Package org.openscience.cdk.io
Class SMILESReader
java.lang.Object
org.openscience.cdk.io.ChemObjectIO
org.openscience.cdk.io.DefaultChemObjectReader
org.openscience.cdk.io.SMILESReader
- All Implemented Interfaces:
Closeable
,AutoCloseable
,IChemObjectIO
,IChemObjectReader
,ISimpleChemObjectReader
This Reader reads files which has one SMILES string on each
line, where the format is given as below:
COC ethoxy ethaneThus first the SMILES, and then after the first space (or tab) on the line a title that is stored as
CDKConstants.TITLE
. For legacy comparability the
title is also placed in a "SMIdbNAME" property. If a line is invalid an empty
molecule is inserted into the container set. The molecule with have the prop
IteratingSMILESReader.BAD_SMILES_INPUT
set to the input line that
could not be read.
For each line a molecule is generated, and multiple Molecules are read as MoleculeSet.
- See Also:
- Source code:
- main
- Belongs to CDK module:
- smiles
- Keywords:
- file format, SMILES
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Nested Class Summary
Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader
IChemObjectReader.Mode
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Field Summary
Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader
errorHandler, mode
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Constructor Summary
ConstructorsConstructorDescriptionSMILESReader
(InputStream input) SMILESReader
(Reader input) Construct a new reader from a Reader and a specified builder object. -
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.Returns theIResourceFormat
class for this IO class.<T extends IChemObject>
Tread
(T object) Reads the content from a XYZ input.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
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Constructor Details
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SMILESReader
Construct a new reader from a Reader and a specified builder object.- Parameters:
input
- The Reader object from which to read structures
-
SMILESReader
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SMILESReader
public SMILESReader()
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Method Details
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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
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setReader
Description copied from interface:IChemObjectReader
Sets the InputStream from which this ChemObjectReader should read the contents.- Throws:
CDKException
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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.
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read
Reads the content from a XYZ input. It can only return aIChemObject
of typeIChemFile
.- Parameters:
object
- class must be of type ChemFile- 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- See Also:
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close
Description copied from interface:IChemObjectIO
Closes this IChemObjectIO's resources.- Throws:
IOException
- when the wrapper IO class cannot be closed.
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