ambit2.dragon

Class AbstractDescriptorShell

java.lang.Object

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

ambit2.dragon.AbstractDescriptorShell

All Implemented Interfaces:

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

Direct Known Subclasses:

DragonShell, VegaShell

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

See Also:

Serialized Form

Field Summary

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
AbstractDescriptorShell()

Method Summary

Modifier and Type	Method and Description
protected boolean	canApply(org.openscience.cdk.interfaces.IAtomContainer atomcontainer)
protected abstract String	getHome()
protected String	getPath(File file)
org.openscience.cdk.interfaces.IAtomContainer	runShell(org.openscience.cdk.interfaces.IAtomContainer mol)
protected org.openscience.cdk.interfaces.IAtomContainer	transform(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, getWorkFolder, initialize, isEnabled, open, parseOutput, parseOutput, prepareInput, process, processStdOut, runShell, setEnabled, setExitCode, setInputFile, setOutputFile, setWorkFolder, transform_input, transform

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractDescriptorShell

public AbstractDescriptorShell()
                        throws ShellException

Throws:

ShellException

Method Detail

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>

runShell

public org.openscience.cdk.interfaces.IAtomContainer runShell(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                       throws ShellException

Overrides:

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

Throws:

ShellException

canApply

protected boolean canApply(org.openscience.cdk.interfaces.IAtomContainer atomcontainer)
                    throws ShellException

Throws:

ShellException

getHome

protected abstract String getHome()
                           throws ShellException

Throws:

ShellException

getPath

protected String getPath(File file)

Overrides:

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