ambit2.core.smiles
Class OpenBabelShell

java.lang.Object
  ambit2.base.external.CommandShell<INPUT,org.openscience.cdk.interfaces.IMolecule>
      ambit2.core.external.ShellSDFoutput<java.lang.String>
          ambit2.core.smiles.OpenBabelShell

All Implemented Interfaces:

ambit2.base.interfaces.IProcessor<java.lang.String,org.openscience.cdk.interfaces.IMolecule>, java.io.Serializable

public class OpenBabelShell
extends ShellSDFoutput<java.lang.String>

See Also:

Serialized Form

Field Summary

protected static java.lang.String[]

libFiles

Fields inherited from class ambit2.core.external.ShellSDFoutput

readOutput

Fields inherited from class ambit2.base.external.CommandShell

enabled, executables, exitCode, inputFile, logger, os_LINUX, os_MAC, os_WINDOWS, os_WINDOWSVISTA, outputFile, prefix, runAsync

Constructor Summary

OpenBabelShell()

Method Summary

protected void	initialize()
protected java.util.List<java.lang.String>	prepareInput(java.lang.String path, java.lang.String mol)
java.lang.String	toString()
protected org.openscience.cdk.interfaces.IMolecule	transform(java.lang.String mol)

Methods inherited from class ambit2.core.external.ShellSDFoutput

isReadOutput, parseOutput, setReadOutput

Methods inherited from class ambit2.base.external.CommandShell

addExecutable, addExecutable, addExecutableLinux, addExecutableMac, addExecutableWin, exitCodeOK, getExecutable, getExecutable, getExitCode, getID, getInputFile, getOutputFile, getPath, isEnabled, process, runShell, runShell, setEnabled, setExitCode, setInputFile, setOutputFile, transform_input, transform

Methods inherited from class java.lang.Object

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

Field Detail

libFiles

protected static java.lang.String[] libFiles

Constructor Detail

OpenBabelShell

public OpenBabelShell()
               throws ambit2.base.external.ShellException

Throws:

ambit2.base.external.ShellException

Method Detail

initialize

protected void initialize()
                   throws ambit2.base.external.ShellException

Overrides:

initialize in class ShellSDFoutput<java.lang.String>

Throws:

ambit2.base.external.ShellException

prepareInput

protected java.util.List<java.lang.String> prepareInput(java.lang.String path,
                                                        java.lang.String mol)
                                                 throws ambit2.base.external.ShellException

Overrides:

prepareInput in class ambit2.base.external.CommandShell<java.lang.String,org.openscience.cdk.interfaces.IMolecule>

Throws:

ambit2.base.external.ShellException

transform

protected org.openscience.cdk.interfaces.IMolecule transform(java.lang.String mol)

Specified by:

transform in class ambit2.base.external.CommandShell<java.lang.String,org.openscience.cdk.interfaces.IMolecule>

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object