ambit2.descriptors

Class AtomEnvironentMatrix

java.lang.Object

ambit2.descriptors.AtomEnvironentMatrix

All Implemented Interfaces:

org.openscience.cdk.fingerprint.IFingerprinter

Direct Known Subclasses:

AtomEnvironmentMatrixDescriptor

public class AtomEnvironentMatrix
extends Object
implements org.openscience.cdk.fingerprint.IFingerprinter

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AtomEnvironentMatrix._param

Field Summary

Fields

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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
String	atomTypeToString(int index)
HashIntDescriptorResult	doCalculation(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
org.openscience.cdk.atomtype.IAtomTypeMatcher	getAtm()
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()
org.openscience.cdk.fingerprint.IBitFingerprint	getBitFingerprint(org.openscience.cdk.interfaces.IAtomContainer container)
org.openscience.cdk.fingerprint.ICountFingerprint	getCountFingerprint(org.openscience.cdk.interfaces.IAtomContainer container)
String[]	getDescriptorNames()
org.openscience.cdk.config.AtomTypeFactory	getFactory()
BitSet	getFingerprint(org.openscience.cdk.interfaces.IAtomContainer container)
int	getMaxLevel()
Map<String,Integer>	getRawFingerprint(org.openscience.cdk.interfaces.IAtomContainer container)
int	getSize()
String	getVersionDescription()
protected String[]	initAtomTypes(org.openscience.cdk.config.AtomTypeFactory factory, org.openscience.cdk.atomtype.IAtomTypeMatcher atm)
boolean	isAddGenericTypes()
void	setAddGenericTypes(boolean addGenericTypes)
void	setAtm(org.openscience.cdk.atomtype.IAtomTypeMatcher atm)
void	setDescriptorNames(String[] descriptorNames)
void	setFactory(org.openscience.cdk.config.AtomTypeFactory factory)
void	setMaxLevel(int maxLevel)

Methods inherited from class java.lang.Object

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

Field Detail

factoryResource

protected String factoryResource

addGenericTypes

protected boolean addGenericTypes

empty

protected boolean empty

map

protected TreeMap<String,Integer> map

descriptorNames

protected String[] descriptorNames

atomTypes

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

Constructor Detail

AtomEnvironentMatrix

public AtomEnvironentMatrix()
                     throws Exception

Throws:

Exception

AtomEnvironentMatrix

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

Throws:

Exception

Method Detail

isAddGenericTypes

public boolean isAddGenericTypes()

setAddGenericTypes

public void setAddGenericTypes(boolean addGenericTypes)

getMaxLevel

public int getMaxLevel()

setMaxLevel

public void setMaxLevel(int maxLevel)

getDescriptorNames

public String[] getDescriptorNames()

setDescriptorNames

public void setDescriptorNames(String[] descriptorNames)

getAtm

public org.openscience.cdk.atomtype.IAtomTypeMatcher getAtm()

setAtm

public void setAtm(org.openscience.cdk.atomtype.IAtomTypeMatcher atm)

getFactory

public org.openscience.cdk.config.AtomTypeFactory getFactory()

setFactory

public void setFactory(org.openscience.cdk.config.AtomTypeFactory factory)

doCalculation

public HashIntDescriptorResult 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

initAtomTypes

protected String[] initAtomTypes(org.openscience.cdk.config.AtomTypeFactory factory,
                                 org.openscience.cdk.atomtype.IAtomTypeMatcher atm)
                          throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

getAtomTypeFactoryStream

protected InputStream getAtomTypeFactoryStream()

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)

getAtomType

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

getBitFingerprint

public org.openscience.cdk.fingerprint.IBitFingerprint getBitFingerprint(org.openscience.cdk.interfaces.IAtomContainer container)
                                                                  throws org.openscience.cdk.exception.CDKException

Specified by:

getBitFingerprint in interface org.openscience.cdk.fingerprint.IFingerprinter

Throws:

org.openscience.cdk.exception.CDKException

getCountFingerprint

public org.openscience.cdk.fingerprint.ICountFingerprint getCountFingerprint(org.openscience.cdk.interfaces.IAtomContainer container)
                                                                      throws org.openscience.cdk.exception.CDKException

Specified by:

getCountFingerprint in interface org.openscience.cdk.fingerprint.IFingerprinter

Throws:

org.openscience.cdk.exception.CDKException

getRawFingerprint

public Map<String,Integer> getRawFingerprint(org.openscience.cdk.interfaces.IAtomContainer container)
                                      throws org.openscience.cdk.exception.CDKException

Specified by:

getRawFingerprint in interface org.openscience.cdk.fingerprint.IFingerprinter

Throws:

org.openscience.cdk.exception.CDKException

getSize

public int getSize()

Specified by:

getSize in interface org.openscience.cdk.fingerprint.IFingerprinter

getFingerprint

public BitSet getFingerprint(org.openscience.cdk.interfaces.IAtomContainer container)
                      throws org.openscience.cdk.exception.CDKException

Specified by:

getFingerprint in interface org.openscience.cdk.fingerprint.IFingerprinter

Throws:

org.openscience.cdk.exception.CDKException

getVersionDescription

public String getVersionDescription()

Specified by:

getVersionDescription in interface org.openscience.cdk.fingerprint.IFingerprinter