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NCBI C++ ToolKit: CBiostruc_model_Base Class Reference
A structural model maps chemical components into a measured three- dimensional space. More...
CBiostruc_model_Base (void) virtual ~CBiostruc_model_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 IsSetType (void) const Check if a value has been assigned to Type data member. More...
bool CanGetType (void) const Check if it is safe to call GetType method. More...
void ResetType (void) Reset Type data member. More...
TType GetType (void) const Get the Type member data. More...
void SetType (TType value) Assign a value to Type data member. More...
TType & SetType (void) Assign a value to Type 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 IsSetModel_space (void) const Check if a value has been assigned to Model_space data member. More...
bool CanGetModel_space (void) const Check if it is safe to call GetModel_space method. More...
void ResetModel_space (void) Reset Model_space data member. More...
const TModel_space & GetModel_space (void) const Get the Model_space member data. More...
void SetModel_space (TModel_space &value) Assign a value to Model_space data member. More...
TModel_space & SetModel_space (void) Assign a value to Model_space data member. More...
bool IsSetModel_coordinates (void) const Check if a value has been assigned to Model_coordinates data member. More...
bool CanGetModel_coordinates (void) const Check if it is safe to call GetModel_coordinates method. More...
void ResetModel_coordinates (void) Reset Model_coordinates data member. More...
const TModel_coordinates & GetModel_coordinates (void) const Get the Model_coordinates member data. More...
TModel_coordinates & SetModel_coordinates (void) Assign a value to Model_coordinates 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 structural model maps chemical components into a measured three- dimensional space.
PDB-derived biostrucs generally contain 4 models, corresponding to "views" of the structure of a biomolecular assemble with increasing levels of complexity. Model types indicate the complexity of the view. The model named "NCBI all atom" represents a view suitable for most computational biology applications. It provides complete atomic coordinate data for a "single best" model, omitting statistical disorder information and/or ensemble structure descriptions provided in the source PDB file. Construction of the single best model is based on the assumption that the contents of the "alternate conformation" field from pdb imply no correlation among the occupancies of multiple sites assigned to sets of atoms: the best site is chosen only on the basis of highest occupancy. Note, however, that alternate conformation sets where correlation is implied are generally constrained in crystallographic refinement to have uniform occupancy, and will thus be selected as a set. For ensemble models the model which assigns coordinates to the most atoms is chosen. If numbers of coordinates are the same, the model occurring first in the PDB file is selected. The single best model includes complete coordinates for all nonpolymer components, but omits those classified as "solvent". Model type is 3 for this model. The model named "NCBI backbone" represents a simple view intended for graphic displays and rapid transmission over a network. It includes only alpha carbon or backbone phosphate coordinates for biopolymers. It is based on selection of alpha-carbon and backbone phosphate atoms from the "NCBI all atom" model. The model type is set to 2. An even simpler model gives only a cartoon representation, using cylinders corresponding to secondary structure elements. This is named "NCBI vector", and has model type 1. The models named "PDB Model 1", "PDB Model 2", etc. represent the complete information provided by PDB, including full descriptions of statistical disorder. The name of the model is based on the contents of the PDB MODEL record, with a default name of "PDB Model 1" for PDB files which contain only a single model. Construction of these models is based on the assumption that contents of the PDB "alternate conformation" field are intended to imply correlation among the occupancies of atom sets flagged by the same identifier. The special flag " " (blank) is assumed to indicate sites occupied in all alternate conformations, and sites flagged otherwise, together with " ", to indicate a distinct member of an ensemble of alternate conformations. Note that construction of ensemble members according to these assumption requires two validation checks on PDB "alternate conformation" flags: they must be unique among sites assigned to the same atom, and that the special " " flag must occur only for unique sites. Sites which violate the first check are flagged as "u", for "unknown"; they are omitted from all ensemble definitions but are nontheless retained in the coordinate list. Sites which violate the second check are flagged "b" for "blank", and are included in an appropriately named ensemble. The model type for pdb all models is 4. Note that in the MMDB database models are stored in the ASN.1 stream in order of increasing model type value. Since models occur as the last item in a biostruc, parsers may avoid reading the entire stream if the desired model is one of the simplified types, which occur first in the stream. This can save considerable I/O time, particularly for large ensemble models from NMR determinations.
CBiostruc_model_Base –
Definition at line 132 of file Biostruc_model_.hpp.
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