ambit2.core.smiles
Class OpenBabelShell

Package class diagram package OpenBabelShell
java.lang.Object
  extended by ambit2.base.external.CommandShell<INPUT,org.openscience.cdk.interfaces.IMolecule>
      extended by ambit2.core.external.ShellSDFoutput<java.lang.String>
          extended by 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