chemaxon.descriptors

Class MolecularDescriptor

java.lang.Object

chemaxon.descriptors.MolecularDescriptor

All Implemented Interfaces:

java.lang.Cloneable

Direct Known Subclasses:

BCUT, ChemicalFingerprint, CustomDescriptor, ECFP, PharmacophoreFingerprint, ReactionFingerprint, ScalarDescriptor, ShapeDescriptor

@PublicAPI
public abstract class MolecularDescriptor
extends java.lang.Object
implements java.lang.Cloneable

Generic definition of molecular descriptors. The MolecularDescriptor class models all kinds of structural keys, fingerprints (hashed, pharmacophoric), MDL keys and many others which can be implemented in derived classes, some of these are implemented in JChem. For the sake of generality the MolecularDescriptor class does not introduce operations that manipulate descriptors on "atomic" level, that is, cells (or bins) of descriptors cannot be accessed either for reading or for writing. This is because cells in various chemical descriptors can have different type (for example bit, integer or floating point value).
Operations between different MolecularDescriptor derivatives are not supported, though for the sake of efficiency no extra type checking is introduced (other than provided by the language itself).
Derived classes should define their own dissimilarity metrics for the sake of efficiency. This is one reason why this class does not define any dissimilarity metric; the other is, that different MolecularDescriptor subclasses may have different representations (for instance integer array vs. float array).

Since:

JChem 2.0

Author:

Miklos Vargyas, Zsuzsanna Szabo, Peter Kovacs (pkovacs84), Adrian Kalaszi

Field Summary

Fields

Modifier and Type	Field and Description
protected MDParameters	params Parameter settings related to the descriptor.

Constructor Summary

Constructors

Constructor and Description
MolecularDescriptor() Default constructor, creates an empty object.
MolecularDescriptor(MDParameters parameters) Creates a new MolecularDescriptor with the given parameters.
MolecularDescriptor(MolecularDescriptor c) Copy constructor, creates am identical copy of the MolecularDescriptor passed as a parameter.

Method Summary

Modifier and Type	Method and Description
abstract MolecularDescriptor	clone() Creates a new instance with identical internal state.
abstract void	fromData(byte[] dbRepr) Builds a MolecularDescriptor object from its external (database) representation.
abstract void	fromFloatArray(float[] descr) Builds a molecular descriptor from its float array representation.
abstract void	fromString(java.lang.String descr) Builds a molecular descriptor from its string representation.
java.lang.String[]	generate(Molecule m) Creates the descriptor for the given Molecule.
java.lang.String[]	generate(java.lang.String molRepr) Creates the descriptor for the given Molecule.
java.awt.Color[]	getAtomSetColors() Determines the coloring of atoms.
int[]	getAtomSetIndexes(Molecule m) Gets the individual atom color indexes.
java.lang.String[]	getAtomSetNames()
abstract float[]	getDefaultDissimilarityMetricThresholds() Gets the default dissimilarity threshold values for all dissimilarity metrics defined.
int	getDefaultMetricIndex() Gets the index of the default metric.
float	getDefaultThreshold(int metricIndex) Gets a metric dependent default threshold value.
abstract float	getDissimilarity(MolecularDescriptor other) Calculates the dissimilarity ratio between two MolecularDescriptor objects using the default metric.
abstract float	getDissimilarity(MolecularDescriptor other, int parametrizedMetricIndex) Calculates the dissimilarity between two MolecularDescriptor objects using the specified metric, apart from that it is the same as getDissimilarity( final MolecularDescriptor other ).
int	getDissimilarityMetricIndex(java.lang.String metricName) Gets the internal index of the given metric.
abstract java.lang.String[]	getDissimilarityMetrics() Gets the dissimilarity metric names in an array.
float	getLowerBound(MolecularDescriptor other) Calculates an estimate for the minimum value of the distance using the default distance metric.
int	getMetricIndex(java.lang.String metricName) Gets the index of the given parameterized metric.
java.lang.String	getMetricName() Gets the name of the current parameterized metric.
java.lang.String	getMetricName(int metricIndex) Gets the name of a metric specified parameterized metric by its index.
java.lang.String	getName() Gets the name of the descriptor.
int	getNumberOfMetrics() Gets the number of parameterized metrics available for the particular descriptor.
int	getNumberOfWeights(java.lang.String dissimilarityMetricName) Gets the number of weight factors used by the specified metric.
MDParameters	getParameters() Gets the parameters associated with the object.
java.lang.String	getParametersClassName() Gets the name of the parameters class corresponding to the descriptor (prefixed with the package name as getClass().getName() would return).
java.lang.String	getShortName() Gets the short name of the descriptor.
float	getThreshold() Gets threshold value of the current parameterized metric.
float	getThreshold(int metricIndex) Gets a metric dependent default threshold value.
static void	main(java.lang.String[] args)
boolean	needsConfig() Indicates if class takes parameters from configuration file.
static MolecularDescriptor	newInstance(java.lang.String descriptorTypeName) Creates a MolecularDescriptor specified by its name.
static MolecularDescriptor	newInstance(java.lang.String descriptorTypeName, java.lang.String parameters) Creates a MolecularDescriptor specified by its name and xml parameter.
static MolecularDescriptor	newInstanceFromXML(java.lang.String parameters) Creates a new MolecularDescriptor instance according to the given parameter string.
static com.google.common.base.Supplier<MolecularDescriptor>	newInstanceSupplier(java.lang.String descriptorTypeName) Creates a Supplier of the specified molecular descriptor.
void	setParameters(MDParameters parameters) Sets the parameters for an already created MolecularDescriptor.
abstract void	setParameters(java.lang.String parameters) Sets the parameters for an already created MolecularDescriptor.
void	setScreeningConfiguration(java.lang.String config) Sets the screening configuration.
java.lang.String	toBinaryString() Creates the binary string representation of a MolecularDescriptor object.
abstract byte[]	toData() Converts the internal (memory) representation of a MolecularDescriptor instance into an external format that can be stored in a database.
abstract java.lang.String	toDecimalString() Creates the string representation of a MolecularDescriptor object.
abstract float[]	toFloatArray() Creates the float array representation of a MolecularDescriptor object.
abstract java.lang.String	toString() Creates the string representation of a MolecularDescriptor object.

Methods inherited from class java.lang.Object

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

Field Detail

params

protected MDParameters params

Parameter settings related to the descriptor. Instances of the MolecularDescriptor class with the same parameter setting share a common MDParameter object, however MolecularDescriptor objects having different parameters are also allowed in the same application. MDParameters can be specialized with inheritance, thus classes derived from MolecularDescriptor are recommended to derive their own MDParameters sub-clusses.

Constructor Detail

MolecularDescriptor

public MolecularDescriptor(MDParameters parameters)

Creates a new MolecularDescriptor with the given parameters.

Parameters:

parameters - parameter settings of the descriptor to be created

Since:

JChem 2.2

MolecularDescriptor

public MolecularDescriptor()

Default constructor, creates an empty object.

MolecularDescriptor

public MolecularDescriptor(MolecularDescriptor c)

Copy constructor, creates am identical copy of the MolecularDescriptor passed as a parameter.

Parameters:

c - a MolecularDescriptor to be copied

Method Detail

newInstance

public static final MolecularDescriptor newInstance(java.lang.String descriptorTypeName,
                                                    java.lang.String parameters)

Creates a MolecularDescriptor specified by its name and xml parameter.

Parameters:

descriptorTypeName - predefined type name or class name If the name doesn't match any of the predefined names, it's assumed that it's a class name parameters xml parameter configuration

Returns:

a new instance of the appropriate MolecularDescriptor

newInstanceSupplier

public static final com.google.common.base.Supplier<MolecularDescriptor> newInstanceSupplier(java.lang.String descriptorTypeName)

Creates a Supplier of the specified molecular descriptor. See newInstance(String).

newInstance

public static final MolecularDescriptor newInstance(java.lang.String descriptorTypeName)

Creates a MolecularDescriptor specified by its name. The descriptor is created with the default parameter settings.

Parameters:

descriptorTypeName - predefined type name or class name If the name does not match any of the predefined names, it is assumed to be a class name

Returns:

a new instance of the appropriate MolecularDescriptor

newInstanceFromXML

public static final MolecularDescriptor newInstanceFromXML(java.lang.String parameters)

Creates a new MolecularDescriptor instance according to the given parameter string. The parameter string is and XML configuration that specifies the type of the MOlecularDescriptor as well as its parmeter settings.

Parameters:

parameters - XML configuration string

Returns:

a new instance of the appropriate MolecularDescriptor

clone

public abstract MolecularDescriptor clone()

Creates a new instance with identical internal state.

Overrides:

clone in class java.lang.Object

Returns:

the newly copied object

getName

public java.lang.String getName()

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

Returns:

the descriptor's name depending on its actual type

getShortName

public java.lang.String getShortName()

Gets the short name of the descriptor.

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 (prefixed with the package name as getClass().getName() would return).

Returns:

the name of the parameters class

setParameters

public void setParameters(MDParameters parameters)

Sets the parameters for an already created MolecularDescriptor.

Parameters:

parameters - parameter settings of the descriptor to be created

setParameters

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

Sets the parameters for an already created MolecularDescriptor.

Parameters:

parameters - parameter settings of the descriptor. If it is null or empty, then the default settings will be used.

Throws:

MDParametersException

getParameters

public MDParameters getParameters()

Gets the parameters associated with the object.

Returns:

parameters settings

needsConfig

public boolean needsConfig()

Indicates if class takes parameters from configuration file. Derived classes have to override this method appropriately.

Returns:

true, most descriptors classes must have a configuration (file)

Since:

JChem 2.2

setScreeningConfiguration

public void setScreeningConfiguration(java.lang.String config)
                               throws MDParametersException

Sets the screening configuration. Overwrites old parameters with the new ones, parameters not affected by the screening configuration remain unchanged.

Parameters:

config - screening configuration string

Throws:

MDParametersException

toData

public abstract byte[] toData()

Converts the internal (memory) representation of a MolecularDescriptor instance into an external format that can be stored in a database.

Returns:

binary representation of the descriptor

fromData

public abstract void fromData(byte[] dbRepr)

Builds a MolecularDescriptor object from its external (database) representation.

Parameters:

dbRepr - an array generated by toData()

toString

public abstract java.lang.String toString()

Creates the string representation of a MolecularDescriptor object. This string value is stored in SDfiles, though the use of this string is not limited to this purpose. Typically, this string is compact, for instance zero values are not necessarily printed.

Overrides:

toString in class java.lang.Object

Returns:

a formatted string of the descriptor

toDecimalString

public abstract java.lang.String toDecimalString()

Creates the string representation of a MolecularDescriptor object. This string value contains all values of the descriptor (including all zeros), values are separated by tabs.

Returns:

a formatted string of the descriptor

toBinaryString

public java.lang.String toBinaryString()

Creates the binary string representation of a MolecularDescriptor object.

Returns:

a 0,1 string of the descriptor

Since:

JChem 2.3

fromString

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

Builds a molecular descriptor from its string representation. Typically used when SDfile is read.

Parameters:

descr - descriptor string, previously generated by toString()

Throws:

java.text.ParseException

toFloatArray

public abstract float[] toFloatArray()

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

Returns:

a formatted float array of the descriptor

Since:

JChem 2.0.1

fromFloatArray

public abstract void fromFloatArray(float[] descr)

Builds a molecular descriptor from its float array representation. Typically used when a hypothesis is created.

Parameters:

descr - descriptor represented in a float array (e.g. generated by toFloatArray())

Since:

JChem 2.0.1

generate

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

Creates the descriptor for the given Molecule.

Returns:

property names set in the molecule passed during generation

Throws:

MDGeneratorException - when failed to generate descriptor

generate

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

Creates the descriptor for the given Molecule.

Parameters:

molRepr - String representation of the molecule eg.: smiles

Returns:

property names set in the molecule passed during generation

Throws:

MDGeneratorException - when failed to generate descriptor

getAtomSetColors

public java.awt.Color[] getAtomSetColors()

Determines the coloring of atoms. This coloring does not reflect element types, instead other categories related to the specific descriptor are considered. Therefore, whenever the parameters are changed, it is advisable to call getAtomSetColors() to obtain the current coloring scheme. Typically, the coloring scheme is defined in the MDParameters object associated with the MolecularDescriptor object.

Returns:

array of colors of different atom categories

getAtomSetNames

public java.lang.String[] getAtomSetNames()

getAtomSetIndexes

public int[] getAtomSetIndexes(Molecule m)

Gets the individual atom color indexes. This allows color mapping and visualization of various properties encoded into the MolecularDescriptor. Prior to this method, getAtomSetColors() has to be called to obtain a color array. This method returns a per atom color index array and the returned indexes refer to to the color array returned by getAtomSetColors.

Parameters:

m - a molecule to assign atom colors to

Returns:

array of color indexes (indexed by atom indexes)

getDissimilarityMetrics

public abstract java.lang.String[] getDissimilarityMetrics()

Gets the dissimilarity metric names in an array.
This method must be overloaded by derived classes in order to get the metrics array depending on the dynamic type. (This is needed because the metrics[] array is a class variable, but class variables are shared among all derived classes.)

Returns:

the metrics array

getDefaultDissimilarityMetricThresholds

public abstract float[] getDefaultDissimilarityMetricThresholds()

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

Returns:

array of dissimilarity threshold values

getDissimilarityMetricIndex

public int getDissimilarityMetricIndex(java.lang.String metricName)
                                throws java.lang.IllegalArgumentException

Gets the internal index of the given metric.

Parameters:

metricName - name of a metric

Returns:

index of the specified metric

Throws:

java.lang.IllegalArgumentException

getNumberOfWeights

public int getNumberOfWeights(java.lang.String dissimilarityMetricName)
                       throws java.lang.IllegalArgumentException

Gets the number of weight factors used by the specified metric. This method can be applied to the dissimilarity metrics provided by the MolecularDescriptor class or its derived classes, but not to parameterized metric.

Parameters:

dissimilarityMetricName - name as returned by getDissimilarityMetrics()

Returns:

number of weights the metric uses

Throws:

java.lang.IllegalArgumentException - if the given parameter is not a valid metric name

getNumberOfMetrics

public int getNumberOfMetrics()

Gets the number of parameterized metrics available for the particular descriptor.

Returns:

number of metrics implemented in this class

getMetricIndex

public int getMetricIndex(java.lang.String metricName)
                   throws java.lang.IllegalArgumentException

Gets the index of the given parameterized metric.

Parameters:

metricName - name of a metric

Returns:

index of the specified metric

Throws:

java.lang.IllegalArgumentException - when given metric name is not valid

getDefaultThreshold

public float getDefaultThreshold(int metricIndex)

Gets a metric dependent default threshold value. The actual value of this wired in parameter is not important, since it is only used in user interfaces to simplify the use of applications for beginners. Note: this method is for compatibility reasons.

Parameters:

metricIndex - index of a parameterized metric

getThreshold

public float getThreshold(int metricIndex)

Gets a metric dependent default threshold value. Ideally, this value should be based on statistics, though the actual value is not too critical, since these are only used in user interfaces to simplify the use of applications for beginners. Note: this method is for compatibility reasons.

Parameters:

metricIndex - index of a parameterized metric

getThreshold

public float getThreshold()

Gets threshold value of the current parameterized metric.

Returns:

threshold value

getMetricName

public java.lang.String getMetricName()

Gets the name of the current parameterized metric.

Returns:

name of the current metric

getMetricName

public java.lang.String getMetricName(int metricIndex)

Gets the name of a metric specified parameterized metric by its index. Note: this method is kept for backward compatibility.

Parameters:

metricIndex - metric index

Returns:

name of the given metric

getDefaultMetricIndex

public int getDefaultMetricIndex()

Gets the index of the default metric. The default metric is one of the available ones that is the most commonly used for the given MolecularDescriptor.

Returns:

metric index of the default metric

getDissimilarity

public abstract float getDissimilarity(MolecularDescriptor other)

Calculates the dissimilarity ratio between two MolecularDescriptor objects using the default metric. Default metric is set in the corresponding MDParameters object. In the case of asymmetric distances swapping the two descriptors can make a big difference.

Parameters:

other - a descriptor, to which the dissimilarity ratio is measured

Returns:

dissimilarity ratio

getDissimilarity

public abstract float getDissimilarity(MolecularDescriptor other,
                                       int parametrizedMetricIndex)

Calculates the dissimilarity between two MolecularDescriptor objects using the specified metric, apart from that it is the same as getDissimilarity( final MolecularDescriptor other ).

Parameters:

other - a descriptor, to which the dissimilarity ratio is measured

parametrizedMetricIndex - the index of the parameterized metric to used

Returns:

dissimilarity ratio

See Also:

MDParameters, PFParameters

getLowerBound

public float getLowerBound(MolecularDescriptor other)

Calculates an estimate for the minimum value of the distance using the default distance metric.

main

public static void main(java.lang.String[] args)