Package org.openscience.cdk.io
Class MDLV3000Reader
java.lang.Object
org.openscience.cdk.io.ChemObjectIO
org.openscience.cdk.io.DefaultChemObjectReader
org.openscience.cdk.io.MDLV3000Reader
- All Implemented Interfaces:
Closeable
,AutoCloseable
,IChemObjectIO
,IChemObjectReader
,ISimpleChemObjectReader
Class that implements the MDL mol V3000 format. This reader reads the
element symbol and 2D or 3D coordinates from the ATOM block.
- Author:
- Egon Willighagen <egonw@users.sf.net>
- Source code:
- main
- IO options:
Name Question Default AddStereo0d Allow stereo created from parity value when no coordinates true AddStereoElements Detect and create IStereoElements for the input. true InterpretHydrogenIsotopes Should D and T be interpreted as hydrogen isotopes? true ForceReadAs3DCoordinates Should coordinates always be read as 3D? false - Belongs to CDK module:
- io
- Keywords:
- MDL molfile V3000
- Created on:
- 2006
- Requires:
- java1.4+
-
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
ConstructorsConstructorDescriptionMDLV3000Reader
(InputStream input) MDLV3000Reader
(InputStream input, IChemObjectReader.Mode mode) MDLV3000Reader
(Reader in) MDLV3000Reader
(Reader in, IChemObjectReader.Mode mode) -
Method Summary
Modifier and TypeMethodDescriptionboolean
accepts
(Class<? extends IChemObject> classObject) Returns whether the givenIChemObject
can be read or written.void
close()
Closes this IChemObjectIO's resources.exhaustStringTokenizer
(StringTokenizer tokenizer) Returns theIResourceFormat
class for this IO class.boolean
isReady()
<T extends IChemObject>
Tread
(T object) Reads an IChemObject of type "object" from input.void
readAtomBlock
(org.openscience.cdk.io.MDLV3000Reader.ReadState state) Reads the atoms, coordinates and charges.void
readBondBlock
(IAtomContainer readData) Reads the bond atoms, order and stereo configuration.readConnectionTable
(IChemObjectBuilder builder) readHeader
(org.openscience.cdk.io.MDLV3000Reader.ReadState state) readLine()
readMolecule
(IChemObjectBuilder builder) void
readSGroup
(IAtomContainer readData) Reads labels.void
setReader
(InputStream input) Sets the InputStream from which this ChemObjectReader should read the contents.void
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
-
MDLV3000Reader
-
MDLV3000Reader
-
MDLV3000Reader
-
MDLV3000Reader
-
MDLV3000Reader
public MDLV3000Reader()
-
-
Method Details
-
getFormat
Description copied from interface:IChemObjectIO
Returns theIResourceFormat
class for this IO class. -
setReader
Description copied from interface:IChemObjectReader
Sets the Reader from which this ChemObjectReader should read the contents.- Throws:
CDKException
-
setReader
Description copied from interface:IChemObjectReader
Sets the InputStream from which this ChemObjectReader should read the contents.- Throws:
CDKException
-
accepts
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
Description copied from interface:ISimpleChemObjectReader
Reads an IChemObject of type "object" from input. The constructor of the actual implementation may take a Reader as input to get a very flexible reader that can read from string, files, etc.- Parameters:
object
- the type of object to return- Returns:
- returns an object of that contains the content (or part) of the input content
- Throws:
CDKException
- it is thrown if the type of information is not available from the input
-
readMolecule
- Throws:
CDKException
-
readConnectionTable
- Throws:
CDKException
-
readHeader
- Returns:
- Last line read
- Throws:
CDKException
- when no file content is detected
-
readAtomBlock
public void readAtomBlock(org.openscience.cdk.io.MDLV3000Reader.ReadState state) throws CDKException Reads the atoms, coordinates and charges.IMPORTANT: it does not support the atom list and its negation!
- Throws:
CDKException
-
readBondBlock
Reads the bond atoms, order and stereo configuration.- Throws:
CDKException
-
readSGroup
Reads labels.- Throws:
CDKException
-
exhaustStringTokenizer
-
readLine
- Throws:
CDKException
-
isReady
- Throws:
CDKException
-
close
Description copied from interface:IChemObjectIO
Closes this IChemObjectIO's resources.- Throws:
IOException
- when the wrapper IO class cannot be closed.
-