Package org.openscience.cdk.io
Class RGroupQueryReader
java.lang.Object
org.openscience.cdk.io.ChemObjectIO
org.openscience.cdk.io.DefaultChemObjectReader
org.openscience.cdk.io.RGroupQueryReader
- All Implemented Interfaces:
Closeable
,AutoCloseable
,IChemObjectIO
,IChemObjectReader
,ISimpleChemObjectReader
A reader for Symyx' Rgroup files (RGFiles).
An RGfile describes a single molecular query with Rgroups.
Each RGfile is a combination of Ctabs defining the root molecule and each
member of each Rgroup in the query.
The RGFile format is described in the manual "CTFile Formats" , Chapter 5.
- Author:
- Mark Rijnbeek
- Source code:
- main
- Belongs to CDK module:
- io
- Keywords:
- Rgroup, R group, R-group
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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
ConstructorsConstructorDescriptionDefault constructor, input not set.Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given InputStream.Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given Reader. -
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) Check input IChemObject and proceed to parse.void
setReader
(InputStream input) Sets the InputStream from which this ChemObjectReader should read the contents.void
Sets the input Reader.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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RGroupQueryReader
public RGroupQueryReader()Default constructor, input not set. -
RGroupQueryReader
Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given InputStream.- Parameters:
in
- The InputStream to read from.
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RGroupQueryReader
Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given Reader.- Parameters:
in
- The Reader to read from.
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Method Details
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setReader
Sets the input Reader.- Parameters:
input
- Reader object- 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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getFormat
Description copied from interface:IChemObjectIO
Returns theIResourceFormat
class for this IO class. -
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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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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read
Check input IChemObject and proceed to parse. Accepts/returns IChemObject of type RGroupQuery only.- Parameters:
object
- class must be of type RGroupQuery- Returns:
- IChemObject read from file
- Throws:
CDKException
- it is thrown if the type of information is not available from the input
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