ambit2.descriptors

Class AtomEnvironmentMatrixDescriptor

java.lang.Object

ambit2.descriptors.AtomEnvironentMatrix

ambit2.descriptors.AtomEnvironmentMatrixDescriptor

All Implemented Interfaces:

org.openscience.cdk.fingerprint.IFingerprinter, org.openscience.cdk.qsar.IDescriptor, org.openscience.cdk.qsar.IMolecularDescriptor

public class AtomEnvironmentMatrixDescriptor
extends AtomEnvironentMatrix
implements org.openscience.cdk.qsar.IMolecularDescriptor

Author:

Nina Jeliazkova
Modified 2013-4-22

Nested Class Summary

Nested classes/interfaces inherited from class ambit2.descriptors.AtomEnvironentMatrix

AtomEnvironentMatrix._param

Field Summary

Fields inherited from class ambit2.descriptors.AtomEnvironentMatrix

addGenericTypes, atomTypes, descriptorNames, empty, factoryResource, map

Constructor Summary

Constructors

Constructor and Description
AtomEnvironmentMatrixDescriptor()
AtomEnvironmentMatrixDescriptor(org.openscience.cdk.atomtype.IAtomTypeMatcher matcher, String factoryResource, int maxLevels)

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainer container) This method calculates the atom environment of an atom.
String[]	getDescriptorNames()
org.openscience.cdk.qsar.result.IDescriptorResult	getDescriptorResultType()
String[]	getParameterNames() Gets the parameterNames attribute of the AtomHybridizationDescriptor object
Object[]	getParameters()
Object	getParameterType(String arg0)
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()
void	initialise(org.openscience.cdk.interfaces.IChemObjectBuilder arg0)
void	setParameters(Object[] allParams) Sets the parameters attribute of the AtomEnvironmentDescriptor object

Methods inherited from class ambit2.descriptors.AtomEnvironentMatrix

atomTypeToString, doCalculation, getAtm, getAtomFingerprintSize, getAtomType, getAtomTypeFactoryStream, getBitFingerprint, getCountFingerprint, getFactory, getFingerprint, getMaxLevel, getRawFingerprint, getSize, getVersionDescription, initAtomTypes, isAddGenericTypes, setAddGenericTypes, setAtm, setDescriptorNames, setFactory, setMaxLevel

Methods inherited from class java.lang.Object

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

Constructor Detail

AtomEnvironmentMatrixDescriptor

public AtomEnvironmentMatrixDescriptor()
                                throws Exception

Throws:

Exception

AtomEnvironmentMatrixDescriptor

public AtomEnvironmentMatrixDescriptor(org.openscience.cdk.atomtype.IAtomTypeMatcher matcher,
                                       String factoryResource,
                                       int maxLevels)
                                throws Exception

Throws:

Exception

Method Detail

initialise

public void initialise(org.openscience.cdk.interfaces.IChemObjectBuilder arg0)

Specified by:

initialise in interface org.openscience.cdk.qsar.IDescriptor

getSpecification

public org.openscience.cdk.qsar.DescriptorSpecification getSpecification()

Specified by:

getSpecification in interface org.openscience.cdk.qsar.IDescriptor

See Also:

IDescriptor.getSpecification()

getDescriptorResultType

public org.openscience.cdk.qsar.result.IDescriptorResult getDescriptorResultType()

Specified by:

getDescriptorResultType in interface org.openscience.cdk.qsar.IMolecularDescriptor

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the AtomHybridizationDescriptor object

Specified by:

getParameterNames in interface org.openscience.cdk.qsar.IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String arg0)

Specified by:

getParameterType in interface org.openscience.cdk.qsar.IDescriptor

See Also:

IDescriptor.getParameterType(java.lang.String)

setParameters

public void setParameters(Object[] allParams)
                   throws org.openscience.cdk.exception.CDKException

Sets the parameters attribute of the AtomEnvironmentDescriptor object

Specified by:

setParameters in interface org.openscience.cdk.qsar.IDescriptor

Parameters:

params - - parameters, as below params[0] MaxLevel, optional , default 3 params[1] perceiveCyclicAtoms, optional , default false params[2] AtomTypeFactory factory, optional, default AtomTypeFactory.getInstance( "org/openscience/cdk/dict/data/sybyl-atom-types.owl") params[3] AtomTypeMatcher atm, optional , default HybridizationStateATMatcher

Throws:

org.openscience.cdk.exception.CDKException

getParameters

public Object[] getParameters()

Specified by:

getParameters in interface org.openscience.cdk.qsar.IDescriptor

See Also:

IDescriptor.getParameters()

calculate

public org.openscience.cdk.qsar.DescriptorValue calculate(org.openscience.cdk.interfaces.IAtomContainer container)

This method calculates the atom environment of an atom.

Specified by:

calculate in interface org.openscience.cdk.qsar.IMolecularDescriptor

Parameters:

container - Parameter is the atom container.

Returns:

int[]

Throws:

org.openscience.cdk.exception.CDKException - Description of the Exception

getDescriptorNames

public String[] getDescriptorNames()

Specified by:

getDescriptorNames in interface org.openscience.cdk.qsar.IDescriptor

Overrides:

getDescriptorNames in class AtomEnvironentMatrix