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

#include <BALL/STRUCTURE/structureMapper.h>

Inheritance diagram for BALL::StructureMapper:

List of all members.

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_

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Detailed Description

Structure mapping class.

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Constructor & Destructor Documentation

BALL::StructureMapper::StructureMapper

(

)

Default constructor

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

Constructor

virtual BALL::StructureMapper::~StructureMapper

(

)

[virtual]

Destructor

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Member Function Documentation

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

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

• 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.

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
	)

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

Assign the two objects to be mapped

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Member Data Documentation

AtomContainer* BALL::StructureMapper::A_ [protected]

AtomContainer* BALL::StructureMapper::B_ [protected]

AtomBijection BALL::StructureMapper::bijection_ [protected]

double BALL::StructureMapper::rmsd_ [protected]