Package org.openscience.cdk.io
Class MoSSOutputReader
java.lang.Object
org.openscience.cdk.io.ChemObjectIO
org.openscience.cdk.io.DefaultChemObjectReader
org.openscience.cdk.io.MoSSOutputReader
- All Implemented Interfaces:
Closeable
,AutoCloseable
,IChemObjectIO
,IChemObjectReader
,ISimpleChemObjectReader
Reader for MoSS output files [Unknown BibTeXML type: BOR2002] which present the results
of a substructure mining study. These files look like:
id,description,nodes,edges,s_abs,s_rel,c_abs,c_rel 1,S-c:c:c:c:c:c,7,6,491,5.055081,5,1.7421603 2,S-c:c:c:c:c,6,5,493,5.0756717,5,1.7421603
Caution: the output contains substructures, not full molecules, even though they are read as such right now.
- Source code:
- main
- Belongs to CDK module:
- smiles
- Keywords:
- MoSS
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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
ConstructorsConstructorDescriptionCreate a reader for MoSS output files from an empty string.MoSSOutputReader
(InputStream input) Create a reader for MoSS output files from anInputStream
.MoSSOutputReader
(Reader input) Create a reader for MoSS output files from aReader
. -
Method Summary
Modifier and TypeMethodDescriptionboolean
accepts
(Class<? extends IChemObject> testClass) 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) Read aIAtomContainerSet
from the input source.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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MoSSOutputReader
Create a reader for MoSS output files from aReader
.- Parameters:
input
- source of CIF data
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MoSSOutputReader
Create a reader for MoSS output files from anInputStream
.- Parameters:
input
- source of CIF data
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MoSSOutputReader
public MoSSOutputReader()Create a reader for MoSS output files from an empty string.
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Method Details
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getFormat
Returns theIResourceFormat
class for this IO class. -
setReader
Sets the Reader from which this ChemObjectReader should read the contents.- Throws:
CDKException
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setReader
Sets the InputStream from which this ChemObjectReader should read the contents.- Throws:
CDKException
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accepts
Returns whether the givenIChemObject
can be read or written.- Parameters:
testClass
-IChemObject
of which is tested if it can be handled.- Returns:
- true, if the
IChemObject
can be handled.
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read
Read aIAtomContainerSet
from the input source.- Parameters:
object
- anIAtomContainerSet
into which the data is stored.- Returns:
- the content in a
IAtomContainerSet
object - Throws:
CDKException
- it is thrown if the type of information is not available from the input
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close
Closes this IChemObjectIO's resources.- Throws:
IOException
- when the wrapper IO class cannot be closed.
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