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java.lang.Object ambit2.base.external.CommandShell<INPUT,org.openscience.cdk.interfaces.IMolecule> ambit2.core.external.ShellSDFoutput<java.lang.String> ambit2.core.smiles.OpenBabelShell
public class OpenBabelShell
Field Summary | |
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protected static java.lang.String[] |
libFiles
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Fields inherited from class ambit2.core.external.ShellSDFoutput |
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readOutput |
Fields inherited from class ambit2.base.external.CommandShell |
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enabled, executables, exitCode, inputFile, logger, os_LINUX, os_MAC, os_WINDOWS, os_WINDOWSVISTA, outputFile, prefix, runAsync |
Constructor Summary | |
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OpenBabelShell()
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Method Summary | |
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protected void |
initialize()
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protected java.util.List<java.lang.String> |
prepareInput(java.lang.String path,
java.lang.String mol)
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java.lang.String |
toString()
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protected org.openscience.cdk.interfaces.IMolecule |
transform(java.lang.String mol)
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Methods inherited from class ambit2.core.external.ShellSDFoutput |
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isReadOutput, parseOutput, setReadOutput |
Methods inherited from class ambit2.base.external.CommandShell |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected static java.lang.String[] libFiles
Constructor Detail |
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public OpenBabelShell() throws ambit2.base.external.ShellException
ambit2.base.external.ShellException
Method Detail |
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protected void initialize() throws ambit2.base.external.ShellException
initialize
in class ShellSDFoutput<java.lang.String>
ambit2.base.external.ShellException
protected java.util.List<java.lang.String> prepareInput(java.lang.String path, java.lang.String mol) throws ambit2.base.external.ShellException
prepareInput
in class ambit2.base.external.CommandShell<java.lang.String,org.openscience.cdk.interfaces.IMolecule>
ambit2.base.external.ShellException
protected org.openscience.cdk.interfaces.IMolecule transform(java.lang.String mol)
transform
in class ambit2.base.external.CommandShell<java.lang.String,org.openscience.cdk.interfaces.IMolecule>
public java.lang.String toString()
toString
in class java.lang.Object
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