Uses of Class
ambit2.base.external.CommandShell

Packages that use CommandShell

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 CommandShell in ambit2.balloon

Subclasses of CommandShell in ambit2.balloon

Modifier and Type	Class and Description
class	ShellBalloon A wrapper for Balloon http://users.abo.fi/mivainio/balloon
class	ShellBalloonWeb Same as ShellBalloon, but gets the BALOON_HOME var from config file Used in web services.

Uses of CommandShell in ambit2.base.external

Fields in ambit2.base.external declared as CommandShell

Modifier and Type	Field and Description
protected CommandShell	ShellException.shell

Constructors in ambit2.base.external with parameters of type CommandShell

Constructor and Description
ShellException(CommandShell shell)
ShellException(CommandShell shell, String message)
ShellException(CommandShell shell, String message, Throwable cause)
ShellException(CommandShell shell, Throwable cause)

Uses of CommandShell in ambit2.core.external

Subclasses of CommandShell in ambit2.core.external

Modifier and Type	Class and Description
class	ShellSDFoutput<INPUT>

Uses of CommandShell in ambit2.core.smiles

Subclasses of CommandShell in ambit2.core.smiles

Modifier and Type	Class and Description
class	OpenBabelAbstractShell<X>
class	OpenBabelDepiction
class	OpenBabelGen3D
class	OpenBabelShell

Uses of CommandShell in ambit2.dragon

Subclasses of CommandShell in ambit2.dragon

Modifier and Type	Class and Description
class	AbstractDescriptorShell
class	DragonShell Launches Dragon6 as an external executable and reads the results back.

Uses of CommandShell in ambit2.mopac

Subclasses of CommandShell in ambit2.mopac

Modifier and Type	Class and Description
class	AbstractMopacShell Runs OpenMopac as an external executable and reads the results back.
class	MopacShell Runs MOPAC and smi2sdf + mengine as means to generate the starting 3D structure
class	MopacShellBalloon
class	MopacShellOB

Uses of CommandShell in ambit2.smi23d

Subclasses of CommandShell in ambit2.smi23d

Modifier and Type	Class and Description
class	ShellMengine A wrapper for Mengine
class	ShellSmi2SDF

Uses of CommandShell in ambit2.some

Subclasses of CommandShell in ambit2.some

Modifier and Type	Class and Description
class	SOMEShell Wrapper for Site Of Metabolism Estimator (SOME) http://www.dddc.ac.cn/adme/myzheng/SOME_1_0.tar.gz.

Uses of CommandShell in ambit2.vega

Subclasses of CommandShell in ambit2.vega

Modifier and Type	Class and Description
class	VegaShell Launches VEGA as external executable