable | |
static void | EnableDebugDump (bool on) |
Private Types | |
typedef CSerialObject | Tparent |
Private Member Functions | |
CResidue_graph_Base (const CResidue_graph_Base &) | |
CResidue_graph_Base & | operator= (const CResidue_graph_Base &) |
Private Attributes | |
Uint4 | m_set_State [1] |
CResidue_graph_id | m_Id |
list< CRef< CBiomol_descr > > | m_Descr |
int | m_Residue_type |
list< string > | m_Iupac_code |
list< CRef< CAtom > > | m_Atoms |
list< CRef< CIntra_residue_bond > > | m_Bonds |
list< CRef< CChiral_center > > | m_Chiral_centers |
Additional Inherited Members | |
Static Public Attributes inherited from CSerialObject | |
static const char * | ms_UnassignedStr = "<*unassigned*>" |
static const char | ms_UnassignedByte = char(0xcd) |
Static Public Attributes inherited from CObject | |
static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
Define possible object states. More... | |
static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
Heap signature was found. More... | |
static const TCount | eCounterBitsPlaceMask |
Mask for 'in heap' state flags. More... | |
static const int | eCounterStep = 1 << 2 |
Skip over the "in heap" bits. More... | |
static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
static const TCount | eCounterStateMask |
Valid object, and object in heap. More... | |
Protected Member Functions inherited from CObject | |
virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
Residue graphs define atomic formulae, connectivity, chirality, and names.
For standard residue graphs from the MMDB dictionary the PDB-assigned residue-type code appears as the name within the residue graph description, and the full trivial name of the residue as a comment within that description. For any nonstandard residue graphs provided with an MMDB biostruc the PDB-assigned residue-type code similarly appears as the name within the description, and any information provided on PDB HET records as a pdb-comment within that description. Note that nonstandard residue graphs for a PDB-derived biostruc may be incomplete. Current PDB format cannot represent connectivity for groups which are disordered, and for which no coordinates are given. In these cases the residue graph defined in MMDB represents only the subgraph that could be identified from available ATOM, HETATM and CONECT records.
Definition at line 94 of file Residue_graph_.hpp.