ambit2.mopac

Class MopacShellOB

java.lang.Object

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

ambit2.mopac.AbstractMopacShell

ambit2.mopac.MopacShellOB

All Implemented Interfaces:

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

public class MopacShellOB
extends AbstractMopacShell

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected OpenBabelGen3D	shell

Fields inherited from class ambit2.mopac.AbstractMopacShell

defaultparams, errorIfDisconnected, inFile, maxAllAtoms, maxHeavyAtoms, MESSAGE_UNSUPPORTED_TYPE, mopac_commands, optimize, outFiles, table, useOriginalStructure

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
MopacShellOB()
MopacShellOB(OpenBabelGen3D shell)

Method Summary

Modifier and Type	Method and Description
protected org.openscience.cdk.interfaces.IAtomContainer	generate3DStructure(org.openscience.cdk.interfaces.IAtomContainer mol)

Methods inherited from class ambit2.mopac.AbstractMopacShell

applyEvenIfDisconnected, getMaxAllAtoms, getMaxHeavyAtoms, getMopac_commands, getOutFile, getPath, initialize, isErrorIfDisconnected, isOptimize, isUseOriginalStructure, parseOutput, prepareInput, process, runShell, setErrorIfDisconnected, setMaxAllAtoms, setMaxHeavyAtoms, setMopac_commands, setOptimize, setUseOriginalStructure, toString, transform_input, transform

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, isEnabled, open, parseOutput, processStdOut, runShell, setEnabled, setExitCode, setInputFile, setOutputFile, setWorkFolder, transform

Methods inherited from class java.lang.Object

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

Field Detail

shell

protected OpenBabelGen3D shell

Constructor Detail

MopacShellOB

public MopacShellOB()
             throws ShellException

Throws:

ShellException

MopacShellOB

public MopacShellOB(OpenBabelGen3D shell)
             throws ShellException

Throws:

ShellException

Method Detail

generate3DStructure

protected org.openscience.cdk.interfaces.IAtomContainer generate3DStructure(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                     throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

generate3DStructure in class AbstractMopacShell

Throws:

net.idea.modbcum.i.exceptions.AmbitException