CModel_space_Base Class Reference

Represents ASN.1 type Model-space defined in file mmdb2.asn

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The model space defines measurement units and any external reference frame. More...

#include <objects/mmdb2/Model_space_.hpp>

Inheritance diagram for CModel_space_Base:

Collaboration diagram for CModel_space_Base:

Public Types
enum	ECoordinate_units { eCoordinate_units_angstroms = 1 , eCoordinate_units_nanometers = 2 , eCoordinate_units_other = 3 , eCoordinate_units_unknown = 255 }
enum	EThermal_factor_units { eThermal_factor_units_b = 1 , eThermal_factor_units_u = 2 , eThermal_factor_units_other = 3 , eThermal_factor_units_unknown = 255 }
enum	EOccupancy_factor_units { eOccupancy_factor_units_fractional = 1 , eOccupancy_factor_units_electrons = 2 , eOccupancy_factor_units_other = 3 , eOccupancy_factor_units_unknown = 255 }
enum	EDensity_units { eDensity_units_electrons_per_unit_volume = 1 , eDensity_units_arbitrary_scale = 2 , eDensity_units_other = 3 , eDensity_units_unknown = 255 }
enum class	E_memberIndex {   e__allMandatory = 0 , e_coordinate_units , e_thermal_factor_units , e_occupancy_factor_units ,   e_density_units , e_reference_frame }
typedef ECoordinate_units	TCoordinate_units
typedef EThermal_factor_units	TThermal_factor_units
typedef EOccupancy_factor_units	TOccupancy_factor_units
typedef EDensity_units	TDensity_units
typedef CReference_frame	TReference_frame
typedef Tparent::CMemberIndex< E_memberIndex, 6 >	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
	CModel_space_Base (void)
virtual	~CModel_space_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetCoordinate_units (void) const
	Check if a value has been assigned to Coordinate_units data member. More...
bool	CanGetCoordinate_units (void) const
	Check if it is safe to call GetCoordinate_units method. More...
void	ResetCoordinate_units (void)
	Reset Coordinate_units data member. More...
TCoordinate_units	GetCoordinate_units (void) const
	Get the Coordinate_units member data. More...
void	SetCoordinate_units (TCoordinate_units value)
	Assign a value to Coordinate_units data member. More...
TCoordinate_units &	SetCoordinate_units (void)
	Assign a value to Coordinate_units data member. More...
bool	IsSetThermal_factor_units (void) const
	Check if a value has been assigned to Thermal_factor_units data member. More...
bool	CanGetThermal_factor_units (void) const
	Check if it is safe to call GetThermal_factor_units method. More...
void	ResetThermal_factor_units (void)
	Reset Thermal_factor_units data member. More...
TThermal_factor_units	GetThermal_factor_units (void) const
	Get the Thermal_factor_units member data. More...
void	SetThermal_factor_units (TThermal_factor_units value)
	Assign a value to Thermal_factor_units data member. More...
TThermal_factor_units &	SetThermal_factor_units (void)
	Assign a value to Thermal_factor_units data member. More...
bool	IsSetOccupancy_factor_units (void) const
	Check if a value has been assigned to Occupancy_factor_units data member. More...
bool	CanGetOccupancy_factor_units (void) const
	Check if it is safe to call GetOccupancy_factor_units method. More...
void	ResetOccupancy_factor_units (void)
	Reset Occupancy_factor_units data member. More...
TOccupancy_factor_units	GetOccupancy_factor_units (void) const
	Get the Occupancy_factor_units member data. More...
void	SetOccupancy_factor_units (TOccupancy_factor_units value)
	Assign a value to Occupancy_factor_units data member. More...
TOccupancy_factor_units &	SetOccupancy_factor_units (void)
	Assign a value to Occupancy_factor_units data member. More...
bool	IsSetDensity_units (void) const
	Check if a value has been assigned to Density_units data member. More...
bool	CanGetDensity_units (void) const
	Check if it is safe to call GetDensity_units method. More...
void	ResetDensity_units (void)
	Reset Density_units data member. More...
TDensity_units	GetDensity_units (void) const
	Get the Density_units member data. More...
void	SetDensity_units (TDensity_units value)
	Assign a value to Density_units data member. More...
TDensity_units &	SetDensity_units (void)
	Assign a value to Density_units data member. More...
bool	IsSetReference_frame (void) const
	Check if a value has been assigned to Reference_frame data member. More...
bool	CanGetReference_frame (void) const
	Check if it is safe to call GetReference_frame method. More...
void	ResetReference_frame (void)
	Reset Reference_frame data member. More...
const TReference_frame &	GetReference_frame (void) const
	Get the Reference_frame member data. More...
void	SetReference_frame (TReference_frame &value)
	Assign a value to Reference_frame data member. More...
TReference_frame &	SetReference_frame (void)
	Assign a value to Reference_frame 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()	ECoordinate_units (void)
	Access to ECoordinate_units's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EThermal_factor_units (void)
	Access to EThermal_factor_units's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EOccupancy_factor_units (void)
	Access to EOccupancy_factor_units's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EDensity_units (void)
	Access to EDensity_units'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
	CModel_space_Base (const CModel_space_Base &)
CModel_space_Base &	operator= (const CModel_space_Base &)

Private Attributes
Uint4	m_set_State [1]
ECoordinate_units	m_Coordinate_units
EThermal_factor_units	m_Thermal_factor_units
EOccupancy_factor_units	m_Occupancy_factor_units
EDensity_units	m_Density_units
CRef< TReference_frame >	m_Reference_frame

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

The model space defines measurement units and any external reference frame.

Coordinates refer to a right-handed orthogonal system defined on axes tagged x, y and z in the coordinate and feature definitions of a biostruc. Coordinates from PDB-derived structures are reported without change, in angstrom units. The units of temperature and occupancy factors are not defined explicitly in PDB, but are inferred from their value range.

CModel_space_Base –

Definition at line 78 of file Model_space_.hpp.

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The documentation for this class was generated from the following files:

• include/objects/mmdb2/Model_space_.hpp
• src/objects/mmdb2/Model_space_.cpp