Package org.openscience.cdk.io
Class MDLReader
java.lang.Object
org.openscience.cdk.io.ChemObjectIO
org.openscience.cdk.io.DefaultChemObjectReader
org.openscience.cdk.io.MDLReader
- All Implemented Interfaces:
Closeable
,AutoCloseable
,IChemObjectIO
,IChemObjectReader
,ISimpleChemObjectReader
Deprecated.
Reads a molecule from the original MDL MOL or SDF file [Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]. An SD files
is read into a
IChemSequence
of IChemModel
's. Each ChemModel will contain one
Molecule. If the MDL molfile contains a property block, the MDLV2000Reader
should be
used.
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);
- Author:
- steinbeck, Egon Willighagen
- See Also:
- Source code:
- main
- IO options:
Name Question Default ForceReadAs3DCoordinates Should coordinates always be read as 3D? false - 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
ConstructorsConstructorDescriptionDeprecated.MDLReader
(InputStream in) Deprecated.Constructs a new MDLReader that can read Molecule from a given InputStream.MDLReader
(InputStream in, IChemObjectReader.Mode mode) Deprecated.Deprecated.Constructs a new MDLReader that can read Molecule from a given Reader.MDLReader
(Reader in, IChemObjectReader.Mode mode) Deprecated. -
Method Summary
Modifier and TypeMethodDescriptionboolean
accepts
(Class<? extends IChemObject> classObject) Deprecated.Returns whether the givenIChemObject
can be read or written.void
close()
Deprecated.Closes this IChemObjectIO's resources.void
Deprecated.Deprecated.Returns theIResourceFormat
class for this IO class.<T extends IChemObject>
Tread
(T object) Deprecated.Takes an object which subclasses IChemObject, e.g.void
setReader
(InputStream input) Deprecated.Sets the InputStream from which this ChemObjectReader should read the contents.void
Deprecated.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 Details
-
MDLReader
public MDLReader()Deprecated. -
MDLReader
Deprecated.Constructs a new MDLReader that can read Molecule from a given InputStream.- Parameters:
in
- The InputStream to read from
-
MDLReader
Deprecated. -
MDLReader
Deprecated.Constructs a new MDLReader that can read Molecule from a given Reader.- Parameters:
in
- The Reader to read from
-
MDLReader
Deprecated.
-
-
Method Details
-
getFormat
Deprecated.Description copied from interface:IChemObjectIO
Returns theIResourceFormat
class for this IO class. -
setReader
Deprecated.Description copied from interface:IChemObjectReader
Sets the Reader from which this ChemObjectReader should read the contents.- Throws:
CDKException
-
setReader
Deprecated.Description copied from interface:IChemObjectReader
Sets the InputStream from which this ChemObjectReader should read the contents.- Throws:
CDKException
-
accepts
Deprecated.Description copied from interface:IChemObjectIO
Returns whether the givenIChemObject
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
Deprecated.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
Deprecated.Description copied from interface:IChemObjectIO
Closes this IChemObjectIO's resources.- Throws:
IOException
- when the wrapper IO class cannot be closed.
-
customizeJob
public void customizeJob()Deprecated.
-
MDLV2000Reader
should be used instead. The V2000 reader can actually read files missing the version tag when in relaxed mode.