BALL::StructureMapper Class Reference

#include <BALL/STRUCTURE/structureMapper.h>

Inheritance diagram for BALL::StructureMapper:

Public Member Functions
void	set (AtomContainer &A, AtomContainer &B)
double	calculateRMSD ()
double	calculateRMSD (const AtomBijection &new_bijection)
bool	calculateTransformation ()
void	calculateDefaultBijection (bool limit_to_selection=false)
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 ()
Public Member Functions inherited from BALL::TransformationProcessor
	TransformationProcessor ()
	TransformationProcessor (const Matrix4x4 &transformation)
void	setTransformation (const Matrix4x4 &transformation)
const Matrix4x4 &	getTransformation () const
virtual Processor::Result	operator() (Atom &atom)
	Applicator method. More...
Public Member Functions inherited from BALL::UnaryProcessor< Atom >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()
virtual bool	start ()
virtual bool	finish ()

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_
Protected Attributes inherited from BALL::TransformationProcessor
Matrix4x4	transformation_

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< Atom, Processor::Result >
typedef Processor::Result	result_type
typedef Atom	argument_type
typedef Atom &	argument_reference
typedef const Atom &	const_argument_reference
typedef Atom *	argument_pointer
typedef const Atom *	const_argument_pointer

Detailed Description

Structure mapping class.

Definition at line 49 of file structureMapper.h.

Constructor & Destructor Documentation

BALL::StructureMapper::StructureMapper

(

)

Default constructor

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

Constructor

virtual BALL::StructureMapper::~StructureMapper ( )

virtual

Destructor

Member Function Documentation

void BALL::StructureMapper::calculateDefaultBijection

(

bool

limit_to_selection = false

)

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

double BALL::StructureMapper::calculateRMSD

(

const AtomBijection &

new_bijection

)

Calculate the root mean squared deviation given a AtomBijection

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 95 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

• 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

Member Data Documentation

AtomContainer* BALL::StructureMapper::A_

protected

Definition at line 153 of file structureMapper.h.

AtomContainer* BALL::StructureMapper::B_

protected

Definition at line 157 of file structureMapper.h.

AtomBijection BALL::StructureMapper::bijection_

protected

Definition at line 162 of file structureMapper.h.

double BALL::StructureMapper::rmsd_

protected

Definition at line 166 of file structureMapper.h.