ambit2.core.smiles

Class OpenBabelGen3D

java.lang.Object

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

ambit2.core.external.ShellSDFoutput<X>

ambit2.core.smiles.OpenBabelAbstractShell<org.openscience.cdk.interfaces.IAtomContainer>

ambit2.core.smiles.OpenBabelGen3D

All Implemented Interfaces:

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

public class OpenBabelGen3D
extends OpenBabelAbstractShell<org.openscience.cdk.interfaces.IAtomContainer>

See Also:

Serialized Form

Field Summary

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
OpenBabelGen3D()

Method Summary

Modifier and Type	Method and Description
protected String	getOBabelHome()
protected String	getOutputFileName()
protected String	getOutputOption()
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

Methods inherited from class ambit2.core.smiles.OpenBabelAbstractShell

getHomeDir, getPath, initialize, isHydrogens, 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

Constructor Detail

OpenBabelGen3D

public OpenBabelGen3D()
               throws ShellException

Throws:

ShellException

Method Detail

getOBabelHome

protected String getOBabelHome()
                        throws ShellException

Overrides:

getOBabelHome in class OpenBabelAbstractShell<org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

getOutputFileName

protected String getOutputFileName()

Overrides:

getOutputFileName in class OpenBabelAbstractShell<org.openscience.cdk.interfaces.IAtomContainer>

getOutputOption

protected String getOutputOption()

Overrides:

getOutputOption in class OpenBabelAbstractShell<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 OpenBabelAbstractShell<org.openscience.cdk.interfaces.IAtomContainer>

Returns:

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

Throws:

ShellException

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