BALL::QSAR::KernelModel Class Reference

#include <BALL/QSAR/kernelModel.h>

Inheritance diagram for BALL::QSAR::KernelModel:

[legend]

List of all members.

Public Member Functions
Constructors and Destructors
	KernelModel (const QSARData &q, int k_type, double p1, double p2)
	KernelModel (const QSARData &q, String f, String g)
	KernelModel (const QSARData &q, Vector< double > &w)
	KernelModel (const QSARData &q, const LinearModel &lm, int column)
	~KernelModel ()
virtual void	saveToFile (string filename)
virtual void	readFromFile (string filename)
virtual Vector< double >	predict (const vector< double > &substance, bool transform)
void	operator= (const Model &m)
Attributes
Kernel *	kernel
Matrix< double >	K_
Input and Output. The following methods can be used to implement the functions saveToFile() and readFromFile() in final classes derived from this base-class
resulting matrix with one column for each modeled activity and with one coefficient for each substance (i.e. one column for each column for Model.Y)
class	RegressionValidation
void	calculateOffsets ()
void	readKernelParametersFromFile (std::ifstream &in)
void	saveKernelParametersToFile (std::ofstream &out)
void	saveTrainingResult (std::ofstream &out)
void	readTrainingResult (std::ifstream &input, int no_substances, int no_y)

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Detailed Description

Definition at line 47 of file kernelModel.h.

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Constructor & Destructor Documentation

BALL::QSAR::KernelModel::KernelModel	(	const QSARData &	q,
		int	k_type,
		double	p1,
		double	p2
	)

BALL::QSAR::KernelModel::KernelModel	(	const QSARData &	q,
		String	f,
		String	g
	)

BALL::QSAR::KernelModel::KernelModel	(	const QSARData &	q,
		Vector< double > &	w
	)

BALL::QSAR::KernelModel::KernelModel	(	const QSARData &	q,
		const LinearModel &	lm,
		int	column
	)

BALL::QSAR::KernelModel::~KernelModel

(

)

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Member Function Documentation

void BALL::QSAR::KernelModel::calculateOffsets

(

)

[protected, virtual]

do nothing for non-kernel models. KernelModel on the other hand overloads this function...

Reimplemented from BALL::QSAR::NonLinearModel.

void BALL::QSAR::KernelModel::operator=

(

const Model &

m

)

[virtual]

copy constructur; creates a model with the same specifications as the given one (same model and kernel parameters). If the given model has been trained, the training result is copied as well.
Note, that the input data that has been read by m to m.descriptor_matrix_ and m.Y_ is NOT copied to new model, since the input data is not part of the specification of a model. If nevertheless, copying of the input data is desired, use function copyData() (afterwards).

Reimplemented from BALL::QSAR::Model.

virtual Vector<double> BALL::QSAR::KernelModel::predict	(	const vector< double > &	substance,
		bool	transform
	)			[virtual]

Predicts the activities of a given substance

Parameters:

	substance	the substance which activity is to be predicted in form of a vecor containing the values for *all* descriptors (if neccessary, relevant descriptors will be selected automatically)
	transform	determines whether the values for each descriptor of the given substance should be transformed before prediction of activity. If (transform==1): each descriptor value is transformed according to the centering of the respective column of QSARData.descriptor_matrix used to train this model. If the substance to be predicted is part of the same input data (e.g. same SD-file) as the training data (as is the case during cross validation), transform should therefore be set to 0.

Returns:

a RowVector containing one value for each predicted activity

Implements BALL::QSAR::Model.

Reimplemented in BALL::QSAR::GPModel.

virtual void BALL::QSAR::KernelModel::readFromFile

(

string

filename

)

[virtual]

reconstruct a saved Model from a file

Reimplemented from BALL::QSAR::RegressionModel.

void BALL::QSAR::KernelModel::readKernelParametersFromFile

(

std::ifstream &

in

)

[protected]

void BALL::QSAR::KernelModel::readTrainingResult	(	std::ifstream &	input,
		int	no_substances,
		int	no_y
	)			[protected]

void BALL::QSAR::KernelModel::saveKernelParametersToFile

(

std::ofstream &

out

)

[protected]

virtual void BALL::QSAR::KernelModel::saveToFile

(

string

filename

)

[virtual]

save Model to a file

Reimplemented from BALL::QSAR::RegressionModel.

void BALL::QSAR::KernelModel::saveTrainingResult

(

std::ofstream &

out

)

[protected]

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Friends And Related Function Documentation

friend class RegressionValidation [friend]

Reimplemented from BALL::QSAR::RegressionModel.

Definition at line 102 of file kernelModel.h.

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Member Data Documentation

Matrix<double> BALL::QSAR::KernelModel::K_ [protected]

Matrix containing the pairwise distances between all substances

Definition at line 85 of file kernelModel.h.

Kernel* BALL::QSAR::KernelModel::kernel

Definition at line 75 of file kernelModel.h.