Uses of Class
ambit2.base.external.ShellException

Packages that use ShellException

Package	Description
ambit2.balloon
ambit2.base.external
ambit2.core.external	Launching external applications by command shell
ambit2.core.smiles	SMILES tools, additional to CDK smiles functionality
ambit2.dragon
ambit2.mopac
ambit2.smi23d
ambit2.some
ambit2.vega

Uses of ShellException in ambit2.balloon

Methods in ambit2.balloon that throw ShellException

Modifier and Type	Method and Description
protected String	ShellBalloon.getBalloonHome()
protected String	ShellBalloonWeb.getBalloonHome()
protected void	ShellBalloon.initialize()
protected org.openscience.cdk.interfaces.IAtomContainer	ShellBalloon.parseOutput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)
protected List<String>	ShellBalloon.prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)

Constructors in ambit2.balloon that throw ShellException

Constructor and Description
ShellBalloon()
ShellBalloonWeb()

Uses of ShellException in ambit2.base.external

Methods in ambit2.base.external that throw ShellException

Modifier and Type	Method and Description
String	CommandShell.addExecutable(String executable, String[] morefiles)
String	CommandShell.addExecutable(String osname, String executable, String[] morefiles)
String	CommandShell.addExecutableFreeBSD(String executable, String[] morefiles)
String	CommandShell.addExecutableLinux(String executable, String[] morefiles)
String	CommandShell.addExecutableLinux64(String executable, String[] morefiles)
String	CommandShell.addExecutableMac(String executable, String[] morefiles)
String	CommandShell.addExecutableWin(String executable, String[] morefiles)
String	CommandShell.getExecutable() invokes CommandShell.getExecutable(String, String) with System.getProperty("os.name") as argument
String	CommandShell.getHomeFromConfig(String propertiesResource, String propertyHome)
protected void	CommandShell.initialize()
protected abstract OUTPUT	CommandShell.parseOutput(String path, INPUT mol) Does nothing, override with smth meaningfull
protected OUTPUT	CommandShell.parseOutput(String path, INPUT mol, int exitVal)
protected List<String>	CommandShell.prepareInput(String path, INPUT mol) Returns empty string, override with smth meaningfull
OUTPUT	CommandShell.runShell(INPUT mol)
protected OUTPUT	CommandShell.runShell(INPUT input, String execString)

Constructors in ambit2.base.external that throw ShellException

Constructor and Description
CommandShell()

Uses of ShellException in ambit2.core.external

Methods in ambit2.core.external that throw ShellException

Modifier and Type	Method and Description
protected void	ShellSDFoutput.initialize()
protected org.openscience.cdk.interfaces.IAtomContainer	ShellSDFoutput.parseOutput(String path, INPUT mol)

Constructors in ambit2.core.external that throw ShellException

Constructor and Description
ShellSDFoutput()

Uses of ShellException in ambit2.core.smiles

Methods in ambit2.core.smiles that throw ShellException

Modifier and Type	Method and Description
protected String	OpenBabelAbstractShell.getOBabelHome()
protected String	OpenBabelGen3D.getOBabelHome()
protected void	OpenBabelAbstractShell.initialize()
protected org.openscience.cdk.interfaces.IAtomContainer	OpenBabelGen3D.parseOutput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)
protected org.openscience.cdk.interfaces.IAtomContainer	OpenBabelDepiction.parseOutput(String path, String mol)
protected List<String>	OpenBabelGen3D.prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)
protected List<String>	OpenBabelAbstractShell.prepareInput(String path, X mol)

Constructors in ambit2.core.smiles that throw ShellException

Constructor and Description
OpenBabelAbstractShell()
OpenBabelDepiction()
OpenBabelGen3D()
OpenBabelShell()

Uses of ShellException in ambit2.dragon

Methods in ambit2.dragon that throw ShellException

Modifier and Type	Method and Description
protected boolean	AbstractDescriptorShell.canApply(org.openscience.cdk.interfaces.IAtomContainer atomcontainer)
protected DragonShell	DescriptorDragonShell.createDragonShell()
protected abstract String	AbstractDescriptorShell.getHome()
protected String	DragonShell.getHome()
protected void	DragonShell.initialize()
protected org.openscience.cdk.interfaces.IAtomContainer	DragonShell.parseOutput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)
protected List<String>	DragonShell.prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.interfaces.IAtomContainer	AbstractDescriptorShell.runShell(org.openscience.cdk.interfaces.IAtomContainer mol)
protected org.openscience.cdk.interfaces.IAtomContainer	DragonShell.transform_input(org.openscience.cdk.interfaces.IAtomContainer mol)

Constructors in ambit2.dragon that throw ShellException

Constructor and Description
AbstractDescriptorShell()
DescriptorDragonShell()
DragonShell()

Uses of ShellException in ambit2.mopac

Methods in ambit2.mopac that throw ShellException

Modifier and Type	Method and Description
protected org.openscience.cdk.interfaces.IAtomContainer	AbstractMopacShell.applyEvenIfDisconnected(org.openscience.cdk.interfaces.IAtomContainer atomcontainer)
protected org.openscience.cdk.interfaces.IAtomContainer	MopacShell.generate3DStructure(org.openscience.cdk.interfaces.IAtomContainer mol)
protected void	AbstractMopacShell.initialize()
protected org.openscience.cdk.interfaces.IAtomContainer	AbstractMopacShell.parseOutput(String mopac_path, org.openscience.cdk.interfaces.IAtomContainer mol)
protected List<String>	AbstractMopacShell.prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.interfaces.IAtomContainer	AbstractMopacShell.runShell(org.openscience.cdk.interfaces.IAtomContainer mol)

Constructors in ambit2.mopac that throw ShellException

Constructor and Description
AbstractMopacShell()
DescriptorMopacShell()
MopacOriginalStructure()
MopacShell()
MopacShellBalloon()
MopacShellBalloon(ShellBalloon balloon)
MopacShellOB()
MopacShellOB(OpenBabelGen3D shell)

Uses of ShellException in ambit2.smi23d

Methods in ambit2.smi23d that throw ShellException

Modifier and Type	Method and Description
protected void	ShellMengine.initialize()
protected void	ShellSmi2SDF.initialize()
protected List<String>	ShellMengine.prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)
protected List<String>	ShellSmi2SDF.prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)

Constructors in ambit2.smi23d that throw ShellException

Constructor and Description
ShellMengine()
ShellSmi2SDF()

Uses of ShellException in ambit2.some

Methods in ambit2.some that throw ShellException

Modifier and Type	Method and Description
protected boolean	SOMEShell.canApply(org.openscience.cdk.interfaces.IAtomContainer atomcontainer)
protected void	SOMEShell.initialize()
protected org.openscience.cdk.interfaces.IAtomContainer	SOMEShell.parseOutput(String mopac_path, org.openscience.cdk.interfaces.IAtomContainer mol)
protected List<String>	SOMEShell.prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.interfaces.IAtomContainer	SOMEShell.runShell(org.openscience.cdk.interfaces.IAtomContainer mol)
protected org.openscience.cdk.interfaces.IAtomContainer	SOMEShell.transform_input(org.openscience.cdk.interfaces.IAtomContainer mol)

Constructors in ambit2.some that throw ShellException

Constructor and Description
DescriptorSOMEShell()
SOMEShell()

Uses of ShellException in ambit2.vega

Methods in ambit2.vega that throw ShellException

Modifier and Type	Method and Description
protected String	VegaShell.getHome()
protected void	VegaShell.initialize()
protected org.openscience.cdk.interfaces.IAtomContainer	VegaShell.parseOutput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)
protected List<String>	VegaShell.prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.interfaces.IAtomContainer	VegaShell.runShell(org.openscience.cdk.interfaces.IAtomContainer mol)
protected org.openscience.cdk.interfaces.IAtomContainer	VegaShell.transform_input(org.openscience.cdk.interfaces.IAtomContainer mol)

Constructors in ambit2.vega that throw ShellException

Constructor and Description
ExternalModelVega()
VegaShell()
VegaShell(String config)