ambit2.core.smiles

Class OpenBabelDepiction

java.lang.Object

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

ambit2.core.external.ShellSDFoutput<X>

ambit2.core.smiles.OpenBabelAbstractShell<String>

ambit2.core.smiles.OpenBabelDepiction

All Implemented Interfaces:

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

public class OpenBabelDepiction
extends OpenBabelAbstractShell<String>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected String	outputFileName
protected int	size

Fields inherited from class ambit2.core.smiles.OpenBabelAbstractShell

hydrogens, OBABEL_EXE, OBABEL_HOME

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
OpenBabelDepiction()

Method Summary

Modifier and Type	Method and Description
BufferedImage	getImage()
protected String	getOutputFileName()
protected String	getOutputOption()
int	getSize()
protected org.openscience.cdk.interfaces.IAtomContainer	parseOutput(String path, String mol) Does nothing, override with smth meaningfull
void	setSize(int size)

Methods inherited from class ambit2.core.smiles.OpenBabelAbstractShell

getHomeDir, getOBabelHome, getPath, initialize, isHydrogens, prepareInput, setHydrogens, toString, transform

Methods inherited from class ambit2.core.external.ShellSDFoutput

isReadOutput, setReadOutput, writeInputSDF

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

outputFileName

protected String outputFileName

size

protected int size

Constructor Detail

OpenBabelDepiction

public OpenBabelDepiction()
                   throws ShellException

Throws:

ShellException

Method Detail

getSize

public int getSize()

setSize

public void setSize(int size)

getOutputOption

protected String getOutputOption()

Overrides:

getOutputOption in class OpenBabelAbstractShell<String>

getOutputFileName

protected String getOutputFileName()

Overrides:

getOutputFileName in class OpenBabelAbstractShell<String>

parseOutput

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

Description copied from class: CommandShell

Does nothing, override with smth meaningfull

Overrides:

parseOutput in class ShellSDFoutput<String>

Throws:

ShellException

getImage

public BufferedImage getImage()
                       throws IOException

Throws:

IOException