ReconstructFragmentProcessor Class Reference
[Miscellaneous]

ReconstructFragmentProcessor. More...

#include <reconstructFragmentProcessor.h>

Inheritance diagram for ReconstructFragmentProcessor:

List of all members.

Public Member Functions
Constructors and Destructors
	ReconstructFragmentProcessor ()
	Default constructor.
	ReconstructFragmentProcessor (const FragmentDB &db)
	Detailed constructor.
	ReconstructFragmentProcessor (const ReconstructFragmentProcessor &db)
	Copy Constructor.
virtual	~ReconstructFragmentProcessor ()
	Destructor.
Processor-related methods
virtual bool	start ()
	Processor start method.
virtual bool	finish ()
	Processor finish method.
virtual Processor::Result	operator() (Fragment &)
	Processor applicaiton method.
Accessors
list< Atom * > &	getInsertedAtoms ()
	Returns a list of inserted atoms.
Size	getNumberOfInsertedAtoms () const
	Returns number of recently inserted atoms.
void	setFragmentDB (const FragmentDB &fragment_db)
	Set the fragment database.
const FragmentDB *	getFragmentDB () const
	Return the current fragment database.
Static Public Member Functions
Static methods.
Matrix4x4	mapThreeVectors (const Vector3 &w1, const Vector3 &w2, const Vector3 &w3, const Vector3 &v1, const Vector3 &v2, const Vector3 &v3)
	Map three vectors onto each other.
Triple< bool, const Atom *, const Atom * >	getTwoReferenceAtoms (const Atom &ref_center_atom, const HashSet< const Atom * > &allowed) throw ()
	Search for the next atoms suitable as reference points.
list< Atom * >	reconstructFragment (Fragment &frag, const Fragment &tplate)
Protected Attributes
const FragmentDB *	fragment_db_
list< Atom * >	inserted_atoms_

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Detailed Description

ReconstructFragmentProcessor.

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Constructor & Destructor Documentation

ReconstructFragmentProcessor::ReconstructFragmentProcessor (   )

Default constructor. Create a new ReconstructFragmentProcessor, which is not yet bound to a FragmentDB , i.e. which cannot yet reconstruct fragments.

ReconstructFragmentProcessor::ReconstructFragmentProcessor (  const FragmentDB &  db  )

Detailed constructor. Create a new ReconstructFragmentProcessor, which is bound to the FragmentDB db.

ReconstructFragmentProcessor::ReconstructFragmentProcessor (  const ReconstructFragmentProcessor &  db  )

Copy Constructor.

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Member Function Documentation

const FragmentDB* ReconstructFragmentProcessor::getFragmentDB (   )  const

Return the current fragment database.

list<Atom*>& ReconstructFragmentProcessor::getInsertedAtoms (   )

Returns a list of inserted atoms.

Size ReconstructFragmentProcessor::getNumberOfInsertedAtoms (   )  const

Returns number of recently inserted atoms.

Triple<bool, const Atom*, const Atom*> ReconstructFragmentProcessor::getTwoReferenceAtoms (  const Atom &  ref_center_atom, const HashSet< const Atom * > &  allowed )  throw () [static]

Search for the next atoms suitable as reference points. This method performs a BFS-like search for atoms in the same residue the ref_center_atom is in. It will consider only atoms contained in the hash set allowed.

Matrix4x4 ReconstructFragmentProcessor::mapThreeVectors (  const Vector3 &  w1, const Vector3 &  w2, const Vector3 &  w3, const Vector3 &  v1, const Vector3 &  v2, const Vector3 &  v3 )  [static]

Map three vectors onto each other. This method computes the transformation which move the three points given in v1, v2, and v3 onto the the three reference points w1, w2, and w3. v1 is always mapped exactly onto w1, and the plane spanned by v1, v2, and v3 is always mapped onto the plane spanned by the three reference points. Furthermore, v2 is mapped such that the vector connecting v1 and v2 is parallel to the vector connecting w1 and w2 after the transformation. Well-defined, but less meaningful transformations are obtained if any of the two point sets is co-linear.

virtual Processor::Result ReconstructFragmentProcessor::operator() (  Fragment &   )  [virtual]

Processor applicaiton method. Tries to reconstruct the current fragment from a matching fragment from the current FragmentDB . Reimplemented from UnaryProcessor< Fragment >.