chemaxon.descriptors
Class ScalarDescriptor

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

All Implemented Interfaces:

java.lang.Cloneable

Direct Known Subclasses:

HAcc, HDon, Heavy, LogD, LogP, Mass, TPSA

public class ScalarDescriptor
extends MolecularDescriptor

Base class for all scalar descriptors. All scalar descriptors should be derived from this class.

Since:

JChem 2.2

Author:

Miklos Vargyas

Field Summary

protected float

descrValue descriptor value

Fields inherited from class chemaxon.descriptors.MolecularDescriptor

params

Constructor Summary

ScalarDescriptor()
Creates a new, empty instance of ScalarDescriptor.

ScalarDescriptor(ScalarDescriptor sd)
Copy constructor.

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

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

Method Summary

void	clear() Clears the descritor: sets its value to zero value.
MolecularDescriptor	clone() Creates a new instance with identical internal state.
void	fromData(byte[] dbRepr) Builds a descriptor from an external data format, created by a previous call to toData().
void	fromFloatArray(float[] descr) Builds the descriptor from a float array of one element.
void	fromString(java.lang.String sd) Builds a descriptpr from its string representation created by toString().
java.lang.String[]	generate(Molecule m) Creates the ScalarDescriptor descriptor for the given Molecule.
float[]	getDefaultDissimilarityMetricThresholds() Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
float	getDefaultThreshold(int metricIndex) Gets a metric dependent default threshold value.
float	getDissimilarity(MolecularDescriptor sd) Calculates the dissimilarity between two scalar descriptor using the default metrics In the present implementation it is always the absolute difference between them.
float	getDissimilarity(MolecularDescriptor sd, int metricIndex) Calculates the dissimilarity between two scalar descriptor using the specified metric.
java.lang.String[]	getDissimilarityMetrics() Gets the dissimilarity metric names
float	getLowerBound(MolecularDescriptor sd) Calculates the lower bound estimate of the dissimilarity from the given descriptor.
java.lang.String	getName() Gets the name of the ScalarDescriptor 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.
void	set(float newValue) Set the value of the descriptor.
void	setParameters(MDParameters parameters) Sets parameters, allocates internal storage if needed and cleans the descriptor.
void	setParameters(java.lang.String parameters) Sets the parameters of an already created ScalarDescriptor object.
byte[]	toData() Converts a ScalarDescriptor object into an array of bytes.
java.lang.String	toDecimalString() Converts the descriptor value into a readable string.
float[]	toFloatArray() Creates the float array representation of the descriptor.
java.lang.String	toString() Converts the descriptor value into a readable string.

Methods inherited from class chemaxon.descriptors.MolecularDescriptor

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

Methods inherited from class java.lang.Object

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

Field Detail

descrValue

protected float descrValue

descriptor value

Constructor Detail

ScalarDescriptor

public ScalarDescriptor()

Creates a new, empty instance of ScalarDescriptor.

ScalarDescriptor

public ScalarDescriptor(SDParameters params)

Creates a new instance of ScalarDescriptor according to the parameters given.

Parameters:

params - parameters settings

ScalarDescriptor

public ScalarDescriptor(java.lang.String params)

Creates a new instance of ScalarDescriptor according to the parameters given.

Parameters:

params - parameter string

ScalarDescriptor

public ScalarDescriptor(ScalarDescriptor sd)

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

Parameters:

sd - a ScalarDescriptor to be copied

Method Detail

clone

public MolecularDescriptor clone()

Creates a new instance with identical internal state.

Specified by:

clone in class MolecularDescriptor

Returns:

the newly copied object

getName

public java.lang.String getName()

Gets the name of the ScalarDescriptor object. The name is not the same as the class name, but a nicer, readable and more meaningful for end-users.

Overrides:

getName in class MolecularDescriptor

Returns:

the nice external name for ScalarDescriptor class objects

getShortName

public java.lang.String getShortName()

Gets the short name of the descriptor.

Overrides:

getShortName in class MolecularDescriptor

Returns:

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

getParametersClassName

public java.lang.String getParametersClassName()

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

Overrides:

getParametersClassName in class MolecularDescriptor

Returns:

the name of the parameters class

setParameters

public void setParameters(MDParameters parameters)

Sets parameters, allocates internal storage if needed and cleans the descriptor.

Overrides:

setParameters in class MolecularDescriptor

Parameters:

parameters - fingerprint parameters

setParameters

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

Sets the parameters of an already created ScalarDescriptor object.

Specified by:

setParameters in class MolecularDescriptor

Parameters:

parameters - parameter settings for the descriptor

Throws:

MDParametersException - any XML error

toData

public byte[] toData()

Converts a ScalarDescriptor object into an array of bytes. This format can be reffered to as an "external representation" since it servers as the data format for storing scalar descriptors in databases.
Use the fromData() method to build the scalar descriptor from this "external" representation.

Specified by:

toData in class MolecularDescriptor

Returns:

byte array representation of the descriptor object

fromData

public void fromData(byte[] dbRepr)

Builds a descriptor from an external data format, created by a previous call to toData().

Specified by:

fromData in class MolecularDescriptor

Parameters:

dbRepr - "external" representation of the ScalarDescriptor object

toFloatArray

public final float[] toFloatArray()

Creates the float array representation of the descriptor.

Specified by:

toFloatArray in class MolecularDescriptor

Returns:

a float array of one element

fromFloatArray

public void fromFloatArray(float[] descr)
                    throws java.lang.RuntimeException

Builds the descriptor from a float array of one element.

Specified by:

fromFloatArray in class MolecularDescriptor

Parameters:

descr - descriptor stored in a (one element) float array

Throws:

java.lang.RuntimeException

clear

public void clear()

Clears the descritor: sets its value to zero value.

toString

public final java.lang.String toString()

Converts the descriptor value into a readable string. This is the default external text format.

Specified by:

toString in class MolecularDescriptor

Returns:

string representation of the descriptor value

toDecimalString

public java.lang.String toDecimalString()

Converts the descriptor value into a readable string. This is the default external text format.

Specified by:

toDecimalString in class MolecularDescriptor

Returns:

string representation of the descriptor value

fromString

public final void fromString(java.lang.String sd)
                      throws java.text.ParseException

Builds a descriptpr from its string representation created by toString().

Specified by:

fromString in class MolecularDescriptor

Parameters:

sd - descriptor value as string

Throws:

java.text.ParseException

set

public void set(float newValue)

Set the value of the descriptor.

Parameters:

newValue - the value to be set

generate

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

Creates the ScalarDescriptor descriptor for the given Molecule. Side-effect!!!!!! Standardizes the input molecule (as defined in MDParameters).

Overrides:

generate in class MolecularDescriptor

Returns:

property names set in the molecule passed during generation

Throws:

MDGeneratorException - when failed to generate descriptor

getDissimilarityMetrics

public java.lang.String[] getDissimilarityMetrics()

Gets the dissimilarity metric names

Specified by:

getDissimilarityMetrics in class MolecularDescriptor

Returns:

the metrics array

getDefaultDissimilarityMetricThresholds

public float[] getDefaultDissimilarityMetricThresholds()

Gets the default dissimilarity threshold values for all dissimilarity metrics defined.

Specified by:

getDefaultDissimilarityMetricThresholds in class MolecularDescriptor

Returns:

array of dissimilarity threshold values

getDefaultThreshold

public float getDefaultThreshold(int metricIndex)

Gets a metric dependent default threshold value.

Overrides:

getDefaultThreshold in class MolecularDescriptor

Parameters:

metricIndex - index of a parameterized metric

getDissimilarity

public float getDissimilarity(MolecularDescriptor sd)

Calculates the dissimilarity between two scalar descriptor using the default metrics In the present implementation it is always the absolute difference between them.

Specified by:

getDissimilarity in class MolecularDescriptor

Parameters:

sd - a scalar descriptor value

Returns:

dissimilarity value

getDissimilarity

public float getDissimilarity(MolecularDescriptor sd,
                              int metricIndex)

Calculates the dissimilarity between two scalar descriptor using the specified metric.

Specified by:

getDissimilarity in class MolecularDescriptor

Parameters:

sd - a scalar descriptor

metricIndex - index of the metric to be used

Returns:

the dissimilarity ratio

See Also:

MDParameters, PFParameters

getLowerBound

public float getLowerBound(MolecularDescriptor sd)

Calculates the lower bound estimate of the dissimilarity from the given descriptor.

Overrides:

getLowerBound in class MolecularDescriptor

Parameters:

sd - a descriptor value

Returns:

always returns 0