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NCBI C++ ToolKit: CAtomic_coordinates_Base Class Reference
Represents ASN.1 type Atomic-coordinates defined in file mmdb2.asn
Search Toolkit Book for CAtomic_coordinates_Base
Literal atomic coordinate values give location, occupancy and order parameters, and a pointer to a specific atom defined in the biostruc graph. More...
#include <objects/mmdb2/Atomic_coordinates_.hpp>
enum class E_memberIndex {
e__allMandatory = 0 , e_number_of_points , e_atoms , e_sites ,
e_temperature_factors , e_occupancies , e_alternate_conf_ids , e_conf_ensembles
} typedef int TNumber_of_points typedef CAtom_pntrs TAtoms typedef CModel_space_points TSites typedef CAtomic_temperature_factors TTemperature_factors typedef CAtomic_occupancies TOccupancies typedef CAlternate_conformation_ids TAlternate_conf_ids typedef list< CRef< CConformation_ensemble > > TConf_ensembles typedef Tparent::CMemberIndex< E_memberIndex, 8 > TmemberIndex 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...
CAtomic_coordinates_Base (void) virtual ~CAtomic_coordinates_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetNumber_of_points (void) const Check if a value has been assigned to Number_of_points data member. More...
bool CanGetNumber_of_points (void) const Check if it is safe to call GetNumber_of_points method. More...
void ResetNumber_of_points (void) Reset Number_of_points data member. More...
TNumber_of_points GetNumber_of_points (void) const Get the Number_of_points member data. More...
void SetNumber_of_points (TNumber_of_points value) Assign a value to Number_of_points data member. More...
TNumber_of_points & SetNumber_of_points (void) Assign a value to Number_of_points 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...
void SetAtoms (TAtoms &value) Assign a value to Atoms data member. More...
TAtoms & SetAtoms (void) Assign a value to Atoms data member. More...
bool IsSetSites (void) const Check if a value has been assigned to Sites data member. More...
bool CanGetSites (void) const Check if it is safe to call GetSites method. More...
void ResetSites (void) Reset Sites data member. More...
const TSites & GetSites (void) const Get the Sites member data. More...
void SetSites (TSites &value) Assign a value to Sites data member. More...
TSites & SetSites (void) Assign a value to Sites data member. More...
bool IsSetTemperature_factors (void) const Check if a value has been assigned to Temperature_factors data member. More...
bool CanGetTemperature_factors (void) const Check if it is safe to call GetTemperature_factors method. More...
void ResetTemperature_factors (void) Reset Temperature_factors data member. More...
const TTemperature_factors & GetTemperature_factors (void) const Get the Temperature_factors member data. More...
void SetTemperature_factors (TTemperature_factors &value) Assign a value to Temperature_factors data member. More...
TTemperature_factors & SetTemperature_factors (void) Assign a value to Temperature_factors data member. More...
bool IsSetOccupancies (void) const Check if a value has been assigned to Occupancies data member. More...
bool CanGetOccupancies (void) const Check if it is safe to call GetOccupancies method. More...
void ResetOccupancies (void) Reset Occupancies data member. More...
const TOccupancies & GetOccupancies (void) const Get the Occupancies member data. More...
void SetOccupancies (TOccupancies &value) Assign a value to Occupancies data member. More...
TOccupancies & SetOccupancies (void) Assign a value to Occupancies data member. More...
bool IsSetAlternate_conf_ids (void) const Check if a value has been assigned to Alternate_conf_ids data member. More...
bool CanGetAlternate_conf_ids (void) const Check if it is safe to call GetAlternate_conf_ids method. More...
void ResetAlternate_conf_ids (void) Reset Alternate_conf_ids data member. More...
const TAlternate_conf_ids & GetAlternate_conf_ids (void) const Get the Alternate_conf_ids member data. More...
void SetAlternate_conf_ids (TAlternate_conf_ids &value) Assign a value to Alternate_conf_ids data member. More...
TAlternate_conf_ids & SetAlternate_conf_ids (void) Assign a value to Alternate_conf_ids data member. More...
bool IsSetConf_ensembles (void) const Check if a value has been assigned to Conf_ensembles data member. More...
bool CanGetConf_ensembles (void) const Check if it is safe to call GetConf_ensembles method. More...
void ResetConf_ensembles (void) Reset Conf_ensembles data member. More...
const TConf_ensembles & GetConf_ensembles (void) const Get the Conf_ensembles member data. More...
TConf_ensembles & SetConf_ensembles (void) Assign a value to Conf_ensembles 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
Literal atomic coordinate values give location, occupancy and order parameters, and a pointer to a specific atom defined in the biostruc graph.
Temperature and occupancy factors have their conventional crystallographic definitions, with units defined in the model space declaration. Atoms, sites, temperature-factors, occupancies and alternate-conformation-ids are parallel arrays, i.e. the have the same number of values as given by number-of-points. Conformation ensembles represent distinct correlated- disorder subsets of the coordinates. They will be present only for certain "views" of PDB structures, as described above. Their derivation from PDB- supplied "alternate-conformation" ids is described below.
CAtomic_coordinates_Base –
Definition at line 91 of file Atomic_coordinates_.hpp.
The documentation for this class was generated from the following files:
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