ambit2.balloon

Class ShellBalloon

java.lang.Object

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

ambit2.core.external.ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer>

ambit2.balloon.ShellBalloon

All Implemented Interfaces:

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

Direct Known Subclasses:

ShellBalloonWeb

public class ShellBalloon
extends ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer>

A wrapper for Balloon http://users.abo.fi/mivainio/balloon

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	BALLOON_EXE
static String	BALLOON_HOME
protected boolean	hydrogens

Fields inherited from class ambit2.core.external.ShellSDFoutput

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
ShellBalloon()

Method Summary

Modifier and Type	Method and Description
protected String	getBalloonHome()
protected String	getHomeDir(File file)
protected String	getOutputFileName()
protected String	getOutputOption()
protected String	getPath(File file)
protected void	initialize()
boolean	isHydrogens()
protected org.openscience.cdk.interfaces.IAtomContainer	parseOutput(String path, org.openscience.cdk.interfaces.IAtomContainer mol) Does nothing, override with smth meaningfull
protected List<String>	prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol) Returns empty string, override with smth meaningfull
void	setHydrogens(boolean hydrogens)
String	toString()
protected org.openscience.cdk.interfaces.IAtomContainer	transform(org.openscience.cdk.interfaces.IAtomContainer mol)
protected String	writeInputSDF(String path, org.openscience.cdk.interfaces.IAtomContainer mol)

Methods inherited from class ambit2.core.external.ShellSDFoutput

isReadOutput, setReadOutput

Methods inherited from class ambit2.base.external.CommandShell

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

Methods inherited from class java.lang.Object

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

Field Detail

BALLOON_EXE

public static final String BALLOON_EXE

See Also:

Constant Field Values

BALLOON_HOME

public static final String BALLOON_HOME

See Also:

Constant Field Values

hydrogens

protected boolean hydrogens

Constructor Detail

ShellBalloon

public ShellBalloon()
             throws ShellException

Throws:

ShellException

Method Detail

isHydrogens

public boolean isHydrogens()

setHydrogens

public void setHydrogens(boolean hydrogens)

getBalloonHome

protected String getBalloonHome()
                         throws ShellException

Throws:

ShellException

initialize

protected void initialize()
                   throws ShellException

Overrides:

initialize in class ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

getOutputFileName

protected String getOutputFileName()

getOutputOption

protected String getOutputOption()

transform

protected org.openscience.cdk.interfaces.IAtomContainer transform(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

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

toString

public String toString()

Overrides:

toString in class Object

getPath

protected String getPath(File file)

Overrides:

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

getHomeDir

protected String getHomeDir(File file)

Overrides:

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

prepareInput

protected List<String> prepareInput(String path,
                                    org.openscience.cdk.interfaces.IAtomContainer mol)
                             throws ShellException

Description copied from class: CommandShell

Returns empty string, override with smth meaningfull

Overrides:

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

Returns:

list of command line parameters (exe name excluded) to be passed to the executable

Throws:

ShellException

writeInputSDF

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

Overrides:

writeInputSDF in class ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer>

Throws:

IOException

org.openscience.cdk.exception.CDKException

parseOutput

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

Description copied from class: CommandShell

Does nothing, override with smth meaningfull

Overrides:

parseOutput in class ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException