Package chemaxon.descriptors
Class ReactionFingerprint
- java.lang.Object
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- chemaxon.descriptors.MolecularDescriptor
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- chemaxon.descriptors.ReactionFingerprint
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- All Implemented Interfaces:
Cloneable
@PublicAPI public class ReactionFingerprint extends MolecularDescriptor
ReactionFingerprint
class.- Since:
- JChem 3.2
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Field Summary
Fields Modifier and Type Field 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
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Constructor Summary
Constructors Constructor 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(String params)
Creates a new instance of ReactionFingerprint according to the parameters given.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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 totoData()
.void
fromFloatArray(float[] descr)
Builds fingerprint from its float array representation.void
fromString(String cfp)
Builds a fingerprint from its string representation created bytoString()
.String[]
generate(Molecule m)
Creates the ReactionFingerprint descriptor for the given Molecule.List<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.String[]
getDissimilarityMetrics()
Gets the dissimilarity metric namesString[]
getDissimilarityMetricsParamDefault()
Gets the dissimilarity metric parameter names -> no parameters.String[]
getDissimilarityMetricsParamHelp()
Gets the dissimilarity metric parameter names -> no parameters.String[]
getDissimilarityMetricsParamNames()
Gets the dissimilarity metric parameter names -> no parameters.int[]
getDissimilarityMetricsParamNum()
Gets the dissimilarity metric parameter number -> no parameters.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.String
getName()
Gets the nice name of theReactionFingerprint
descriptor object.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.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()
Returnstrue
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(String[] argv)
void
setParameters(MDParameters parameters)
Sets parameters, allocates internal storage if needed and cleans the descriptor.void
setParameters(String parameters)
Sets the parameters of an already createdReactionFingerprint
object.String
toBinaryString()
Converts the fingerprint into a 0,1 string.byte[]
toData()
Converts a reaction fingerprint object into a byte array.String
toDecimalString()
Converts the fingerprint into a tab separated string.float[]
toFloatArray()
Creates the float array representation of the fingerprint.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
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Constructor Detail
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ReactionFingerprint
public ReactionFingerprint()
Creates a new, empty instance of ReactionFingerprint without allocating internal storage.
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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
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ReactionFingerprint
public ReactionFingerprint(String params)
Creates a new instance of ReactionFingerprint according to the parameters given.- Parameters:
params
- parameter settings
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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 sameRFParameters
object.- Parameters:
rfp
- fingerprint to be copied
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Method Detail
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clone
public ReactionFingerprint clone()
Creates a copy with identical internal state. The new instances share the sameRFParameters
object with the copied one.- Specified by:
clone
in classMolecularDescriptor
- Returns:
- the newly created object
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getName
public String getName()
Gets the nice name of theReactionFingerprint
descriptor object. This name is not the same as the class name: it is nicer, and more meaningful for end-users.- Overrides:
getName
in classMolecularDescriptor
- Returns:
- the nice, external name for ReactionFingerprint descriptor class objects
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getShortName
public String getShortName()
Gets the short name of the descriptor. This name appears in text outputs.- Overrides:
getShortName
in classMolecularDescriptor
- Returns:
- the short name used in text outputs (tables etc.)
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getParametersClassName
public String getParametersClassName()
Gets the name of the parameters class corresponding to the descriptor.- Overrides:
getParametersClassName
in classMolecularDescriptor
- Returns:
- the name of the parameters class
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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
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setParameters
public void setParameters(MDParameters parameters)
Sets parameters, allocates internal storage if needed and cleans the descriptor.- Overrides:
setParameters
in classMolecularDescriptor
- Parameters:
parameters
- fingerprint parameters
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setParameters
public void setParameters(String parameters) throws MDParametersException
Sets the parameters of an already createdReactionFingerprint
object.- Specified by:
setParameters
in classMolecularDescriptor
- Parameters:
parameters
- parameter settings for the descriptor- Throws:
MDParametersException
- any XML error
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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 thefromData()
method to build the fingerprint from this "external" representation.- Specified by:
toData
in classMolecularDescriptor
- Returns:
- byte array representation of the fingerprint object
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fromData
public void fromData(byte[] dbRepr)
Builds a fingerprint from an external data format, created by a previous call totoData()
.- Specified by:
fromData
in classMolecularDescriptor
- Parameters:
dbRepr
- "external" representation of ReactionFingerprint
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clear
public final void clear()
Clears the fingerprint: sets all bins to store zero value.
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toString
public final 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 classMolecularDescriptor
- Returns:
- string representation of the fingerprint
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toDecimalString
public final String toDecimalString()
Converts the fingerprint into a tab separated string.- Specified by:
toDecimalString
in classMolecularDescriptor
- Returns:
- string representation of the fingerprint
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toBinaryString
public String toBinaryString()
Converts the fingerprint into a 0,1 string.- Overrides:
toBinaryString
in classMolecularDescriptor
- Returns:
- binary string representation of the fingerprint
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fromString
public final void fromString(String cfp) throws ParseException
Builds a fingerprint from its string representation created bytoString()
.- Specified by:
fromString
in classMolecularDescriptor
- Parameters:
cfp
- fingerprint string- Throws:
ParseException
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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 classMolecularDescriptor
- Returns:
- a float array representation of the fingerprint
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fromFloatArray
public void fromFloatArray(float[] descr) throws RuntimeException
Builds fingerprint from its float array representation. Typically used when a hypothesis is created.- Specified by:
fromFloatArray
in classMolecularDescriptor
- Parameters:
descr
- fingerprint represented in a float array (e.g. generated bytoFloatArray()
)- Throws:
RuntimeException
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generate
public String[] generate(Molecule m) throws MDGeneratorException
Creates the ReactionFingerprint descriptor for the given Molecule. Calls the generator created by the correspondingMDParameters
class.- Overrides:
generate
in classMolecularDescriptor
- Returns:
- property names set in the molecule passed during generation
- Throws:
MDGeneratorException
- when failed to generate descriptor
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isReactionMappingIncomplete
public boolean isReactionMappingIncomplete()
Returnstrue
if reaction molecule was not mapped completely during reaction fingerprint generation. Should be called aftergenerate(Molecule)
.- Returns:
true
if the reaction molecule was not mapped completely- Since:
- JChem 5.1.2
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getDissimilarityMetrics
public String[] getDissimilarityMetrics()
Gets the dissimilarity metric names- Specified by:
getDissimilarityMetrics
in classMolecularDescriptor
- Returns:
- the metrics array
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getDissimilarityMetricsParamNum
public int[] getDissimilarityMetricsParamNum()
Gets the dissimilarity metric parameter number -> no parameters.- Returns:
- the metrics array
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getDissimilarityMetricsParamNames
public String[] getDissimilarityMetricsParamNames()
Gets the dissimilarity metric parameter names -> no parameters.- Returns:
- the metrics array
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getDissimilarityMetricsParamRanges
public String[] getDissimilarityMetricsParamRanges()
Gets the dissimilarity metric parameter ranges -> no parameters.- Returns:
- the metrics array
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getDissimilarityMetricsParamDefault
public String[] getDissimilarityMetricsParamDefault()
Gets the dissimilarity metric parameter names -> no parameters.- Returns:
- the metrics array
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getDissimilarityMetricsParamHelp
public String[] getDissimilarityMetricsParamHelp()
Gets the dissimilarity metric parameter names -> no parameters.- Returns:
- the metrics array
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getDefaultDissimilarityMetricThresholds
public float[] getDefaultDissimilarityMetricThresholds()
Gets the default dissimilarity threshold values for all dissimilarity metrics defined.- Specified by:
getDefaultDissimilarityMetricThresholds
in classMolecularDescriptor
- Returns:
- array of dissimilarity threshold values
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getDefaultMetricIndex
public int getDefaultMetricIndex()
Gets the index of the default metric. In the case of this class this is Tanimoto.- Overrides:
getDefaultMetricIndex
in classMolecularDescriptor
- Returns:
- metric index of the default metric
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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 classMolecularDescriptor
- Parameters:
metricIndex
- index of a parameterized metric
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getCommonBitCount
public int getCommonBitCount(ReactionFingerprint f)
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getReactantTanimoto
public float getReactantTanimoto(ReactionFingerprint f)
Returns the tanimoto distance of the reactant sides.- Parameters:
f
- the distance fromf
is calculated- Returns:
- the tanimoto distance (dissimilarity coefficient)
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getProductTanimoto
public float getProductTanimoto(ReactionFingerprint f)
Returns the tanimoto distance of the product sides.- Parameters:
f
- the distance fromf
is calculated- Returns:
- the tanimoto distance (dissimilarity coefficient)
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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 fromf
is calculated- Returns:
- the tanimoto distance (dissimilarity coefficient)
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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 fromf
is calculated- Returns:
- the tanimoto distance (dissimilarity coefficient)
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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 fromf
is calculated- Returns:
- the tanimoto distance (dissimilarity coefficient)
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getDissimilarity
public float getDissimilarity(MolecularDescriptor fp2)
Calculates the dissimilarity between two reaction fingerprints using the default distance measure.- Specified by:
getDissimilarity
in classMolecularDescriptor
- Parameters:
fp2
- the other reaction fingerprint- Returns:
- dissimilarity ratio
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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 classMolecularDescriptor
- Parameters:
fp2
- the reaction fingerprint from which the distance is measuredmetricIndex
- index of the metric to be used- Returns:
- the dissimilarity ratio
- See Also:
MDParameters
,PFParameters
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getLowerBound
public float getLowerBound(MolecularDescriptor fp2)
Calculates the lower bound estimate of the dissimilarity from the given fingerprint. In the case ofReactionFingerprint
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 classMolecularDescriptor
- Parameters:
fp2
- reaction fingerprint from which distance is measured- Returns:
- estimate of the minimum distance
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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
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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 endlength
- 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
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main
public static void main(String[] argv)
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