ambit2.core.external

Class ShellSDFoutput<INPUT>

java.lang.Object

ambit2.base.external.CommandShell<INPUT,org.openscience.cdk.interfaces.IAtomContainer>

ambit2.core.external.ShellSDFoutput<INPUT>

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<INPUT,org.openscience.cdk.interfaces.IAtomContainer>

Direct Known Subclasses:

OpenBabelAbstractShell, ShellBalloon, ShellMengine, ShellSmi2SDF

public abstract class ShellSDFoutput<INPUT>
extends CommandShell<INPUT,org.openscience.cdk.interfaces.IAtomContainer>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	readOutput

Fields inherited from class ambit2.base.external.CommandShell

enabled, executables, exitCode, inputFile, logger, os_FreeBSD, os_LINUX, os_LINUX64, os_MAC, os_WINDOWS, os_WINDOWS7, os_WINDOWSVISTA, outputFile, prefix, runAsync, workFolder

Constructor Summary

Constructors

Constructor and Description
ShellSDFoutput()

Method Summary

Modifier and Type	Method and Description
protected void	initialize()
boolean	isReadOutput()
protected org.openscience.cdk.interfaces.IAtomContainer	parseOutput(String path, INPUT mol) Does nothing, override with smth meaningfull
void	setReadOutput(boolean readOutput)
protected String	writeInputSDF(String path, org.openscience.cdk.interfaces.IAtomContainer mol)

Methods inherited from class ambit2.base.external.CommandShell

addExecutable, addExecutable, addExecutableFreeBSD, addExecutableLinux, addExecutableLinux64, addExecutableMac, addExecutableWin, close, exitCodeOK, getExecutable, getExecutable, getExitCode, getHomeDir, getHomeFromConfig, getID, getInputFile, getMsgemptymolecule, getOutputFile, getPath, getWorkFolder, isEnabled, open, parseOutput, prepareInput, process, processStdOut, runShell, runShell, setEnabled, setExitCode, setInputFile, setOutputFile, setWorkFolder, transform_input, transform, transform

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

readOutput

protected boolean readOutput

Constructor Detail

ShellSDFoutput

public ShellSDFoutput()
               throws ShellException

Throws:

ShellException

Method Detail

initialize

protected void initialize()
                   throws ShellException

Overrides:

initialize in class CommandShell<INPUT,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

parseOutput

protected org.openscience.cdk.interfaces.IAtomContainer parseOutput(String path,
                                                                    INPUT mol)
                                                             throws ShellException

Description copied from class: CommandShell

Does nothing, override with smth meaningfull

Specified by:

parseOutput in class CommandShell<INPUT,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

isReadOutput

public boolean isReadOutput()

setReadOutput

public void setReadOutput(boolean readOutput)

writeInputSDF

protected String writeInputSDF(String path,
                               org.openscience.cdk.interfaces.IAtomContainer mol)
                        throws IOException,
                               org.openscience.cdk.exception.CDKException

Throws:

IOException

org.openscience.cdk.exception.CDKException