@PublicAPI public class BCUT extends MolecularDescriptor implements chemaxon.license.Licensable
Modifier and Type | Field and Description |
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protected float[][] |
highestEigenvalues |
protected float[][] |
lowestEigenvalues |
params
Constructor and Description |
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BCUT()
Creates a new, empty BCUT descriptor.
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BCUT(BCUT sd)
Copy constructor.
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BCUT(BCUTParameters params)
Creates a new instance according to the parameters.
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BCUT(java.lang.String params)
Creates a new instance according to the parameters.
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Modifier and Type | Method and Description |
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void |
clear()
Clears the descriptor, all values are set to zero.
|
BCUT |
clone()
Creates a new instance with identical internal state.
|
void |
fromData(byte[] dbRepr)
Builds a
BCUT descriptor from an external data format,
created by a previous call to toData() . |
void |
fromFloatArray(float[] descr)
Builds a
BCUT descriptor from its float array representation
(generated by toFloatArray() ). |
void |
fromString(java.lang.String bcut)
Builds a
BCUT descriptor from its string representation
created by toString() . |
java.lang.String[] |
generate(Molecule m)
Creates the BCUT descriptor for the given Molecule.
|
java.util.List<java.lang.String> |
getAliasNames() |
float[] |
getDefaultDissimilarityMetricThresholds()
Gets the default dissimilarity threshold values for all dissimilarity
metrics defined.
|
float |
getDissimilarity(MolecularDescriptor other)
Calculates the dissimilarity ratio between two
BCUT
objects using the current default metric. |
float |
getDissimilarity(MolecularDescriptor other,
int parametrizedMetricIndex)
Calculates the dissimilarity between two
BCUT
objects using the specified metric, apart from that it is the same as
getDissimilarity( final MolecularDescriptor other ) . |
java.lang.String[] |
getDissimilarityMetrics()
Gets the dissimilarity metric names introduced for this class of
MolecularDescriptor . |
float |
getEuclidean(BCUT descr)
Calculates the Euclidean distance.
|
float |
getHighestEigenvalue(int desc,
int index)
Gets the specified highest eigenvalue.
|
float |
getLowestEigenvalue(int desc,
int index)
Gets the specified lowest eigenvalue.
|
java.lang.String |
getName()
Gets the name of the
BCUT descriptor 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.
|
float |
getWeightedEuclidean(BCUT descr)
Calculates the weighted Euclidean distance.
|
boolean |
isLicensed()
Returns information about the licensing of the product.
|
void |
setLicenseEnvironment(java.lang.String env)
Sets the license environment.
|
void |
setParameters(MDParameters parameters)
Sets the parameters of an already created
BCUT object. |
void |
setParameters(java.lang.String parameters)
Sets the parameters of an already created
BCUT object. |
byte[] |
toData()
Converts a
BCUT object into a byte array. |
java.lang.String |
toDecimalString()
Converts the
BCUT descriptor into a tab separated string. |
float[] |
toFloatArray()
Creates the float array representation of a
BCUT descriptor
object. |
java.lang.String |
toString()
Converts the descriptor into a readable string.
|
generate, getAtomSetColors, getAtomSetIndexes, getAtomSetNames, getDefaultMetricIndex, getDefaultThreshold, getDissimilarityMetricIndex, getLowerBound, getMetricIndex, getMetricName, getMetricName, getNumberOfMetrics, getNumberOfWeights, getParameters, getThreshold, getThreshold, main, needsConfig, newInstance, newInstance, newInstanceFromXML, newInstanceSupplier, setScreeningConfiguration, toBinaryString
protected float[][] lowestEigenvalues
protected float[][] highestEigenvalues
public BCUT()
public BCUT(BCUTParameters params)
params
- configuration parameterspublic BCUT(java.lang.String params)
params
- parameter settingspublic BCUT(BCUT sd)
BCUT
passed is created. The old and the new instances share the same
BCUTParameters
object.sd
- BCUT descriptor to be copiedpublic BCUT clone()
clone
in class MolecularDescriptor
public boolean isLicensed()
isLicensed
in interface chemaxon.license.Licensable
public void setLicenseEnvironment(java.lang.String env)
setLicenseEnvironment
in interface chemaxon.license.Licensable
public byte[] toData()
BCUT
object into a byte array.
This format can be reffered to as an "external representation" since
it servers as the data format for storing BCUT descriptors in databases.
fromData()
method to build the BCUT
object from this "external" representation.toData
in class MolecularDescriptor
public void fromData(byte[] dbRepr)
BCUT
descriptor from an external data format,
created by a previous call to toData()
.fromData
in class MolecularDescriptor
dbRepr
- "external" representation of a BCUT
objectpublic java.lang.String getName()
BCUT
descriptor object. This name is
not the same as the class name: nicer, and more meaningful for end-users
too.getName
in class MolecularDescriptor
public java.lang.String getShortName()
getShortName
in class MolecularDescriptor
public void setParameters(java.lang.String parameters) throws MDParametersException
BCUT
object.setParameters
in class MolecularDescriptor
parameters
- parameter settings for the descriptorMDParametersException
- any XML errorpublic void setParameters(MDParameters parameters) throws MDParametersException
BCUT
object.setParameters
in class MolecularDescriptor
parameters
- parameter settings for the descriptorMDParametersException
- any XML errorpublic java.lang.String getParametersClassName()
getParametersClassName
in class MolecularDescriptor
public void clear()
public float getLowestEigenvalue(int desc, int index)
desc
- the index of descriptorindex
- the index of one of the lowest eigenvalues to be
retrieved (0 is the smallest).public float getHighestEigenvalue(int desc, int index)
desc
- the index of descriptorindex
- the index of one of the highest eigenvalues to be
retrieved (0 is the largest)public final void fromString(java.lang.String bcut) throws java.text.ParseException
BCUT
descriptor from its string representation
created by toString()
.fromString
in class MolecularDescriptor
bcut
- BCUT
descriptor stringjava.text.ParseException
public final java.lang.String toString()
BCUT
descriptor, and it is also
the format which is be stored in SDfiles. Lowest eigenvalues are printed
first, and they are comma separated. Lowest and highest eigenvalue are
separated by a semicolon, which is printed if there is at least one
highest eigenvalue calculated (even if no lowest values are needed).toString
in class MolecularDescriptor
public final java.lang.String toDecimalString()
BCUT
descriptor into a tab separated string.toDecimalString
in class MolecularDescriptor
public float[] toFloatArray()
BCUT
descriptor
object.toFloatArray
in class MolecularDescriptor
public void fromFloatArray(float[] descr)
BCUT
descriptor from its float array representation
(generated by toFloatArray()
).
Typically use is hypothesis generation.fromFloatArray
in class MolecularDescriptor
descr
- descriptor represented in a float arraypublic java.lang.String[] generate(Molecule m) throws MDGeneratorException
BCUTParameters
class.generate
in class MolecularDescriptor
MDGeneratorException
- when failed to generate descriptorpublic java.lang.String[] getDissimilarityMetrics()
MolecularDescriptor
.getDissimilarityMetrics
in class MolecularDescriptor
public float[] getDefaultDissimilarityMetricThresholds()
getDefaultDissimilarityMetricThresholds
in class MolecularDescriptor
public final float getEuclidean(BCUT descr)
descr
- another descriptor from which the distance is measuredpublic final float getWeightedEuclidean(BCUT descr)
BCUTParameters
object.descr
- a descriptor from which the distance is measuredpublic float getDissimilarity(MolecularDescriptor other)
BCUT
objects using the current default metric.
Default metric is set in the corresponding BCUTParameters
object by setCurrentParametrizedMetric( int metricIndex )
.
In the case of assymetric distances swapping the two descriptors can
make big difference.getDissimilarity
in class MolecularDescriptor
other
- a descriptor, to which the dissimilarity ratio is measuredpublic float getDissimilarity(MolecularDescriptor other, int parametrizedMetricIndex)
BCUT
objects using the specified metric, apart from that it is the same as
getDissimilarity( final MolecularDescriptor other )
.getDissimilarity
in class MolecularDescriptor
other
- a descriptor, to which the dissimilarity ratio is measuredparametrizedMetricIndex
- the index of the parametrized metric to usedMDParameters
,
BCUTParameters
public java.util.List<java.lang.String> getAliasNames()