org.openscience.cdk.io

Class MDLV2000Reader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

org.openscience.cdk.io.MDLV2000Reader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

public class MDLV2000Reader
extends DefaultChemObjectReader

Reads content from MDL molfiles and SD files. It can read a IAtomContainer or IChemModel from an MDL molfile, and a IChemFile from a SD file, with a IChemSequence of IChemModel's, where each IChemModel will contain one IAtomContainer.

From the Atom block it reads atomic coordinates, element types and formal charges. From the Bond block it reads the bonds and the orders. Additionally, it reads 'M CHG', 'G ', 'M RAD' and 'M ISO' lines from the property block.

If all z coordinates are 0.0, then the xy coordinates are taken as 2D, otherwise the coordinates are read as 3D.

The title of the MOL file is read and can be retrieved with:

   molecule.getProperty(CDKConstants.TITLE);
 

RGroups which are saved in the MDL molfile as R#, are renamed according to their appearance, e.g. the first R# is named R1. With PseudAtom.getLabel() "R1" is returned (instead of R#). This is introduced due to the SAR table generation procedure of Scitegics PipelinePilot.

Author:

steinbeck, Egon Willighagen

This class is affected by these bug(s):

1587283

Source code:

master

IO options:

Name	Question	Default
ForceReadAs3DCoordinates	Should coordinates always be read as 3D?	false
AddStereoElements	Detect and create IStereoElements for the input.	true
InterpretHydrogenIsotopes	Should D and T be interpreted as hydrogen isotopes?	true

Belongs to CDK module:

io

Keywords:

file format, MDL molfile, file format, SDF

Created on:

2000-10-02

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 and Description
MDLV2000Reader()
MDLV2000Reader(InputStream in) Constructs a new MDLReader that can read Molecule from a given InputStream.
MDLV2000Reader(InputStream in, IChemObjectReader.Mode mode)
MDLV2000Reader(Reader in) Constructs a new MDLReader that can read Molecule from a given Reader.
MDLV2000Reader(Reader in, IChemObjectReader.Mode mode)

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class<? extends IChemObject> classObject)
void	close()
void	customizeJob()
IResourceFormat	getFormat()
<T extends IChemObject> T	read(T object) Takes an object which subclasses IChemObject, e.g.
void	setReader(InputStream input)
void	setReader(Reader input)

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

MDLV2000Reader

public MDLV2000Reader()

MDLV2000Reader

public MDLV2000Reader(InputStream in)

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

Parameters:

in - The InputStream to read from

MDLV2000Reader

public MDLV2000Reader(InputStream in,
                      IChemObjectReader.Mode mode)

MDLV2000Reader

public MDLV2000Reader(Reader in)

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

Parameters:

in - The Reader to read from

MDLV2000Reader

public MDLV2000Reader(Reader in,
                      IChemObjectReader.Mode mode)

Method Detail

getFormat

public IResourceFormat getFormat()

setReader

public void setReader(Reader input)
               throws CDKException

Throws:

CDKException

setReader

public void setReader(InputStream input)
               throws CDKException

Throws:

CDKException

accepts

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

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

close

public void close()
           throws IOException

Throws:

IOException

customizeJob

public void customizeJob()