ambit2.mopac

Class MopacShell

java.lang.Object

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

ambit2.mopac.AbstractMopacShell

ambit2.mopac.MopacShell

All Implemented Interfaces:

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

public class MopacShell
extends AbstractMopacShell

Runs MOPAC and smi2sdf + mengine as means to generate the starting 3D structure

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ShellMengine	mengine
protected ShellSmi2SDF	smi2sdf

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
MopacShell()

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

smi2sdf

protected ShellSmi2SDF smi2sdf

mengine

protected ShellMengine mengine

Constructor Detail

MopacShell

public MopacShell()
           throws ShellException

Throws:

ShellException

Method Detail

generate3DStructure

protected org.openscience.cdk.interfaces.IAtomContainer generate3DStructure(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                     throws ShellException

Specified by:

generate3DStructure in class AbstractMopacShell

Throws:

ShellException