ambit2.descriptors

Class PKASmartsDescriptor

java.lang.Object

ambit2.descriptors.PKASmartsDescriptor

All Implemented Interfaces:

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

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

pKa calculation

Adam C. Lee, Jing-yu Yu, and Gordon M. Crippen, pKa Prediction of Monoprotic Small Molecules the SMARTS Way

http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/asap/abs/ci8001815.html

Author:

nina

Field Summary

Fields

Modifier and Type	Field and Description
protected static Logger	logger
protected PKANode	root
static String[]	title
protected Hashtable<Integer,PKANode>	tree

Constructor Summary

Constructors

Constructor and Description
PKASmartsDescriptor()

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainer arg0)
String[]	getDescriptorNames()
org.openscience.cdk.qsar.result.IDescriptorResult	getDescriptorResultType()
String[]	getParameterNames()
Object[]	getParameters()
Object	getParameterType(String arg0)
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()
Hashtable<Integer,PKANode>	getTree()
void	initialise(org.openscience.cdk.interfaces.IChemObjectBuilder arg0)
protected PKANode	initialize()
void	setParameters(Object[] arg0)
protected PKANode	traverse(org.openscience.cdk.interfaces.IAtomContainer ac, PKANode node, ArrayList<String> trace)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static Logger logger

title

public static String[] title

tree

protected Hashtable<Integer,PKANode> tree

root

protected PKANode root

Constructor Detail

PKASmartsDescriptor

public PKASmartsDescriptor()

Method Detail

initialise

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

Specified by:

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

calculate

public org.openscience.cdk.qsar.DescriptorValue calculate(org.openscience.cdk.interfaces.IAtomContainer arg0)

Specified by:

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

getTree

public Hashtable<Integer,PKANode> getTree()

getDescriptorResultType

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

Specified by:

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

getParameterNames

public String[] getParameterNames()

Specified by:

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

getParameterType

public Object getParameterType(String arg0)

Specified by:

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

getParameters

public Object[] getParameters()

Specified by:

getParameters 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

setParameters

public void setParameters(Object[] arg0)
                   throws org.openscience.cdk.exception.CDKException

Specified by:

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

Throws:

org.openscience.cdk.exception.CDKException

traverse

protected PKANode traverse(org.openscience.cdk.interfaces.IAtomContainer ac,
                           PKANode node,
                           ArrayList<String> trace)
                    throws SMARTSException

Throws:

SMARTSException

initialize

protected PKANode initialize()
                      throws IOException

Throws:

IOException

getDescriptorNames

public String[] getDescriptorNames()

Specified by:

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