StructureMapper Class Reference
[Mapping of molecular structures]

Structure mapping class. More...

#include <structureMapper.h>

Inheritance diagram for StructureMapper:

List of all members.

Public Member Functions
void	set (AtomContainer &A, AtomContainer &B)
	Assign the two objects to be mapped.
double	calculateRMSD ()
	Calculate the root mean squared deviation.
bool	calculateTransformation ()
	Calculate the transformation to map the first of two isomorphous AtomContainer objects onto the second.
void	calculateDefaultBijection ()
	Calculate a reasonable bijection for the mapping of A and B.
const AtomBijection &	getBijection () const
	Return the current bijection.
AtomBijection	calculateFragmentBijection (const vector< Fragment * > &A, const vector< Fragment * > &B)
	Calculates a bijection to map two arrays of fragments onto each other.
bool	mapFragments (const vector< Fragment * > &A, const vector< Fragment * > &B, Matrix4x4 *transformation, double upper_bound=8.0, double lower_bound=2.5)
	Maps two fragments onto each other.
Size	mapResiduesByBackbone (const list< Residue * > &l1, const list< Residue * > &l2)
vector< vector< Fragment * > > &	searchPattern (vector< Fragment * > &pattern, AtomContainer &composite, double max_rmsd=4.0, double max_center_tolerance=2.0, double upper_bound=8.0, double lower_bound=4.0)
Matrix4x4	mapProteins (Protein &P1, Protein &P2, std::map< String, Size > &type_map, Size &no_matched_ca, double &rmsd, double upper_bound=8.0, double lower_bound=4.0, double tolerance=0.6)
	Map two proteins onto each other.
Constructors and Destructors
	StructureMapper ()
	Default constructor.
	StructureMapper (AtomContainer &A, AtomContainer &B)
	Constructor.
virtual	~StructureMapper ()
	Destructor.
Static Public Member Functions
Matrix4x4	matchPoints (const Vector3 &w1, const Vector3 &w2, const Vector3 &w3, const Vector3 &v1, const Vector3 &v2, const Vector3 &v3)
	Map three points onto each other.
Matrix4x4	matchBackboneAtoms (const Residue &r1, const Residue &r2)
Protected Member Functions
Size	countFragments_ (const AtomContainer &ac) const
Protected Attributes
AtomContainer *	A_
AtomContainer *	B_
AtomBijection	bijection_
double	rmsd_

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Detailed Description

Structure mapping class.

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Member Function Documentation

AtomBijection StructureMapper::calculateFragmentBijection (  const vector< Fragment * > &  A, const vector< Fragment * > &  B )

Calculates a bijection to map two arrays of fragments onto each other.

Matrix4x4 StructureMapper::mapProteins (  Protein &  P1, Protein &  P2, std::map< String, Size > &  type_map, Size &  no_matched_ca, double &  rmsd, double  upper_bound = 8.0, double  lower_bound = 4.0, double  tolerance = 0.6 )

Map two proteins onto each other.

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

Map three points onto each other. Computes a transformation that maps the point w1 onto the point v1, the point w2 onto the ray that starts in v1 and goes through v2, the point w3 into the plane generated by v1, v2, and v3.