#include <fitness.hpp>
Inherited by paradocks::MiniFF, paradocks::MPSP08, paradocks::PMF04, paradocks::POTMIX, and paradocks::PScore.
Public Member Functions | |
Fitness (vector< string > ¶meter) | |
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. |
virtual void paradocks::Fitness::initProtein | ( | const ChainList & | prot, | |
const Vec3_t & | as, | |||
Float_t | r | |||
) | [virtual] |
Initialise the fitness function with the protein.
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!
virtual void paradocks::Fitness::initLigand | ( | const ChainList & | lig | ) | [pure virtual] |
Initialise the Fitness function with the ligand. Pure virtual function!
lig | The ligand as ChainList. |
virtual unsigned int paradocks::Fitness::RotCount | ( | ) | [inline, virtual] |
Return the number rotatable bonds.
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!
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.
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.
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 |