ambit2.core.io
Class MDLV2000ReaderExtended

java.lang.Object
  org.openscience.cdk.io.DefaultChemObjectReader
      ambit2.core.io.MDLV2000ReaderExtended

All Implemented Interfaces:

org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectReader

public class MDLV2000ReaderExtended
extends org.openscience.cdk.io.DefaultChemObjectReader

Supports SGroups. Reads a molecule from an MDL MOL or SDF file {cdk.cite DAL92}. An SD files is read into a ChemSequence of ChemModel's. Each ChemModel will contain one Molecule.

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 file 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. cdk.module io cdk.svnrev $Revision: 9684 $

Nested Class Summary

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

org.openscience.cdk.io.IChemObjectReader.Mode

Field Summary

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

mode

Constructor Summary

MDLV2000ReaderExtended()

MDLV2000ReaderExtended(java.io.InputStream in)
Contructs a new MDLReader that can read Molecule from a given InputStream.

MDLV2000ReaderExtended(java.io.InputStream in, org.openscience.cdk.io.IChemObjectReader.Mode mode)

MDLV2000ReaderExtended(java.io.Reader in)
Contructs a new MDLReader that can read Molecule from a given Reader.

MDLV2000ReaderExtended(java.io.Reader in, org.openscience.cdk.io.IChemObjectReader.Mode mode)

Method Summary

boolean	accepts(java.lang.Class classObject)
void	close()
void	customizeJob()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
org.openscience.cdk.io.setting.IOSetting[]	getIOSettings()
org.openscience.cdk.interfaces.IChemObject	read(org.openscience.cdk.interfaces.IChemObject object) Takes an object which subclasses IChemObject, e.g.
void	setReader(java.io.InputStream input)
void	setReader(java.io.Reader input)

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

addChemObjectIOListener, fireFrameRead, fireIOSettingQuestion, removeChemObjectIOListener, setReaderMode

Methods inherited from class java.lang.Object

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

Constructor Detail

MDLV2000ReaderExtended

public MDLV2000ReaderExtended()

MDLV2000ReaderExtended

public MDLV2000ReaderExtended(java.io.InputStream in)

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

Parameters:

in - The InputStream to read from

MDLV2000ReaderExtended

public MDLV2000ReaderExtended(java.io.InputStream in,
                              org.openscience.cdk.io.IChemObjectReader.Mode mode)

MDLV2000ReaderExtended

public MDLV2000ReaderExtended(java.io.Reader in)

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

Parameters:

in - The Reader to read from

MDLV2000ReaderExtended

public MDLV2000ReaderExtended(java.io.Reader in,
                              org.openscience.cdk.io.IChemObjectReader.Mode mode)

Method Detail

getFormat

public org.openscience.cdk.io.formats.IResourceFormat getFormat()

setReader

public void setReader(java.io.Reader input)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

setReader

public void setReader(java.io.InputStream input)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

accepts

public boolean accepts(java.lang.Class classObject)

read

public org.openscience.cdk.interfaces.IChemObject read(org.openscience.cdk.interfaces.IChemObject object)
                                                throws org.openscience.cdk.exception.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:

org.openscience.cdk.exception.CDKException

close

public void close()
           throws java.io.IOException

Throws:

java.io.IOException

customizeJob

public void customizeJob()

getIOSettings

public org.openscience.cdk.io.setting.IOSetting[] getIOSettings()

Specified by:

getIOSettings in interface org.openscience.cdk.io.IChemObjectIO

Overrides:

getIOSettings in class org.openscience.cdk.io.DefaultChemObjectReader