Search Toolkit Book for CIntra_residue_bond_Base
Intra-residue-bond specifies connectivity between atoms in Residue-graph. More...
#include <objects/mmdb1/Intra_residue_bond_.hpp>
Inheritance diagram for CIntra_residue_bond_Base:
Collaboration diagram for CIntra_residue_bond_Base:
Public Types | |
| enum | EBond_order { eBond_order_single = 1 , eBond_order_partial_double = 2 , eBond_order_aromatic = 3 , eBond_order_double = 4 , eBond_order_triple = 5 , eBond_order_other = 6 , eBond_order_unknown = 255 } |
| enum class | E_memberIndex { e__allMandatory = 0 , e_atom_id_1 , e_atom_id_2 , e_bond_order } |
| typedef CAtom_id | TAtom_id_1 |
| typedef CAtom_id | TAtom_id_2 |
| typedef int | TBond_order |
| typedef Tparent::CMemberIndex< E_memberIndex, 4 > | TmemberIndex |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
Public Member Functions | |
| CIntra_residue_bond_Base (void) | |
| virtual | ~CIntra_residue_bond_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetAtom_id_1 (void) const |
| Check if a value has been assigned to Atom_id_1 data member. More... | |
| bool | CanGetAtom_id_1 (void) const |
| Check if it is safe to call GetAtom_id_1 method. More... | |
| void | ResetAtom_id_1 (void) |
| Reset Atom_id_1 data member. More... | |
| const TAtom_id_1 & | GetAtom_id_1 (void) const |
| Get the Atom_id_1 member data. More... | |
| void | SetAtom_id_1 (const TAtom_id_1 &value) |
| Assign a value to Atom_id_1 data member. More... | |
| TAtom_id_1 & | SetAtom_id_1 (void) |
| Assign a value to Atom_id_1 data member. More... | |
| bool | IsSetAtom_id_2 (void) const |
| Check if a value has been assigned to Atom_id_2 data member. More... | |
| bool | CanGetAtom_id_2 (void) const |
| Check if it is safe to call GetAtom_id_2 method. More... | |
| void | ResetAtom_id_2 (void) |
| Reset Atom_id_2 data member. More... | |
| const TAtom_id_2 & | GetAtom_id_2 (void) const |
| Get the Atom_id_2 member data. More... | |
| void | SetAtom_id_2 (const TAtom_id_2 &value) |
| Assign a value to Atom_id_2 data member. More... | |
| TAtom_id_2 & | SetAtom_id_2 (void) |
| Assign a value to Atom_id_2 data member. More... | |
| bool | IsSetBond_order (void) const |
| Check if a value has been assigned to Bond_order data member. More... | |
| bool | CanGetBond_order (void) const |
| Check if it is safe to call GetBond_order method. More... | |
| void | ResetBond_order (void) |
| Reset Bond_order data member. More... | |
| TBond_order | GetBond_order (void) const |
| Get the Bond_order member data. More... | |
| void | SetBond_order (TBond_order value) |
| Assign a value to Bond_order data member. More... | |
| TBond_order & | SetBond_order (void) |
| Assign a value to Bond_order 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() | EBond_order (void) |
| Access to EBond_order'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 | |
| CIntra_residue_bond_Base (const CIntra_residue_bond_Base &) | |
| CIntra_residue_bond_Base & | operator= (const CIntra_residue_bond_Base &) |
Private Attributes | |
| Uint4 | m_set_State [1] |
| CAtom_id | m_Atom_id_1 |
| CAtom_id | m_Atom_id_2 |
| int | m_Bond_order |
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... | |
Detailed Description
Intra-residue-bond specifies connectivity between atoms in Residue-graph.
Unlike Inter-residue-bond defined later, its participating atoms are part of a residue subgraph dictionary, not part of a specific biostruc-graph. For residue graphs in the standard MMDB dictionary bonds are defined from the known chemical structures of amino acids and nucleotides. For nonstandard residue graphs bonds are defined from PDB CONECT records, with validation for consistency with coordinate data, and from stereochemical calculation to identify unreported bonds. Validation and bond identification are based on comparison of inter-atomic distances to the sum of covalent radii for the corresponding elements.
Definition at line 82 of file Intra_residue_bond_.hpp.
The documentation for this class was generated from the following files:
- include/objects/mmdb1/Intra_residue_bond_.hpp
- src/objects/mmdb1/Intra_residue_bond_.cpp
