BALL
1.4.1
|
#include <BALL/STRUCTURE/structureMapper.h>
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_ |
Structure mapping class.
Definition at line 49 of file structureMapper.h.
Default constructor
Constructor
virtual BALL::StructureMapper::~StructureMapper | ( | ) | [virtual] |
Destructor
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] |
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
w1
onto the point v1
,w2
onto the ray that starts in v1
and goes through v2
,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
AtomContainer* BALL::StructureMapper::A_ [protected] |
Definition at line 149 of file structureMapper.h.
AtomContainer* BALL::StructureMapper::B_ [protected] |
Definition at line 153 of file structureMapper.h.
AtomBijection BALL::StructureMapper::bijection_ [protected] |
Definition at line 158 of file structureMapper.h.
double BALL::StructureMapper::rmsd_ [protected] |
Definition at line 162 of file structureMapper.h.