ambit2.core.smiles

Class OpenBabelAbstractShell<X>

java.lang.Object

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

ambit2.core.external.ShellSDFoutput<X>

ambit2.core.smiles.OpenBabelAbstractShell<X>

All Implemented Interfaces:

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

Direct Known Subclasses:

OpenBabelDepiction, OpenBabelGen3D, OpenBabelShell

public class OpenBabelAbstractShell<X>
extends ShellSDFoutput<X>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	hydrogens
static String	OBABEL_EXE
static String	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
OpenBabelAbstractShell()

Method Summary

Modifier and Type	Method and Description
protected String	getHomeDir(File file)
protected String	getOBabelHome()
protected String	getOutputFileName()
protected String	getOutputOption()
protected String	getPath(File file)
protected void	initialize()
boolean	isHydrogens()
protected List<String>	prepareInput(String path, X mol) Returns empty string, override with smth meaningfull
void	setHydrogens(boolean hydrogens)
String	toString()
protected org.openscience.cdk.interfaces.IAtomContainer	transform(X mol)

Methods inherited from class ambit2.core.external.ShellSDFoutput

isReadOutput, parseOutput, 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

OBABEL_EXE

public static final String OBABEL_EXE

See Also:

Constant Field Values

OBABEL_HOME

public static final String OBABEL_HOME

See Also:

Constant Field Values

hydrogens

protected boolean hydrogens

Constructor Detail

OpenBabelAbstractShell

public OpenBabelAbstractShell()
                       throws ShellException

Throws:

ShellException

Method Detail

isHydrogens

public boolean isHydrogens()

setHydrogens

public void setHydrogens(boolean hydrogens)

getOBabelHome

protected String getOBabelHome()
                        throws ShellException

Throws:

ShellException

initialize

protected void initialize()
                   throws ShellException

Overrides:

initialize in class ShellSDFoutput<X>

Throws:

ShellException

getOutputFileName

protected String getOutputFileName()

getOutputOption

protected String getOutputOption()

transform

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

Specified by:

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

getHomeDir

protected String getHomeDir(File file)

Overrides:

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

prepareInput

protected List<String> prepareInput(String path,
                                    X mol)
                             throws ShellException

Description copied from class: CommandShell

Returns empty string, override with smth meaningfull

Overrides:

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

Returns:

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

Throws:

ShellException