chemaxon.descriptors.scalars
Class TPSA

java.lang.Object
  chemaxon.descriptors.MolecularDescriptor
      chemaxon.descriptors.ScalarDescriptor
          chemaxon.descriptors.scalars.TPSA

All Implemented Interfaces:

java.lang.Cloneable

public class TPSA
extends ScalarDescriptor

Implements TPSA (Topological Polar Surface Area) value as a scalar descriptor.

Since:

JChem 2.2

Author:

Miklos Vargyas

Field Summary

Fields inherited from class chemaxon.descriptors.ScalarDescriptor

descrValue

Fields inherited from class chemaxon.descriptors.MolecularDescriptor

params

Constructor Summary

TPSA()
Creates a new, empty logD descriptor.

TPSA(ScalarDescriptor sd)
Copy constructor.

TPSA(SDParameters params)
Creates a new instance according to the parameters given.

TPSA(java.lang.String params)
Creates a new instance according to the parameters given.

Method Summary

MolecularDescriptor	clone() Creates a new instance with identical internal state.
java.lang.String[]	generate(Molecule m) Creates the TPSA descriptor for the given Molecule.
java.lang.String	getName() Gets the name of the TPSA descriptor object.
java.lang.String	getParametersClassName() Gets the name of the parameters class corresponding to the descriptor.
java.lang.String	getShortName() Gets the short name of the descriptor.
boolean	needsConfig() Indicates if class takes parameters from configuration file.
void	setParameters(java.lang.String parameters) Sets the parameters of an already created TPSA object.

Methods inherited from class chemaxon.descriptors.ScalarDescriptor

clear, fromData, fromFloatArray, fromString, getDefaultDissimilarityMetricThresholds, getDefaultThreshold, getDissimilarity, getDissimilarity, getDissimilarityMetrics, getLowerBound, set, setParameters, toData, toDecimalString, toFloatArray, toString

Methods inherited from class chemaxon.descriptors.MolecularDescriptor

generate, getAtomSetColors, getAtomSetIndexes, getAtomSetNames, getDefaultMetricIndex, getDissimilarityMetricIndex, getMetricIndex, getMetricName, getMetricName, getNumberOfMetrics, getNumberOfWeights, getParameters, getThreshold, getThreshold, main, newInstance, newInstance, newInstanceFromXML, setScreeningConfiguration, toBinaryString

Methods inherited from class java.lang.Object

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

Constructor Detail

TPSA

public TPSA()

Creates a new, empty logD descriptor.

TPSA

public TPSA(SDParameters params)

Creates a new instance according to the parameters given.

Parameters:

params - parameters

TPSA

public TPSA(java.lang.String params)

Creates a new instance according to the parameters given.

Parameters:

params - parameter settings

TPSA

public TPSA(ScalarDescriptor sd)

Copy constructor. An identical copy of the ScalarDescriptor passed is created. The old and the new instances share the same TPSAParameters object.

Parameters:

sd - a fingerprint to be copied

Method Detail

clone

public MolecularDescriptor clone()

Creates a new instance with identical internal state.

Overrides:

clone in class ScalarDescriptor

Returns:

the newly copied object

getName

public java.lang.String getName()

Gets the name of the TPSA descriptor object. The name is not the same as the class name, but nicer, and more meaningful for end-users too.

Overrides:

getName in class ScalarDescriptor

Returns:

the nice, external name for logD descriptor class objects

getShortName

public java.lang.String getShortName()

Gets the short name of the descriptor.

Overrides:

getShortName in class ScalarDescriptor

Returns:

the short name used in text outputs (tables etc.)

setParameters

public void setParameters(java.lang.String parameters)
                   throws MDParametersException

Sets the parameters of an already created TPSA object.

Overrides:

setParameters in class ScalarDescriptor

Parameters:

parameters - parameter settings for the descriptor

Throws:

ConfigurationException - any XML error

MDParametersException - any XML error

getParametersClassName

public java.lang.String getParametersClassName()

Gets the name of the parameters class corresponding to the descriptor.

Overrides:

getParametersClassName in class ScalarDescriptor

Returns:

the name of the parameters class

needsConfig

public boolean needsConfig()

Indicates if class takes parameters from configuration file.

Overrides:

needsConfig in class MolecularDescriptor

Returns:

false

generate

public java.lang.String[] generate(Molecule m)
                            throws MDGeneratorException

Creates the TPSA descriptor for the given Molecule. Calls the generator created by the corresponding TPSAParameters class.

Overrides:

generate in class ScalarDescriptor

Returns:

property names set in the molecule passed during generation

Throws:

MDGeneratorException - when failed to generate descriptor