ambit2.mopac

Class AbstractMopacShell

java.lang.Object

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

ambit2.mopac.AbstractMopacShell

All Implemented Interfaces:

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

Direct Known Subclasses:

MopacShell, MopacShellBalloon, MopacShellOB

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

Runs OpenMopac as an external executable and reads the results back. The resulting molecule is assigned 3D coordinates as well as properties as EHOMO, ELUMO, ELECTRONIC_ENERGY, etc.

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	defaultparams
protected boolean	errorIfDisconnected
protected String	inFile
protected int	maxAllAtoms
protected int	maxHeavyAtoms
static String	MESSAGE_UNSUPPORTED_TYPE
protected String	mopac_commands
protected boolean	optimize
protected String[]	outFiles
protected String[]	table
protected boolean	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
AbstractMopacShell()

Method Summary

Modifier and Type	Method and Description
protected org.openscience.cdk.interfaces.IAtomContainer	applyEvenIfDisconnected(org.openscience.cdk.interfaces.IAtomContainer atomcontainer)
protected abstract org.openscience.cdk.interfaces.IAtomContainer	generate3DStructure(org.openscience.cdk.interfaces.IAtomContainer mol)
int	getMaxAllAtoms()
int	getMaxHeavyAtoms()
String	getMopac_commands()
protected String	getOutFile(int i, String os)
protected String	getPath(File file)
protected void	initialize()
boolean	isErrorIfDisconnected()
boolean	isOptimize()
boolean	isUseOriginalStructure()
protected org.openscience.cdk.interfaces.IAtomContainer	parseOutput(String mopac_path, org.openscience.cdk.interfaces.IAtomContainer mol) Does nothing, override with smth meaningfull
protected List<String>	prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol) Returns empty string, override with smth meaningfull
org.openscience.cdk.interfaces.IAtomContainer	process(org.openscience.cdk.interfaces.IAtomContainer target)
org.openscience.cdk.interfaces.IAtomContainer	runShell(org.openscience.cdk.interfaces.IAtomContainer mol)
void	setErrorIfDisconnected(boolean errorIfDisconnected)
void	setMaxAllAtoms(int maxAllAtoms)
void	setMaxHeavyAtoms(int maxHeavyAtoms)
void	setMopac_commands(String mopac_commands)
void	setOptimize(boolean optimize)
void	setUseOriginalStructure(boolean useOriginalStructure)
String	toString()
protected org.openscience.cdk.interfaces.IAtomContainer	transform_input(org.openscience.cdk.interfaces.IAtomContainer mol) This is not thread safe!
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, 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

maxHeavyAtoms

protected int maxHeavyAtoms

maxAllAtoms

protected int maxAllAtoms

defaultparams

public static String[] defaultparams

mopac_commands

protected String mopac_commands

useOriginalStructure

protected boolean useOriginalStructure

optimize

protected boolean optimize

inFile

protected String inFile

outFiles

protected String[] outFiles

errorIfDisconnected

protected boolean errorIfDisconnected

MESSAGE_UNSUPPORTED_TYPE

public static String MESSAGE_UNSUPPORTED_TYPE

table

protected String[] table

Constructor Detail

AbstractMopacShell

public AbstractMopacShell()
                   throws ShellException

Throws:

ShellException

Method Detail

isUseOriginalStructure

public boolean isUseOriginalStructure()

setUseOriginalStructure

public void setUseOriginalStructure(boolean useOriginalStructure)

isOptimize

public boolean isOptimize()

setOptimize

public void setOptimize(boolean optimize)

getMopac_commands

public String getMopac_commands()

setMopac_commands

public void setMopac_commands(String mopac_commands)

getMaxHeavyAtoms

public int getMaxHeavyAtoms()

setMaxHeavyAtoms

public void setMaxHeavyAtoms(int maxHeavyAtoms)

getMaxAllAtoms

public int getMaxAllAtoms()

setMaxAllAtoms

public void setMaxAllAtoms(int maxAllAtoms)

isErrorIfDisconnected

public boolean isErrorIfDisconnected()

setErrorIfDisconnected

public void setErrorIfDisconnected(boolean errorIfDisconnected)

initialize

protected void initialize()
                   throws ShellException

Overrides:

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

Throws:

ShellException

generate3DStructure

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

Throws:

net.idea.modbcum.i.exceptions.AmbitException

transform_input

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

This is not thread safe!

Overrides:

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

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getOutFile

protected String getOutFile(int i,
                            String os)

getPath

protected String getPath(File file)

Overrides:

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

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

parseOutput

protected org.openscience.cdk.interfaces.IAtomContainer parseOutput(String mopac_path,
                                                                    org.openscience.cdk.interfaces.IAtomContainer mol)
                                                             throws ShellException

Description copied from class: CommandShell

Does nothing, override with smth meaningfull

Specified by:

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

Throws:

ShellException

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

applyEvenIfDisconnected

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

Throws:

ShellException

toString

public String toString()

Overrides:

toString in class Object

process

public org.openscience.cdk.interfaces.IAtomContainer process(org.openscience.cdk.interfaces.IAtomContainer target)
                                                      throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

process in interface net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Overrides:

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

Throws:

net.idea.modbcum.i.exceptions.AmbitException