chemaxon.descriptors

Class CustomDescriptor

java.lang.Object

chemaxon.descriptors.MolecularDescriptor

chemaxon.descriptors.CustomDescriptor

All Implemented Interfaces:

java.lang.Cloneable

@PublicAPI
public class CustomDescriptor
extends MolecularDescriptor

The CustomDescriptor class implements a generic molecular descriptor class which supports third party or use defined descriptors. Such descriptors can be used throughout the entire JChem system as any other MolecularDescriptor with only one exception: they cannot be generated by this class, they must be provided by the user of this class. CustomDescriptor supports the management (storage/retrival) and dissimilarity calculations of such descriptors. These descriptors can have three distinct types: float, int or binary, their dimension is not limited. All metrics implemented in the Metrics class are supported and can be optimized.

Since:

JChem 2.3

Author:

Miklos Vargyas

Field Summary

Fields

Modifier and Type	Field and Description
protected float[]	floatDescr storage for the floating point descriptors
protected int[]	intDescr storage for the integer or binary descriptors

Fields inherited from class chemaxon.descriptors.MolecularDescriptor

params

Constructor Summary

Constructors

Constructor and Description
CustomDescriptor() Creates a new, empty instance of CustomDescriptor without allocating internal storage for its value.
CustomDescriptor(CDParameters params) Creates a new instance of CustomDescriptor according to the parameters given.
CustomDescriptor(CustomDescriptor cd) Copy constructor.
CustomDescriptor(int type, int length) Creates a new, empty instance of CustomDescriptor and allocates internal storage to store values.
CustomDescriptor(java.lang.String params) Creates a new instance of CustomDescriptor according to the parameters given.

Method Summary

Modifier and Type	Method and Description
void	clear() Clears the descriptor: sets all cells to store zero value.
CustomDescriptor	clone() Creates a new instance with identical internal state.
void	fromData(byte[] dbRepr) Builds a CustomDescriptor from an external data format, created by a previous call to toData().
void	fromFloatArray(float[] descr) Builds a molecular descriptor from its float array representation.
void	fromString(java.lang.String descr) Builds a descriptor from its string representation created by toString().
float	getAsymmetricEuclidean(CustomDescriptor f) Calculates the asymmetric Euclidean distance.
int	getBit(int cell)
float[]	getDefaultDissimilarityMetricThresholds() Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
float	getDissimilarity(MolecularDescriptor descr) Calculates the dissimilarity between two pharmacophore fingerprints using the default distance measure.
float	getDissimilarity(MolecularDescriptor descr, int metricIndex) Calculates the dissimilarity between two descriptors using the specified parametrized dissimilarity metric.
java.lang.String[]	getDissimilarityMetrics() Gets the dissimilarity metric names.
float	getEuclidean(CustomDescriptor f) Calculates the Euclidean distance.
float	getFloat(int cell)
int	getInt(int cell)
java.lang.String	getName() Gets the name of the CustomDescriptor object.
java.lang.String	getParametersClassName() Gets the name of the parameters class corresponding to the descriptor.
float	getScaledTanimoto(CustomDescriptor f) Gets the Tanimoto dissimilarity coefficient.
java.lang.String	getShortName() Gets the short name of the descriptor.
float	getTanimoto(CustomDescriptor f) Gets the Tanimoto dissimilarity coefficient.
float	getWeightedAsymmetricEuclidean(CustomDescriptor f) Calculates the weighted asymmetric Euclidean distance.
float	getWeightedEuclidean(CustomDescriptor f) Calculates the weighted Euclidean distance.
void	set(int cell, float value) Sets the value of one cell of the descriptor.
void	set(int cell, float[] values) Sets values of the descriptor.
void	set(int cell, int value) Sets the value of one cell of the descriptor.
void	set(int cell, int[] values) Sets values of the descriptor.
void	setParameters(CDParameters parameters) Sets parameters, allocates internal storage if needed and clears the descriptor.
void	setParameters(java.lang.String parameters) Sets the parameters of an already created CustomDescriptor object.
byte[]	toData() Converts a CustomDescriptor object into a byte array.
java.lang.String	toDecimalString() Converts the descriptor into a readable string of decimal numbers (float or integer, depending on descriptor type).
float[]	toFloatArray() Creates the float array representation of a CustomDescriptor object.
java.lang.String	toString() Converts the descriptor into a readable string.

Methods inherited from class chemaxon.descriptors.MolecularDescriptor

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

Methods inherited from class java.lang.Object

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

Field Detail

floatDescr

protected float[] floatDescr

storage for the floating point descriptors

intDescr

protected int[] intDescr

storage for the integer or binary descriptors

Constructor Detail

CustomDescriptor

public CustomDescriptor()

Creates a new, empty instance of CustomDescriptor without allocating internal storage for its value.

CustomDescriptor

public CustomDescriptor(int type,
                        int length)

Creates a new, empty instance of CustomDescriptor and allocates internal storage to store values.

Parameters:

type - type of each cell of the descriptor (binary, int, float)

length - size (dimension) of the descriptor

CustomDescriptor

public CustomDescriptor(CDParameters params)

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

Parameters:

params - parameter configuration

CustomDescriptor

public CustomDescriptor(java.lang.String params)

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

Parameters:

params - parameter configuration (XML) string

CustomDescriptor

public CustomDescriptor(CustomDescriptor cd)

Copy constructor. An identical copy of the CustomDescriptor object passed is created. The original and the copy share the same CDParameters object.

Parameters:

cd - descriptor object to be copied

Method Detail

clone

public CustomDescriptor 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 CustomDescriptor object. This name is not the same as the class name, it is nicer, more readable and meaningful for end-users too.

Overrides:

getName in class MolecularDescriptor

Returns:

the nice, external name for CCustomDescriptor 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(CDParameters parameters)

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

Parameters:

parameters - descriptor parameters

setParameters

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

Sets the parameters of an already created CustomDescriptor 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 CustomDescriptor object into a byte array. This format can be reffered to as an "external representation" since it servers for storing fingerprints in databases.
Use the fromData() method to build the object 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 CustomDescriptor from an external data format, created by a previous call to toData().

Specified by:

fromData in class MolecularDescriptor

Parameters:

dbRepr - "external" representation of CustomDescriptor

set

public void set(int cell,
                float[] values)

Sets values of the descriptor.

Parameters:

cell - the index of the first cell (dimension) to be modified

values - new values to be stored

set

public void set(int cell,
                float value)

Sets the value of one cell of the descriptor.

Parameters:

cell - the index of the first cell to be modified

value - new value to be stored

set

public void set(int cell,
                int[] values)

Sets values of the descriptor. This method is used in the case of integer and binary descriptors.

Parameters:

cell - the index of the first cell (dimension) to be modified

values - new values to be stored

set

public void set(int cell,
                int value)

Sets the value of one cell of the descriptor.

Parameters:

cell - the index of the first cell to be modified

value - new value to be stored

getBit

public int getBit(int cell)

getInt

public int getInt(int cell)

getFloat

public float getFloat(int cell)

clear

public void clear()

Clears the descriptor: sets all cells to store zero value.

toString

public java.lang.String toString()

Converts the descriptor into a readable string. This is the default external text format of any CustomDescriptor.

Specified by:

toString in class MolecularDescriptor

Returns:

string representation of the descriptor

toDecimalString

public java.lang.String toDecimalString()

Converts the descriptor into a readable string of decimal numbers (float or integer, depending on descriptor type).

Specified by:

toDecimalString in class MolecularDescriptor

Returns:

string representation of the descriptor

fromString

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

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

Specified by:

fromString in class MolecularDescriptor

Parameters:

descr - a custom descriptor string of decimal values

Throws:

java.text.ParseException

toFloatArray

public float[] toFloatArray()

Creates the float array representation of a CustomDescriptor object. This array contains all values of the descriptor (including all zeros) in the elements of the array.

Specified by:

toFloatArray in class MolecularDescriptor

Returns:

float array of the descriptor cells

fromFloatArray

public void fromFloatArray(float[] descr)

Builds a molecular descriptor from its float array representation.

Specified by:

fromFloatArray in class MolecularDescriptor

Parameters:

descr - descriptor represented in a float array

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

getTanimoto

public float getTanimoto(CustomDescriptor f)

Gets the Tanimoto dissimilarity coefficient.

Parameters:

f - the descriptor form which distance is measured

Returns:

dissimilarity coefficient

getScaledTanimoto

public float getScaledTanimoto(CustomDescriptor f)

Gets the Tanimoto dissimilarity coefficient. Both scale factor and the scaling hypothesis is stored in the corresponding CDParameters object.

Parameters:

f - the descriptor form which distance is measured

Returns:

dissimilarity coefficient

getEuclidean

public float getEuclidean(CustomDescriptor f)

Calculates the Euclidean distance. The dissimilarity coefficient returned ranges from 0 to MAX_FLOAT, this coefficient is not normalized.

Parameters:

f - another fingerprint from which the distance is measured

Returns:

euclidean distance of the two descriptors

getAsymmetricEuclidean

public float getAsymmetricEuclidean(CustomDescriptor f)

Calculates the asymmetric Euclidean distance. This metric is often referred to as directed Euclidean. The dissimilarity coefficient returned ranges from 0 to MAX_FLOAT, this coefficient is not normalized. Asymmetry factor is stored in the corresponding CDParameters object.

Parameters:

f - another fingerprint from which the distance is measured

Returns:

asymmetric euclidean distance of the two descriptors

getWeightedEuclidean

public float getWeightedEuclidean(CustomDescriptor f)

Calculates the weighted Euclidean distance. Weights are taken from the associated CDParameters object.

Parameters:

f - a fingerprint from which the distance is measured

Returns:

weighted euclidean distance of the two descriptors

getWeightedAsymmetricEuclidean

public float getWeightedAsymmetricEuclidean(CustomDescriptor f)

Calculates the weighted asymmetric Euclidean distance. Weights and asymmetry ratio are taken from the associated CDParameters object.

Parameters:

f - a fingerprint from which the distance is measured

Returns:

weighted asymmetric euclidean distance of the two descriptors

getDissimilarity

public float getDissimilarity(MolecularDescriptor descr)

Calculates the dissimilarity between two pharmacophore fingerprints using the default distance measure.

Specified by:

getDissimilarity in class MolecularDescriptor

Parameters:

descr - the other descriptor

Returns:

dissimilarity ratio

getDissimilarity

public float getDissimilarity(MolecularDescriptor descr,
                              int metricIndex)

Calculates the dissimilarity between two descriptors using the specified parametrized dissimilarity metric.

Specified by:

getDissimilarity in class MolecularDescriptor

Parameters:

descr - the descriptor from which the distance is measured

metricIndex - index of the parametrized metric to be used

Returns:

the dissimilarity ratio

See Also:

MDParameters, PFParameters