BALL::StructureMapper Class Reference
[Mapping of molecular structures]

Inheritance diagram for BALL::StructureMapper:

Public Member Functions
void	set (AtomContainer &A, AtomContainer &B)
double	calculateRMSD ()
bool	calculateTransformation ()
void	calculateDefaultBijection ()
const AtomBijection &	getBijection () const
AtomBijection	calculateFragmentBijection (const vector< Fragment * > &A, const vector< Fragment * > &B)
bool	mapFragments (const vector< Fragment * > &A, const vector< Fragment * > &B, Matrix4x4 *transformation, double upper_bound=8.0, double lower_bound=2.5)
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)
Constructors and Destructors

	StructureMapper ()
	StructureMapper (AtomContainer &A, AtomContainer &B)
virtual	~StructureMapper ()
Static Public Member Functions
static Matrix4x4	matchPoints (const Vector3 &w1, const Vector3 &w2, const Vector3 &w3, const Vector3 &v1, const Vector3 &v2, const Vector3 &v3)
static 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_

Detailed Description

Structure mapping class.

Definition at line 49 of file structureMapper.h.

BALL::StructureMapper::StructureMapper ( )

Default constructor

BALL::StructureMapper::StructureMapper	(	AtomContainer &	A,
		AtomContainer &	B
	)

Constructor

virtual BALL::StructureMapper::~StructureMapper ( ) [virtual]

Destructor

void BALL::StructureMapper::calculateDefaultBijection ( )

Calculate a reasonable bijection for the mapping of A and B

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

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

double BALL::StructureMapper::calculateRMSD ( )

Calculate the root mean squared deviation

bool BALL::StructureMapper::calculateTransformation ( )

Calculate the transformation to map the first of two isomorphous AtomContainer objects onto the second

Size BALL::StructureMapper::countFragments_ ( const AtomContainer & ac ) const [protected]

const AtomBijection& BALL::StructureMapper::getBijection ( ) const [inline]

Return the current bijection

Definition at line 91 of file structureMapper.h.

bool BALL::StructureMapper::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

Matrix4x4 BALL::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.

Size BALL::StructureMapper::mapResiduesByBackbone	(	const list< Residue * > &	l1,
		const list< Residue * > &	l2
	)

static Matrix4x4 BALL::StructureMapper::matchBackboneAtoms	(	const Residue &	r1,
		const Residue &	r2
	)			`[static]`

static Matrix4x4 BALL::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

vector<vector<Fragment*> >& BALL::StructureMapper::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`
	)