Surface

Defines a collection of SurfaceParticle's that make up the surface of a molecule. The class hosts a reader that reads output out of a Shou surface file.

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AUTHORS
CHANGES LOG
GOALS
USAGE

Class Summary

class Surface
: public Molecule< SurfacePoint>

{
public:
Surface();
int readShouFile(istream& shouStream);
int readSurfaceFile(istream& inFile);
int readSurfaceFile(const string fileName);
float area() const;
void outputVRML(ostream& VRMLstream, const float red , const float green , const float blue ) const;
protected:
}; // Surface

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AUTHORS

Zipi Fligelman (zipo@math.tau.ac.il)

Copyright: SAMBA group, Tel-Aviv Univ. Israel, 1997.

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CHANGES LOG

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GOALS

Holds a list of surface points. Surfcae points are defined using the surface point and the normal to the surface at the point. The class is descendant of Molecule<SurfacePoint> and hosts all the methods supported by the Molecule template.

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USAGE

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Surface();

Default constructor - empty Surface. 

  Surface();

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int readShouFile(istream& shouStream);

We read a Surface file/s and we add them to the list of surface point with the appropriate constructor. 

  int readShouFile(istream& shouStream);

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int readSurfaceFile(istream& inFile);

Same as readShouFile 

  int readSurfaceFile(istream& inFile);

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int readSurfaceFile(const string fileName);

  int readSurfaceFile(const string fileName);

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float area() const;

computes surface area by summing the areas of all the points 

  float area() const;

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void outputVRML(ostream& VRMLstream, const float red , const float green , const float blue ) const;

Output the molecular surface as a VRML 1.0 model. This function may be used to display the molecular surfac as a 3d model. 

  void outputVRML(ostream& VRMLstream,
                  const float red = 1.0,
                  const float green = 1.0,
                  const float blue = 1.0) const;

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All Members

public:
// Adding Particles.
template< class StreamT> int readPDBfile(StreamT& PDBstream, const PDB::Selector& selector ));
template< class StreamT> int readHetAtomsFromPDBfile(StreamT& PDBstream, const PDB::Selector& selector ));
int readAllPDBfile(const string& pdbFile, const PDB::Selector& selector ));
template< class StreamT> int readAllPDBfile(StreamT& PDBstream, const PDB::Selector& selector ));
class Selector ;
class ChainSelector ;
class WaterHydrogenUnSelector ;
class CaSelector ;
class BackboneSelector ;
int select (const Selector& selector);
int select (const Selector& selector, Molecule< ParticleT>& m) const;
void add(const ParticleT& p);
vector< Vector3> getDiameterTriple() const;
// 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(const Molecule& m);
Molecule splitOnIndex(const int i);
Molecule& operator+=(const Vector3& v);
Molecule& operator*=(const Matrix3& lt);
Molecule& operator*=(const RigidTrans3& rt);
Molecule& operator=(const Molecule& m);
template< class T> friend ostream& operator<< (ostream& s, const Molecule& m);
int readShouFile(istream& shouStream);
int readSurfaceFile(istream& inFile);
int readSurfaceFile(const string fileName);
float area() const;
void outputVRML(ostream& VRMLstream, const float red , const float green , const float blue ) const;
protected:

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Ancestors

Inheritance chain for Surface:

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Descendants

Class is not inherited by any others.

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