ambit2.descriptors

Class AtomEnvironmentDescriptor

java.lang.Object

ambit2.descriptors.AtomEnvironmentDescriptor

All Implemented Interfaces:

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

public class AtomEnvironmentDescriptor
extends Object
implements org.openscience.cdk.qsar.IMolecularDescriptor

implements atom environment fingerprint following Xing, L., Glen, R.C. Novel Methods for the prediction of logger P, pKa and log D. J. Chem. Inf. Comput. Sci. 2002, 42, 796-805

Author:

Nina Jeliazkova
Modified 2005-6-15

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AtomEnvironmentDescriptor._param

Field Summary

Fields

Modifier and Type	Field and Description
protected org.openscience.cdk.interfaces.IAtomType[]	atomTypes
protected boolean	empty
protected TreeMap<String,Integer>	map

Constructor Summary

Constructors

Constructor and Description
AtomEnvironmentDescriptor()

Method Summary

Modifier and Type	Method and Description
String	atomTypeToString(int index)
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainer container) This method calculates the atom environment of an atom.
int[][]	doCalculation(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
int	getAtomFingerprintSize() to hold counts of all atom types defined by factory for maxlevel and one additional entry for undefined atom types
org.openscience.cdk.interfaces.IAtomType	getAtomType(int index)
protected InputStream	getAtomTypeFactoryStream()
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 java.lang.Object

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

Field Detail

empty

protected boolean empty

atomTypes

protected org.openscience.cdk.interfaces.IAtomType[] atomTypes

map

protected TreeMap<String,Integer> map

Constructor Detail

AtomEnvironmentDescriptor

public AtomEnvironmentDescriptor()

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

getAtomFingerprintSize

public int getAtomFingerprintSize()

to hold counts of all atom types defined by factory for maxlevel and one additional entry for undefined atom types

Returns:

atomTypeToString

public String atomTypeToString(int index)

doCalculation

public int[][] doCalculation(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
                      throws org.openscience.cdk.exception.CDKException

Parameters:

arg0 -

result - result[i] contains the level at which ith atom is from the current atom (one set by setParameters)

Throws:

org.openscience.cdk.exception.CDKException

getAtomTypeFactoryStream

protected InputStream getAtomTypeFactoryStream()

getAtomType

public org.openscience.cdk.interfaces.IAtomType getAtomType(int index)