paradocks::Fitness Class Reference
[ParaDockS Fitness function Interface]

Fitness class. Virtual base class interface definition for all Fitness class implementations. More...

#include <fitness.hpp>

Inherited by paradocks::MiniFF, paradocks::MPSP08, paradocks::PMF04, paradocks::POTMIX, and paradocks::PScore.

List of all members.

Public Member Functions

 Fitness (vector< string > &parameter)
 Constructor.
virtual ~Fitness ()
 Destructor.
virtual void initProtein (const ChainList &prot, const Vec3_t &as, Float_t r)
 Initialise the fitness function with the protein.
virtual unsigned int TermsCount ()=0
 Return the number of terms implemented in the fitness function. Pure virtual function!
virtual void initLigand (const ChainList &lig)=0
 Initialise the Fitness function with the ligand. Pure virtual function!
virtual unsigned int RotCount ()
 Return the number rotatable bonds.
virtual void eval (const Vec3_t &pos, const Quat_t &ori, const vector< Float_t > &angle, vector< Float_t > *&result)=0
 Evaluate the current configuration. This method evaluates the configuration of the ligand specified in the parameter and returns a field of scoring values. Pure virtual function!
void writeOptimum (const Vec3_t &pos, const Quat_t &ori, const vector< Float_t > &angle, ostream &outfile)
 Write out a ligands configuration as Tripos MOL2 data. This method writes out a ligands configuration as Tripos MOL2 data to a stream.
void restoreLigand ()
 write initial coordinates back
Vec3_t Offset ()
 return ligand offset

Public Attributes

stringstream log
 All output from the fitness class should go into this stringstream.

Protected Member Functions

void initLigand (const ChainList &lig, unsigned int h_handling)
 Provides some code for initLigand(const ChainList& lig). This method finds rotatable bonds in the ligand and does some preparation.


Detailed Description

Fitness class. Virtual base class interface definition for all Fitness class implementations.

Member Function Documentation

virtual void paradocks::Fitness::initProtein ( const ChainList &  prot,
const Vec3_t &  as,
Float_t  r 
) [virtual]

Initialise the fitness function with the protein.

Parameters:
prot The protein as ChainList.
as Center of the active site.
r Radius of the active site.

virtual unsigned int paradocks::Fitness::TermsCount (  )  [pure virtual]

Return the number of terms implemented in the fitness function. Pure virtual function!

Returns:
Number of fitness (scoring) terms returned by eval.

virtual void paradocks::Fitness::initLigand ( const ChainList &  lig  )  [pure virtual]

Initialise the Fitness function with the ligand. Pure virtual function!

Parameters:
lig The ligand as ChainList.
Returns:
Number of rotatable bonds in the ligand.

virtual unsigned int paradocks::Fitness::RotCount (  )  [inline, virtual]

Return the number rotatable bonds.

Returns:
Number of rotatable bonds in the current ligand.

virtual void paradocks::Fitness::eval ( const Vec3_t &  pos,
const Quat_t &  ori,
const vector< Float_t > &  angle,
vector< Float_t > *&  result 
) [pure virtual]

Evaluate the current configuration. This method evaluates the configuration of the ligand specified in the parameter and returns a field of scoring values. Pure virtual function!

Parameters:
pos Position of the centerfragment.
ori Orientation of the centerfragment.
angle Vector of the ligand's torsion angles. The size needs to be equal to TermsCount().
result A pointer to the vector with the results.

void paradocks::Fitness::writeOptimum ( const Vec3_t &  pos,
const Quat_t &  ori,
const vector< Float_t > &  angle,
ostream &  outfile 
)

Write out a ligands configuration as Tripos MOL2 data. This method writes out a ligands configuration as Tripos MOL2 data to a stream.

Parameters:
pos Position of the centerfragment.
ori Orientation of the centerfragment.
angle Vector of the ligand's torsion angles. The size needs to be equal to TermsCount().
outfile The Tripos MOL2 data will be writen to this stream.

void paradocks::Fitness::initLigand ( const ChainList &  lig,
unsigned int  h_handling 
) [protected]

Provides some code for initLigand(const ChainList& lig). This method finds rotatable bonds in the ligand and does some preparation.

Parameters:
lig The ligand as ChainList.
h_handling Handling of hydrogens:
0 - no hydrogens are rotated
1 - polar hydrogens are rotated
2 - all hydrogens are rotated


The documentation for this class was generated from the following file:

Generated on Mon Nov 23 08:31:44 2009 for ParaDockS by  doxygen 1.5.8