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 MemCore::StrongPtr< class Object, class ObjectBase > | |
| typedef WeakPtr< Object, ObjectBase >::ObjectBase_t | ObjectBase_t |
| Public Types inherited from MemCore::WeakPtr< class Object, class 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< class Object, class 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 MemCore::StrongPtr< class Object, class 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< class Object, class ObjectBase > | |
| pointer_t | getPtrValue () const |
| pointer_t | operator-> () const |
| refvalue_t & | operator* () const |
| size_t | operator~ () const |
| 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) | |
| WeakPtr & | assignWeak (const WeakPtr &other) |
| WeakPtr & | operator= (const WeakPtr &other) |
| Public Member Functions inherited from MemCore::DynPtr< class Object, class 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< class Object, class 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< class Object, class ObjectBase > | |
| WeakPtr (Object *that, const SelfInitialize &) | |
| Protected Member Functions inherited from MemCore::DynPtr< class Object, class 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.
