TMolecule

Extension of the Molecule class. Holds 3 reference points, usually the most farthest points, that are used to answer the clustering question - the distance between two transformations.

[ Lib_General64 | Source | Keywords | Summary | Ancestors | All Members | Descendants ]

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Class Summary

class TMolecule
: public FMolecule< TPoint>
{

public:
typedef TPoint	Ptype;
typedef FMolecule< TPoint>	BaseMoleculeType;
static float	st_fThr;
	TMolecule(const string& filename);
	TMolecule(const string& filename,const FMolecule< TPoint>&);
explicit	TMolecule() ;
string	getFileName()const ;
void	setFileName(const string& sFileName) ;
Vector3	getRefPoint(int i) ;
bool	equalTrans(const RigidTrans3&,const RigidTrans3&);
bool	equalTransMax(const RigidTrans3&,const RigidTrans3&,const float thr );
bool	matched(const Vector3& u1, const Vector3& u2, const Vector3& u3, const RigidTrans3& trans, const Vector3& v1, const Vector3& v2, const Vector3& v3);
protected:

}; // TMolecule

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KEYWORD

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AUTHORS

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CHANGES LOG

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GOALS

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USAGE

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typedef TPoint Ptype;

  typedef TPoint Ptype;

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typedef FMolecule< TPoint> BaseMoleculeType;

  typedef FMolecule< TPoint> BaseMoleculeType;

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float st_fThr;

for calc RMSD between ref points should be set to 3*epsilon^2

  static float st_fThr;

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TMolecule(const string& filename);

  TMolecule(const string& filename);

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TMolecule(const string& filename,const FMolecule< TPoint>&);

  TMolecule(const string& filename,const FMolecule< TPoint>&);

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explicit TMolecule() ;

  explicit TMolecule()  
;

Function is currently defined inline.

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string getFileName()const ;

  string getFileName()const                     
;

Function is currently defined inline.

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void setFileName(const string& sFileName) ;

  void setFileName(const string& sFileName)                        
;

Function is currently defined inline.

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Vector3 getRefPoint(int i) ;

  Vector3 getRefPoint(int i)                         
;

Function is currently defined inline.

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bool equalTrans(const RigidTrans3&,const RigidTrans3&);

  bool equalTrans(const RigidTrans3&,const RigidTrans3&);

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bool equalTransMax(const RigidTrans3&,const RigidTrans3&,const float thr );

  bool equalTransMax(const RigidTrans3&,const RigidTrans3&,const float thr=3.0);

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bool matched(const Vector3& u1, const Vector3& u2, const Vector3& u3, const RigidTrans3& trans, const Vector3& v1, const Vector3& v2, const Vector3& v3);

  bool matched(const Vector3& u1,
	       const Vector3& u2,
	       const Vector3& u3,
	       const RigidTrans3& trans,
	       const Vector3& v1,
	       const Vector3& v2,
	       const Vector3& v3);

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All Members

public:

	// Adding Particles.
int readPDBfile(istream& PDBstream, const	PDB::Selector& selector ));
class	Selector ;
class	CaSelector ;
void	add(const ParticleT& p);
int	select (const Selector& selector);

	// Inspection.
Vector3	operator()(unsigned int particle) const ;
Vector3	centroid() const;

	// Operators.
void	transform(const Matrix3& lt);
void	translate(const Vector3& move);
void	rigidTrans(const RigidTrans3& rt);
void	concat(FMolecule& m);
FMolecule	splitOnIndex(const int i);
FMolecule&	operator+=(const Vector3& v);
FMolecule&	operator*=(const Matrix3& lt);
FMolecule&	operator*=(const RigidTrans3& rt);
FMolecule&	operator=(const FMolecule& m);
template<class ParticleTT> friend ostream&	operator<<(ostream& s, const FMolecule<ParticleTT>& m);
typedef TPoint	Ptype;
typedef FMolecule< TPoint>	BaseMoleculeType;
static float	st_fThr;
explicit	TMolecule() ;
string	getFileName()const ;
void	setFileName(const string& sFileName) ;
Vector3	getRefPoint(int i) ;
bool	equalTrans(const RigidTrans3&,const RigidTrans3&);
bool	equalTransMax(const RigidTrans3&,const RigidTrans3&,const float thr );
bool	matched(const Vector3& u1, const Vector3& u2, const Vector3& u3, const RigidTrans3& trans, const Vector3& v1, const Vector3& v2, const Vector3& v3);
protected:

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Ancestors

Inheritance chain for TMolecule:

vector
FMolecule

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Descendants

Class is not inherited by any others.

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Generated from source by the Cocoon utilities on Tue Jan 5 18:47:31 2010 .

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