toxTree.tree.rules

Class InChILookupFile

java.lang.Object

toxTree.tree.rules.InChILookupFile

All Implemented Interfaces:

ILookupFile

public class InChILookupFile
extends Object
implements ILookupFile

In-memory InChI lookup. Should be fine for few hundreds compounds found in bodymol & foodmol.

Author:

nina

Field Summary

Fields

Modifier and Type	Field and Description
protected File	file
protected ambit2.core.processors.structure.InchiProcessor	inchiProcessor
protected List<String>	inchis

Constructor Summary

Constructors

Constructor and Description
InChILookupFile(File file)

Method Summary

Modifier and Type	Method and Description
boolean	find(org.openscience.cdk.interfaces.IAtomContainer mol)
File	getFile()
boolean	isEnabled()
void	readFile()
void	readFileInchi()
static List<String>	readFileSDF(File file, ambit2.core.processors.structure.InchiProcessor inchiProcessor)
void	setFile(File file)
int	size()
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

file

protected File file

inchiProcessor

protected ambit2.core.processors.structure.InchiProcessor inchiProcessor

inchis

protected List<String> inchis

Constructor Detail

InChILookupFile

public InChILookupFile(File file)
                throws IOException,
                       org.openscience.cdk.exception.CDKException

Throws:

IOException

org.openscience.cdk.exception.CDKException

Method Detail

find

public boolean find(org.openscience.cdk.interfaces.IAtomContainer mol)
             throws DecisionMethodException

Specified by:

find in interface ILookupFile

Throws:

DecisionMethodException

readFileInchi

public void readFileInchi()
                   throws Exception

Throws:

Exception

readFile

public void readFile()
              throws Exception

Throws:

Exception

readFileSDF

public static List<String> readFileSDF(File file,
                                       ambit2.core.processors.structure.InchiProcessor inchiProcessor)
                                throws Exception

Throws:

Exception

isEnabled

public boolean isEnabled()

Specified by:

isEnabled in interface ILookupFile

getFile

public File getFile()

Specified by:

getFile in interface ILookupFile

setFile

public void setFile(File file)
             throws IOException

Specified by:

setFile in interface ILookupFile

Throws:

IOException

toString

public String toString()

Overrides:

toString in class Object

size

public int size()

Specified by:

size in interface ILookupFile