BALL::Rescoring Class Reference

#include <BALL/SCORING/FUNCTIONS/rescoring.h>

Inheritance diagram for BALL::Rescoring:

Classes
class	RescoreQSARData

Public Member Functions
	Rescoring (AtomContainer &receptor, AtomContainer &reference_ligand, Options &options, String free_energy_label, ScoringFunction *sf)
virtual	~Rescoring ()
void	addScoreContributions (Molecule *mol)
void	recalibrate ()
virtual double	rescore (Molecule *mol)
void	saveModel (String filename)
void	loadModel (String filename)
void	calculateQuality (double &correlation, double &q2, double &std_error)
const String &	getName ()

Protected Member Functions
virtual void	generateScoreContributions_ (Molecule *, vector< vector< double > > *, vector< double > *)
void	setup_ ()

Protected Attributes
ScoringFunction *	scoring_function_
RescoreQSARData	data_
QSAR::RegressionModel *	model_
String	free_energy_label_
String	ff_filename_
bool	convert_
bool	use_calibration_
vector< double >	predicted_affinities_
vector< double >	experimental_affinities_
bool	check_applicability_
String	name_
std::ofstream	stddev_out_

Detailed Description

Definition at line 17 of file rescoring.h.

Constructor & Destructor Documentation

BALL::Rescoring::Rescoring	(	AtomContainer &	receptor,
		AtomContainer &	reference_ligand,
		Options &	options,
		String	free_energy_label,
		ScoringFunction *	sf
	)

virtual BALL::Rescoring::~Rescoring ( )

virtual

Member Function Documentation

void BALL::Rescoring::addScoreContributions

(

Molecule *

mol

)

add score and experimentally determined binding affinity for one molecule to training data set

void BALL::Rescoring::calculateQuality	(	double &	correlation,
		double &	q2,
		double &	std_error
	)

Calculated quality statistics for the rescoring that was done by all previous uses of rescore().

virtual void BALL::Rescoring::generateScoreContributions_ ( Molecule *  , vector< vector< double > > *  , vector< double > *    )

inlineprotectedvirtual

If the Rescoring-approach uses training and a QSAR-model, this function should be implemented in the derived class and should generate score-contributions for the given molecule and add them to 'matrix' or, if matrix == NULL, to 'v'. The default function of this base-class does nothing.

Reimplemented in BALL::Rescoring3D.

Definition at line 61 of file rescoring.h.

const String& BALL::Rescoring::getName

(

)

Return the name of the rescoring approach.

void BALL::Rescoring::loadModel

(

String

filename

)

If the derived class uses a QSAR-model, it can be loaded from a file by use of this method

void BALL::Rescoring::recalibrate

(

)

train a model based on the data entered by use of addScoreContributions() for each molecule

virtual double BALL::Rescoring::rescore ( Molecule *  mol )

virtual

Rescores the given molecule. Depending on the derived class, this method may or may not use a QSAR-Model. If you reimplement this method in a derived class, make sure to make it add the predicted and the experimentally determined affinity value to predicted_affinities_ resp. experimental_affinities_.

void BALL::Rescoring::saveModel

(

String

filename

)

If a QSAR-model was created, it can be saved to file by use of this method

void BALL::Rescoring::setup_ ( )

protected

Member Data Documentation

bool BALL::Rescoring::check_applicability_

protected

Determines whether an applicability domain check should be done before rescoring each ligand. If the ligand is outside of the applicability domain, the score obtained by use of the scoring function will be returned without any model-based rescoring.

Definition at line 83 of file rescoring.h.

bool BALL::Rescoring::convert_

protected

Definition at line 71 of file rescoring.h.

RescoreQSARData BALL::Rescoring::data_

protected

Definition at line 67 of file rescoring.h.

vector<double> BALL::Rescoring::experimental_affinities_

protected

vector containing one experimentally determined affinity value for each molecule that was rescored by use of rescore().

Definition at line 80 of file rescoring.h.

String BALL::Rescoring::ff_filename_

protected

Definition at line 70 of file rescoring.h.

String BALL::Rescoring::free_energy_label_

protected

Definition at line 69 of file rescoring.h.

QSAR::RegressionModel* BALL::Rescoring::model_

protected

Definition at line 68 of file rescoring.h.

String BALL::Rescoring::name_

protected

the name of the rescoring approach

Definition at line 86 of file rescoring.h.

vector<double> BALL::Rescoring::predicted_affinities_

protected

vector containing one predicted affinity value for each molecule that was rescored by use of rescore().

Definition at line 77 of file rescoring.h.

ScoringFunction* BALL::Rescoring::scoring_function_

protected

Definition at line 65 of file rescoring.h.

std::ofstream BALL::Rescoring::stddev_out_

protected

Definition at line 88 of file rescoring.h.

bool BALL::Rescoring::use_calibration_

protected

determines whether the Rescoring approach uses training/calibration

Definition at line 74 of file rescoring.h.