BALL  1.4.1
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Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes
BALL::StructureMapper Class Reference

#include <BALL/STRUCTURE/structureMapper.h>

Inheritance diagram for BALL::StructureMapper:
BALL::TransformationProcessor BALL::UnaryProcessor< Atom > BALL::UnaryFunctor< Atom, Processor::Result >

List of all members.

Public Member Functions

void set (AtomContainer &A, AtomContainer &B)
double calculateRMSD ()
bool calculateTransformation ()
void calculateDefaultBijection ()
const AtomBijectiongetBijection () 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

AtomContainerA_
AtomContainerB_
AtomBijection bijection_
double rmsd_

Detailed Description

Structure mapping class.

Definition at line 49 of file structureMapper.h.


Constructor & Destructor Documentation

Default constructor

Constructor

Destructor


Member Function Documentation

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.

Calculate the root mean squared deviation

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

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

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

  • 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 
)

Assign the two objects to be mapped


Member Data Documentation

Definition at line 149 of file structureMapper.h.

Definition at line 153 of file structureMapper.h.

Definition at line 158 of file structureMapper.h.

Definition at line 162 of file structureMapper.h.

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