5 #ifndef BALL_STRUCTURE_STRUCTUREMAPPER_H
6 #define BALL_STRUCTURE_STRUCTUREMAPPER_H
12 #ifndef BALL_CONCEPT_PROCESSOR_H
16 #ifndef BALL_STRUCTURE_GEOMETRICTRANSFORMATIONS_H
20 #ifndef BALL_DATATYPE_STRING_H
24 #ifndef BALL_KERNEL_PROTEIN_H
28 #ifndef BALL_KERNEL_ATOM_H
32 #ifndef BALL_MATHS_MATRIX44_H
36 #ifndef BALL_STRUCTURE_ATOMBIJECTION_H
100 (
const vector<Fragment*>& A,
const vector<Fragment*>& B);
105 (
const vector<Fragment*>& A,
const vector<Fragment*>& B,
106 Matrix4x4* transformation,
double upper_bound = 8.0,
double lower_bound = 2.5);
132 double max_rmsd = 4.0,
double max_center_tolerance = 2.0,
133 double upper_bound = 8.0,
double lower_bound = 4.0);
139 std::map<String, Size>& type_map,
142 double upper_bound = 8.0,
143 double lower_bound = 4.0,
144 double tolerance = 0.6);
static Matrix4x4 matchPoints(const Vector3 &w1, const Vector3 &w2, const Vector3 &w3, const Vector3 &v1, const Vector3 &v2, const Vector3 &v3)
void set(AtomContainer &A, AtomContainer &B)
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)
Size countFragments_(const AtomContainer &ac) const
virtual ~StructureMapper()
StructureMapper(AtomContainer &A, AtomContainer &B)
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)
static Matrix4x4 matchBackboneAtoms(const Residue &r1, const Residue &r2)
const AtomBijection & getBijection() const
AtomBijection calculateFragmentBijection(const vector< Fragment * > &A, const vector< Fragment * > &B)
Size mapResiduesByBackbone(const list< Residue * > &l1, const list< Residue * > &l2)
bool mapFragments(const vector< Fragment * > &A, const vector< Fragment * > &B, Matrix4x4 *transformation, double upper_bound=8.0, double lower_bound=2.5)
void calculateDefaultBijection(bool limit_to_selection=false)
bool calculateTransformation()
double calculateRMSD(const AtomBijection &new_bijection)