Fiber::MDHistory Class Reference

A convenience grid type for molecules. More...

#include <MDHistory.hpp>

Inheritance diagram for Fiber::MDHistory:

Public Types
typedef uint16_t	AtomType_t
Public Types inherited from Eagle::StrongPtr< Object, ObjectBase >
typedef WeakPtr< Object, ObjectBase >::ObjectBase_t	ObjectBase_t
Public Types inherited from MemCore::WeakPtr< Object, ObjectBase >
typedef Object	object_t
typedef ObjectBase	ObjectBase_t
typedef RefPtrTypeTrait< Object, ObjectBase >::ReferencePointerType	pointer_t
typedef RefPtrTypeTrait< Object, ObjectBase >::ReferenceValueType	refvalue_t
Public Types inherited from MemCore::DynPtr< Object, ObjectBase >
typedef Object	object_t
Public Types inherited from Fiber::Edges
typedef EdgeCell32	EdgeCell_t
typedef TriangleCell32	TriangleCell_t
typedef TypedArray< Eagle::PhysicalSpace::point >	CoordsArray_t
typedef MemArray< 1, Eagle::PhysicalSpace::point >	CoordsMemArray_t
typedef MultiArray< 1, Eagle::PhysicalSpace::point >	CoordsMultiArray_m_t
typedef MemArray< 1, EdgeCell_t >	EdgesArray_t
typedef MemArray< 1, TriangleCell_t >	TriArray_t
typedef MemArray< 1, std::vector< index_t > >	IndexSetArray_t
typedef MemArray< 1, Eagle::tvector3 >	TangentialVector_t
typedef std::vector< index_t >	EdgesPerVertex_t
	Edges per vertex: variable length!
typedef MemArray< 1, EdgesPerVertex_t >	EdgesPerVertexMemArray_t

Public Member Functions
	MDHistory (const RefPtr< Grid > &grid)
bool	assign (const RefPtr< Grid > &theGrid)
bool	isValid ()
RefPtr< MemArray< 1, Dihedral_t > >	getDihedrals (const RefPtr< FragmentID > &frag=NullPtr())
void	getAtomTypeNames (std::vector< string > &names, const RefPtr< FragmentID > &frag=NullPtr()) const
void	extractChains (const std::vector< string > &atom_filter, unsigned mindepth, unsigned maxdepth, std::vector< std::list< uint32_t > > &AllChains, std::vector< string > &dict_arr, MultiArray< 1, MDHistory::AtomType_t > &type_arr, MultiArray< 1, EdgeCell32 > &edge_arr) const
void	recursiveChainFinder (std::list< uint32_t > &chain, const std::vector< std::list< uint32_t > > &neighbors, std::vector< std::list< uint32_t > > &AllChains, unsigned mindepth, unsigned maxdepth, std::vector< string > &dict_arr, MultiArray< 1, MDHistory::AtomType_t > &type_arr, const std::vector< string > &atom_filter) const
void	extractSingleCluster (uint32_t root, const std::vector< string > &atom_filter, unsigned maxdepth, std::list< uint32_t > &cluster, std::vector< string > &dict_arr, MultiArray< 1, MDHistory::AtomType_t > &type_arr, MultiArray< 1, EdgeCell32 > &edge_arr) const
void	recursiveClusterFinder (std::list< uint32_t > &cluster, uint32_t node, const std::vector< std::list< uint32_t > > &neighbors, unsigned maxdepth, std::vector< string > &dict_arr, MultiArray< 1, MDHistory::AtomType_t > &type_arr, const std::vector< string > &atom_filter) const
template<class T, class C>
bool	isMember (const T &str, const C &atom_filter) const
Public Member Functions inherited from Fiber::GridWithCartesianVertices
	GridWithCartesianVertices (const RefPtr< Grid > &theGrid=nullptr)
bool	assign (const RefPtr< Grid > &theGrid)
bool	isValid () const
Public Member Functions inherited from Fiber::TypedGrid
bool	assign (const RefPtr< Grid > &theGrid)
bool	invalidate ()
	Invalidate the stored Grid pointer and return false.
Public Member Functions inherited from Eagle::StrongPtr< Object, ObjectBase >
StrongPtr &	assignStrong (const DynPtr_t &other)
StrongPtr &	assignStrong (const ReferenceBase< ObjectBase_t > *Obj)
StrongPtr &	assignStrong (const std::nullptr_t &)
auto	operator() (Arguments...parameters) const -> decltype((*this->getPtrValue())(parameters...))
refvalue_t &	operator* () const
pointer_t	operator-> () const
StrongPtr &	operator= (const DynPtr_t &other)
StrongPtr &	operator= (const ReferenceBase< ObjectBase_t > *Obj)
StrongPtr &	operator= (const std::initializer_list< StrongPtr > &other)
StrongPtr &	operator= (const std::nullptr_t &)
StrongPtr &	operator= (const StrongPtr &other)
auto	operator[] (const IndexType &I) const -> decltype((*this->getPtrValue())[I])
	StrongPtr (const ReferenceBase< ObjectBase_t > *Obj)
	StrongPtr (const ReferenceBase< ObjectBase_t > *Obj, const NotNullPtr &)
	StrongPtr (const std::nullptr_t &)
	StrongPtr (const StrongPtr< ChildObject, ObjectBase > &Other)
	StrongPtr (const StrongPtr< Object, ObjectBase > &Other)
	StrongPtr (const WeakPtr< ChildObject, ObjectBase_t > &Other)
Public Member Functions inherited from MemCore::WeakPtr< Object, ObjectBase >
	WeakPtr (const std::nullptr_t &)
	WeakPtr (const ReferenceBase< ObjectBase > *Obj)
	WeakPtr (const ReferenceBase< ObjectBase > *Obj, const NotNullPtr &)
	WeakPtr (const WeakPtr< AnyObject, ObjectBase > &Other)
	WeakPtr (const WeakPtr &Other)
pointer_t	getPtrValue () const
pointer_t	operator-> () const
refvalue_t &	operator* () const
size_t	operator~ () const
WeakPtr &	assignWeak (const WeakPtr &other)
WeakPtr &	operator= (const WeakPtr &other)
Public Member Functions inherited from MemCore::DynPtr< Object, ObjectBase >
const DynPtr &	getDynPtr () const noexcept
const type_info &	getType () const noexcept
bool	isAssignable (const DynPtr< ObjectBase, ObjectBase > &Other) const noexcept
	operator void * () const noexcept
bool	operator! () const noexcept
void	speak (const char *s, const char *prefix="") const noexcept
void	Speak (const char *s, const char *prefix="") const
Public Member Functions inherited from Fiber::Edges
	Edges (const RefPtr< Grid > &G)
	Retrieve a Edge information from a Grid object.
	~Edges ()
	Destructor, cleans up references.

Static Public Member Functions
static SkeletonID	getDihedralSkeletonID ()
static RefPtr< Field >	createDihedralPositionsField (const RefPtr< Grid > &grid)
Static Public Member Functions inherited from Fiber::GridWithCartesianVertices
static GridWithCartesianVertices	create (Grid &myGrid, int Dims, const RefPtr< Field > &Positions)
Static Public Member Functions inherited from MemCore::DynPtr< Object, ObjectBase >
static const DynPtr &	getNullPtr () noexcept
Static Public Member Functions inherited from Fiber::Edges
static SkeletonID	EdgeSkeletonID ()
	Return the skeleton ID that refers to the Edges property of a cw-complex.
static SkeletonID	ID ()
	Return a skeleton ID that is characteristic for Grid objects that carry Edge information.
static RefPtr< Skeleton >	getEdgeSkeleton (const RefPtr< Grid > &G, bool CreateIfNotFound)
	Return the Skeleton that holds all the information that is given on Edges of a Grid object.
static RefPtr< Representation >	getVerticesPerEdge (const RefPtr< Grid > &G, bool CreateIfNotFound)
	Find the information how edges are represented as Vertices, which is two vertices are given per Edge ID.
static RefPtr< Field >	getVerticesPerEdgeField (const RefPtr< Grid > &G)
	Return the Positions field of the edges given as vertices.
static RefPtr< EdgesArray_t >	getVerticesPerEdgeArray (const RefPtr< Grid > &G)
	Return the data array that holds the edges as vertices.
static bool	addVerticesPerEdgeField (const RefPtr< Grid > &G, const RefPtr< Field > &theField)
	Add a new Field describing the Edge information to a certain Grid object.
static bool	addVerticesPerEdgeArray (const RefPtr< Grid > &G, const RefPtr< EdgesArray_t > &Data)
	Add a new array of edges to the Edge information of a certain Grid object.
static bool	addVerticesPerEdgeArray (const RefPtr< Grid > &G, const RefPtr< MemCore::TypedChunk< EdgeCell_t > > &EdgeData)
static RefPtr< Representation >	getEdgesPerVertex (const RefPtr< Grid > &G, bool CreateIfNotFound)
	Find the information how vertices are related to edges, which can be varying, the element type of the Positions field is thus dependent on the type of mesh.
static RefPtr< Field >	getEdgesPerVertexField (const RefPtr< Grid > &G, bool CreateIfNotFound)
static RefPtr< EdgesArray_t >	getEdgesPerVertexArray (const RefPtr< Grid > &G)
static bool	addEdgesPerVertex (const RefPtr< Grid > &G, const RefPtr< Field > &theField)
static RefPtr< EdgesPerVertexMemArray_t >	createEdgesPerVertex (const RefPtr< Grid > &G, bool storeThem)
	Get all edges of each vertex;.

Public Attributes
RefPtr< Skeleton >	DihedralSkeleton
RefPtr< Representation >	DihedralsAsVertices
RefPtr< Field >	DihedralPositions
RefPtr< Field >	AtomTypes
Public Attributes inherited from Fiber::GridWithCartesianVertices
RefPtr< Skeleton >	Vertices
RefPtr< Representation >	CartesianVertices
	Collection of all fields given on vertices relative to cartesian coordinates.
RefPtr< Field >	CartesianPositions
Public Attributes inherited from Fiber::Edges
RefPtr< Skeleton >	EdgeSkeleton
RefPtr< Representation >	VerticesPerEdge
RefPtr< Field >	VerticesPerEdgeField
RefPtr< EdgesArray_t >	VerticesPerEdgeArray

Additional Inherited Members
Protected Member Functions inherited from MemCore::WeakPtr< Object, ObjectBase >
	WeakPtr (Object *that, const SelfInitialize &)
Protected Member Functions inherited from MemCore::DynPtr< Object, ObjectBase >
	DynPtr (const DynPtr< AnyObject, ObjectBase > &Other) noexcept
	DynPtr (const std::nullptr_t &) noexcept

Detailed Description

A convenience grid type for molecules.

Adds a skeleton for dihedrals. Adds a backbone.

Author

: marcel