Package org.openscience.cdk.io

Class MDLRXNV2000Reader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

org.openscience.cdk.io.MDLRXNV2000Reader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

public class MDLRXNV2000Reader
extends DefaultChemObjectReader

Reads a molecule from an MDL RXN file [Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]. This MDL RXN reader uses the MDLV2000Reader to read each mol file.

This reader has two modes: IChemObjectReader.Mode.STRICT and IChemObjectReader.Mode.RELAXED. It defaults to mode RELAXED.

In mode RELAXED it supports an entry for agents on the count line. It also silently accepts any molecular entities that are not declared on the counts line as agents.

In STRICT mode this reader throws a CDKException if

• there is an entry for agents on the counts line or
• the number of molecular entities is greater than the sum of the number of reactants and the number of products (i.e., there are undeclared agents)

Additionally, MDLV2000Reader used for reading the individual molecular entities comes with its own set of constraints when running in STRICT mode.

Author:

Egon Willighagen, Thomas Kuhn, Uli Fechner

This class is affected by these bug(s):

1849923

Source code:

main

Belongs to CDK module:

io

Keywords:

file format, MDL RXN

Created on:

2003-07-24

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader

IChemObjectReader.Mode

Field Summary

Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader

errorHandler, mode

Constructor Summary

Constructors

Constructor	Description
MDLRXNV2000Reader()
MDLRXNV2000Reader(InputStream input)
MDLRXNV2000Reader(InputStream input, IChemObjectReader.Mode mode)
MDLRXNV2000Reader(Reader in)	Constructs a new MDLReader that can read Molecule from a given Reader.
MDLRXNV2000Reader(Reader in, IChemObjectReader.Mode mode)

Method Summary

Modifier and Type	Method	Description
boolean	accepts(Class<? extends IChemObject> classObject)	Returns whether the given IChemObject can be read or written.
boolean	accepts(IChemObject object)
void	close()	Closes this IChemObjectIO's resources.
IResourceFormat	getFormat()	Returns the IResourceFormat class for this IO class.
<T extends IChemObject> T	read(T object)	Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).
void	setReader(InputStream input)	Sets the InputStream from which this ChemObjectReader should read the contents.
void	setReader(Reader input)	Sets the Reader from which this ChemObjectReader should read the contents.

Methods inherited from class org.openscience.cdk.io.DefaultChemObjectReader

fireFrameRead, handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

Methods inherited from class org.openscience.cdk.io.ChemObjectIO

addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.io.IChemObjectIO

addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Constructor Detail

MDLRXNV2000Reader

public MDLRXNV2000Reader(Reader in)

Constructs a new MDLReader that can read Molecule from a given Reader.

Parameters:

in - Reader to read from

MDLRXNV2000Reader

public MDLRXNV2000Reader(Reader in,
                         IChemObjectReader.Mode mode)

MDLRXNV2000Reader

public MDLRXNV2000Reader(InputStream input)

MDLRXNV2000Reader

public MDLRXNV2000Reader(InputStream input,
                         IChemObjectReader.Mode mode)

MDLRXNV2000Reader

public MDLRXNV2000Reader()

Method Detail

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setReader

public void setReader(Reader input)
               throws CDKException

Description copied from interface: IChemObjectReader

Sets the Reader from which this ChemObjectReader should read the contents.

Throws:

CDKException

setReader

public void setReader(InputStream input)
               throws CDKException

Description copied from interface: IChemObjectReader

Sets the InputStream from which this ChemObjectReader should read the contents.

Throws:

CDKException

accepts

public boolean accepts(Class<? extends IChemObject> classObject)

Description copied from interface: IChemObjectIO

Returns whether the given IChemObject can be read or written.

Parameters:

classObject - IChemObject of which is tested if it can be handled.

Returns:

true, if the IChemObject can be handled.

read

public <T extends IChemObject> T read(T object)
                               throws CDKException

Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc). If the specific implementation does not support a specific IChemObject it will throw an Exception.

Parameters:

object - The object that subclasses IChemObject

Returns:

The IChemObject read

Throws:

CDKException - thrown in case the type of provided object is not supported

accepts

public boolean accepts(IChemObject object)

close

public void close()
           throws IOException

Description copied from interface: IChemObjectIO

Closes this IChemObjectIO's resources.

Throws:

IOException - when the wrapper IO class cannot be closed.