chemaxon.descriptors
Class MDMetricOptimizer

java.lang.Object
  chemaxon.descriptors.MDMetricOptimizer

public class MDMetricOptimizer
extends java.lang.Object

Optimization of metric parameters for dissimilarity based screening. Parameter optimization is uniform for each metric: it is based on the optimization of the performance of the metrics when used for screening molecules. Optimization is performed defining the parameters as variables, its goal is to maximize the selected evaluator function of the given MDHitEvaluator object during screening performed on a test set. The test set consists of actives (similar set) mixed with molecules randomly selected from the target set of screening (dissimilar set).

Parameters are written into the common MDParameters object, determined from the query descriptors.

The MDHitEvaluator object must be set up, for its usage see MDHitEvaluator. Parametrized metrics must be set (weighted, asymmetric, scaled, etc.) MDReaders also must be set up, for usage see MDReader.

Typical usage:

 MDMetricOptimizer metrOpt = new MDMetricOPtimizer( evaluator );
 metrOpt.optimizeParameters( pfp2DIndex, euclideanIndex, similarReader, dissimilarReader );
 

Since:

JChem 2.0

Author:

Zsuzsanna Szabo

Field Summary

float	maxErrorInF Maximal allowed dofference in last two calculated values of the enrichment ratio function for termination.
float	maxErrorInX Maximal allowed dofference in last two calculated values of the weight variables for termination.
int	nrOfIterations Maximal allowed number of iterations
float	percentage Consider enrichment ratio values only in cases, when at least the given percent of similars is selected as hits.

Constructor Summary

MDMetricOptimizer(MDHitEvaluator evaluator)
Constructor of parameter optimizer.

Method Summary

void	optimizeParameters(int mdIndex, int metricIndex, MDReader similarSet, MDReader dissimilarSet) Finds optimal parameter values for the given metric.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

nrOfIterations

public int nrOfIterations

Maximal allowed number of iterations

maxErrorInF

public float maxErrorInF

Maximal allowed dofference in last two calculated values of the enrichment ratio function for termination.

maxErrorInX

public float maxErrorInX

Maximal allowed dofference in last two calculated values of the weight variables for termination.

percentage

public float percentage

Consider enrichment ratio values only in cases, when at least the given percent of similars is selected as hits.

Constructor Detail

MDMetricOptimizer

public MDMetricOptimizer(MDHitEvaluator evaluator)

Constructor of parameter optimizer.

Parameters:

evaluator - Evaluator of acive/inactive hits

Method Detail

optimizeParameters

public void optimizeParameters(int mdIndex,
                               int metricIndex,
                               MDReader similarSet,
                               MDReader dissimilarSet)
                        throws MDReaderException

Finds optimal parameter values for the given metric. Parameters are set and can be withdrawn from the common MDParameters object.

Parameters:

mdIndex - Index of molecular descriptor

metricIndex - Index of metric

similarSet - Reader of the set containing actives to be selected as hits

dissimilarSet - Reader of target fingerprints

Throws:

MDReaderException