chemaxon.descriptors

Class ReactionFingerprint

java.lang.Object

chemaxon.descriptors.MolecularDescriptor

chemaxon.descriptors.ReactionFingerprint

All Implemented Interfaces:

java.lang.Cloneable

@PublicAPI
public class ReactionFingerprint
extends MolecularDescriptor

ReactionFingerprint class.

Since:

JChem 3.2

Version:

5.1.2 09/24/2008

Author:

Zsolt Mohacsi

Field Summary

Fields

Modifier and Type	Field and Description
protected int	brightness number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less plausible)
protected int[]	fp storage for the fingerprint

Fields inherited from class chemaxon.descriptors.MolecularDescriptor

params

Constructor Summary

Constructors

Constructor and Description
ReactionFingerprint() Creates a new, empty instance of ReactionFingerprint without allocating internal storage.
ReactionFingerprint(ReactionFingerprint rfp) Copy constructor.
ReactionFingerprint(RFParameters params) Creates a new instance of ReactionFingerprint according to the parameters given.
ReactionFingerprint(java.lang.String params) Creates a new instance of ReactionFingerprint according to the parameters given.

Method Summary

Modifier and Type	Method and Description
void	clear() Clears the fingerprint: sets all bins to store zero value.
ReactionFingerprint	clone() Creates a copy with identical internal state.
void	fromData(byte[] dbRepr) Builds a fingerprint from an external data format, created by a previous call to toData().
void	fromFloatArray(float[] descr) Builds fingerprint from its float array representation.
void	fromString(java.lang.String cfp) Builds a fingerprint from its string representation created by toString().
java.lang.String[]	generate(Molecule m) Creates the ReactionFingerprint descriptor for the given Molecule.
java.util.List<java.lang.String>	getAliasNames()
int	getBrightness() Gets the brightness of the fingerprint.
static int[]	getChemicalHashedFingerprint(int[] reactionFingerprint, int length) Creates chemical hashed fingerpint from reaction fingerprint.
float	getCoarseReactionTanimoto(ReactionFingerprint f) Returns the tanimoto distance of the reaction centers.
int	getCommonBitCount(ReactionFingerprint f)
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.
float	getDissimilarity(MolecularDescriptor fp2) Calculates the dissimilarity between two reaction fingerprints using the default distance measure.
float	getDissimilarity(MolecularDescriptor fp2, int metricIndex) Calculates the dissimilarity between two reaction fingerprints using the specified distance metric.
java.lang.String[]	getDissimilarityMetrics() Gets the dissimilarity metric names
java.lang.String[]	getDissimilarityMetricsParamDefault() Gets the dissimilarity metric parameter names -> no parameters.
java.lang.String[]	getDissimilarityMetricsParamHelp() Gets the dissimilarity metric parameter names -> no parameters.
java.lang.String[]	getDissimilarityMetricsParamNames() Gets the dissimilarity metric parameter names -> no parameters.
int[]	getDissimilarityMetricsParamNum() Gets the dissimilarity metric parameter number -> no parameters.
java.lang.String[]	getDissimilarityMetricsParamRanges() Gets the dissimilarity metric parameter ranges -> no parameters.
float	getLowerBound(MolecularDescriptor fp2) Calculates the lower bound estimate of the dissimilarity from the given fingerprint.
float	getMediumReactionTanimoto(ReactionFingerprint f) Returns the tanimoto distance of the reaction centers and their neighbouring atoms and bonds.
java.lang.String	getName() Gets the nice name of the ReactionFingerprint descriptor object.
java.lang.String	getParametersClassName() Gets the name of the parameters class corresponding to the descriptor.
float	getProductTanimoto(ReactionFingerprint f) Returns the tanimoto distance of the product sides.
float	getReactantTanimoto(ReactionFingerprint f) Returns the tanimoto distance of the reactant sides.
java.lang.String	getShortName() Gets the short name of the descriptor.
float	getStrictReactionTanimoto(ReactionFingerprint f) Returns the tanimoto distance of the reaction centers, their immediate neighbour atoms and bonds, and the neighbours' neighbouring atoms and bonds.
boolean	isReactionMappingIncomplete() Returns true if reaction molecule was not mapped completely during reaction fingerprint generation.
boolean	isSubSetOf(ReactionFingerprint f) Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter.
static void	main(java.lang.String[] argv)
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 ReactionFingerprint object.
java.lang.String	toBinaryString() Converts the fingerprint into a 0,1 string.
byte[]	toData() Converts a reaction fingerprint object into a byte array.
java.lang.String	toDecimalString() Converts the fingerprint into a tab separated string.
float[]	toFloatArray() Creates the float array representation of the fingerprint.
java.lang.String	toString() Converts the fingerprint into a readable string.

Methods inherited from class chemaxon.descriptors.MolecularDescriptor

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

Methods inherited from class java.lang.Object

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

Field Detail

fp

protected int[] fp

storage for the fingerprint

brightness

protected int brightness

number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less plausible)

Constructor Detail

ReactionFingerprint

public ReactionFingerprint()

Creates a new, empty instance of ReactionFingerprint without allocating internal storage.

ReactionFingerprint

public ReactionFingerprint(RFParameters params)

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

Parameters:

params - parameters used in fingerprint generation and handling

ReactionFingerprint

public ReactionFingerprint(java.lang.String params)

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

Parameters:

params - parameter settings

ReactionFingerprint

public ReactionFingerprint(ReactionFingerprint rfp)

Copy constructor. An identical copy of the reaction fingerprint passed is created. The old and the new instances share the same RFParameters object.

Parameters:

rfp - fingerprint to be copied

Method Detail

clone

public ReactionFingerprint clone()

Creates a copy with identical internal state. The new instances share the same RFParameters object with the copied one.

Specified by:

clone in class MolecularDescriptor

Returns:

the newly created object

getName

public java.lang.String getName()

Gets the nice name of the ReactionFingerprint descriptor object. This name is not the same as the class name: it is nicer, and more meaningful for end-users.

Overrides:

getName in class MolecularDescriptor

Returns:

the nice, external name for ReactionFingerprint descriptor class objects

getShortName

public java.lang.String getShortName()

Gets the short name of the descriptor. This name appears in text outputs.

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

getBrightness

public int getBrightness()

Gets the brightness of the fingerprint. Actually, sometimes this is called the darkness. To be precise, this methods gets the numbers of 1 (one) bits in the fingerprint.

Returns:

number of bits set to 1

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 ReactionFingerprint 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 reaction fingerprint object into a byte array. This format can be reffered to as an "external representation" since it servers as the data format for storing fingerprints in databases..
Use the fromData() method to build the fingerprint from this "external" representation.

Specified by:

toData in class MolecularDescriptor

Returns:

byte array representation of the fingerprint object

fromData

public void fromData(byte[] dbRepr)

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

Specified by:

fromData in class MolecularDescriptor

Parameters:

dbRepr - "external" representation of ReactionFingerprint

clear

public final void clear()

Clears the fingerprint: sets all bins to store zero value.

toString

public final java.lang.String toString()

Converts the fingerprint into a readable string. This is the default external text format of the fingerprint, which can also be stored into an SDfile.

Specified by:

toString in class MolecularDescriptor

Returns:

string representation of the fingerprint

toDecimalString

public final java.lang.String toDecimalString()

Converts the fingerprint into a tab separated string.

Specified by:

toDecimalString in class MolecularDescriptor

Returns:

string representation of the fingerprint

toBinaryString

public java.lang.String toBinaryString()

Converts the fingerprint into a 0,1 string.

Overrides:

toBinaryString in class MolecularDescriptor

Returns:

binary string representation of the fingerprint

fromString

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

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

Specified by:

fromString in class MolecularDescriptor

Parameters:

cfp - fingerprint string

Throws:

java.text.ParseException

toFloatArray

public final float[] toFloatArray()

Creates the float array representation of the fingerprint. This array contains all values of the fingerprint (including all zeros) in the elements of the array.

Specified by:

toFloatArray in class MolecularDescriptor

Returns:

a float array representation of the fingerprint

fromFloatArray

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

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

Specified by:

fromFloatArray in class MolecularDescriptor

Parameters:

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

Throws:

java.lang.RuntimeException

generate

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

Creates the ReactionFingerprint descriptor for the given Molecule. Calls the generator created by the corresponding MDParameters class.

Overrides:

generate in class MolecularDescriptor

Returns:

property names set in the molecule passed during generation

Throws:

MDGeneratorException - when failed to generate descriptor

isReactionMappingIncomplete

public boolean isReactionMappingIncomplete()

Returns true if reaction molecule was not mapped completely during reaction fingerprint generation. Should be called after generate(Molecule).

Returns:

true if the reaction molecule was not mapped completely

Since:

JChem 5.1.2

getDissimilarityMetrics

public java.lang.String[] getDissimilarityMetrics()

Gets the dissimilarity metric names

Specified by:

getDissimilarityMetrics in class MolecularDescriptor

Returns:

the metrics array

getDissimilarityMetricsParamNum

public int[] getDissimilarityMetricsParamNum()

Gets the dissimilarity metric parameter number -> no parameters.

Returns:

the metrics array

getDissimilarityMetricsParamNames

public java.lang.String[] getDissimilarityMetricsParamNames()

Gets the dissimilarity metric parameter names -> no parameters.

Returns:

the metrics array

getDissimilarityMetricsParamRanges

public java.lang.String[] getDissimilarityMetricsParamRanges()

Gets the dissimilarity metric parameter ranges -> no parameters.

Returns:

the metrics array

getDissimilarityMetricsParamDefault

public java.lang.String[] getDissimilarityMetricsParamDefault()

Gets the dissimilarity metric parameter names -> no parameters.

Returns:

the metrics array

getDissimilarityMetricsParamHelp

public java.lang.String[] getDissimilarityMetricsParamHelp()

Gets the dissimilarity metric parameter names -> no parameters.

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

getDefaultMetricIndex

public int getDefaultMetricIndex()

Gets the index of the default metric. In the case of this class this is Tanimoto.

Overrides:

getDefaultMetricIndex in class MolecularDescriptor

Returns:

metric index of the default metric

getDefaultThreshold

public float getDefaultThreshold(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.

Overrides:

getDefaultThreshold in class MolecularDescriptor

Parameters:

metricIndex - index of a parameterized metric

getCommonBitCount

public int getCommonBitCount(ReactionFingerprint f)

getReactantTanimoto

public float getReactantTanimoto(ReactionFingerprint f)

Returns the tanimoto distance of the reactant sides.

Parameters:

f - the distance from f is calculated

Returns:

the tanimoto distance (dissimilarity coefficient)

getProductTanimoto

public float getProductTanimoto(ReactionFingerprint f)

Returns the tanimoto distance of the product sides.

Parameters:

f - the distance from f is calculated

Returns:

the tanimoto distance (dissimilarity coefficient)

getCoarseReactionTanimoto

public float getCoarseReactionTanimoto(ReactionFingerprint f)

Returns the tanimoto distance of the reaction centers. The direction of the reaction is considered.

Parameters:

f - the distance from f is calculated

Returns:

the tanimoto distance (dissimilarity coefficient)

getMediumReactionTanimoto

public float getMediumReactionTanimoto(ReactionFingerprint f)

Returns the tanimoto distance of the reaction centers and their neighbouring atoms and bonds. The direction of the reaction is considered.

Parameters:

f - the distance from f is calculated

Returns:

the tanimoto distance (dissimilarity coefficient)

getStrictReactionTanimoto

public float getStrictReactionTanimoto(ReactionFingerprint f)

Returns the tanimoto distance of the reaction centers, their immediate neighbour atoms and bonds, and the neighbours' neighbouring atoms and bonds. The direction of the reaction is considered.

Parameters:

f - the distance from f is calculated

Returns:

the tanimoto distance (dissimilarity coefficient)

getDissimilarity

public float getDissimilarity(MolecularDescriptor fp2)

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

Specified by:

getDissimilarity in class MolecularDescriptor

Parameters:

fp2 - the other reaction fingerprint

Returns:

dissimilarity ratio

getDissimilarity

public float getDissimilarity(MolecularDescriptor fp2,
                              int metricIndex)

Calculates the dissimilarity between two reaction fingerprints using the specified distance metric. The index of the required metric can be obtained by calling getMetricIndex( String metricName ) .
New metrics implemented by this class have to be added at the end of the existing ones.

Specified by:

getDissimilarity in class MolecularDescriptor

Parameters:

fp2 - the reaction fingerprint from which the distance is measured

metricIndex - index of the metric to be used

Returns:

the dissimilarity ratio

See Also:

MDParameters, PFParameters

getLowerBound

public float getLowerBound(MolecularDescriptor fp2)

Calculates the lower bound estimate of the dissimilarity from the given fingerprint. In the case of ReactionFingerprint a good estimate for the minimum distance cannot be obtained efficiently (that is, significantly faster than calculating the proper distance) therefore 0 is returned. This trivial distance bound estimation will lead to calling getDistance.

Overrides:

getLowerBound in class MolecularDescriptor

Parameters:

fp2 - reaction fingerprint from which distance is measured

Returns:

estimate of the minimum distance

isSubSetOf

public boolean isSubSetOf(ReactionFingerprint f)

Checks if this fingerprint is a subset of another fingerprint that is passed as method parameter. A binary fingerprint is considered to be a subset of another if none of its bits is larger than that of the other's.

Parameters:

f - a descriptor which is supposed to be a superset

Returns:

true if this descriptor is a subset of the parameter

getChemicalHashedFingerprint

public static int[] getChemicalHashedFingerprint(int[] reactionFingerprint,
                                                 int length)

Creates chemical hashed fingerpint from reaction fingerprint.

Parameters:

reactionFingerprint - the fingeprint as was generated by ReactionFingerprint, may contain additional data (e.g. structural keys) at the end

length - the length of the FP part in integers to consider (the remainder will be ignored, e.g. structural keys)

Returns:

the chemical hashed fingerprint of the total reaction

main

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

getAliasNames

public java.util.List<java.lang.String> getAliasNames()

Returns:

alias names of the given descriptor in lower case