ambit2.smi23d

Class ShellMengine

java.lang.Object

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

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

ambit2.smi23d.ShellMengine

All Implemented Interfaces:

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

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

A wrapper for Mengine

Author:

nina

See Also:

Serialized Form

Field Summary

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
ShellMengine()

Method Summary

Modifier and Type	Method and Description
protected void	initialize()
protected List<String>	prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol) Returns empty string, override with smth meaningfull
String	toString()
protected org.openscience.cdk.interfaces.IAtomContainer	transform(org.openscience.cdk.interfaces.IAtomContainer 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, getHomeDir, getHomeFromConfig, getID, getInputFile, getMsgemptymolecule, getOutputFile, getPath, 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

ShellMengine

public ShellMengine()
             throws ShellException

Throws:

ShellException

Method Detail

initialize

protected void initialize()
                   throws ShellException

Overrides:

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

Throws:

ShellException

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

toString

public String toString()

Overrides:

toString in class Object

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>