ambit2.dragon

Class DragonShell

java.lang.Object

ambit2.base.external.CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

ambit2.dragon.AbstractDescriptorShell

ambit2.dragon.DragonShell

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

public class DragonShell
extends AbstractDescriptorShell

Launches Dragon6 as an external executable and reads the results back.

Author:

nina

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DragonShell._options

Field Summary

Fields

Modifier and Type	Field and Description
protected DragonDescriptorDictionary	descriptors
static String	DRAGON_EXE
static String	DRAGON_HOME
protected String[]	inFile
protected String[]	outFile

Fields inherited from class ambit2.base.external.CommandShell

enabled, executables, exitCode, inputFile, logger, os_FreeBSD, os_LINUX, os_LINUX64, os_MAC, os_WINDOWS, os_WINDOWS7, os_WINDOWSVISTA, outputFile, prefix, runAsync, workFolder

Constructor Summary

Constructors

Constructor and Description
DragonShell()

Method Summary

Modifier and Type	Method and Description
String[]	getDescriptorNames()
String	getDescriptorNamesAsString()
DragonDescriptorDictionary	getDescriptors()
protected String	getHome()
protected String	getHomeDir(File file)
protected void	initialize()
protected org.openscience.cdk.interfaces.IAtomContainer	parseOutput(String path, org.openscience.cdk.interfaces.IAtomContainer mol) Does nothing, override with smth meaningfull
protected List<String>	prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol) Returns empty string, override with smth meaningfull
Object[]	setDescriptors()
void	setDescriptors(Object[] names) Descriptor or block names expected
String	toString()
protected org.openscience.cdk.interfaces.IAtomContainer	transform_input(org.openscience.cdk.interfaces.IAtomContainer mol)

Methods inherited from class ambit2.dragon.AbstractDescriptorShell

canApply, getPath, runShell, transform

Methods inherited from class ambit2.base.external.CommandShell

addExecutable, addExecutable, addExecutableFreeBSD, addExecutableLinux, addExecutableLinux64, addExecutableMac, addExecutableWin, close, exitCodeOK, getExecutable, getExecutable, getExitCode, getHomeFromConfig, getID, getInputFile, getMsgemptymolecule, getOutputFile, getWorkFolder, isEnabled, open, parseOutput, process, processStdOut, runShell, setEnabled, setExitCode, setInputFile, setOutputFile, setWorkFolder, transform

Methods inherited from class java.lang.Object

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

Field Detail

descriptors

protected DragonDescriptorDictionary descriptors

DRAGON_EXE

public static final String DRAGON_EXE

See Also:

Constant Field Values

DRAGON_HOME

public static final String DRAGON_HOME

See Also:

Constant Field Values

inFile

protected String[] inFile

outFile

protected String[] outFile

Constructor Detail

DragonShell

public DragonShell()
            throws ShellException

Throws:

ShellException

Method Detail

getDescriptors

public DragonDescriptorDictionary getDescriptors()

getDescriptorNamesAsString

public String getDescriptorNamesAsString()

getDescriptorNames

public String[] getDescriptorNames()

setDescriptors

public void setDescriptors(Object[] names)
                    throws org.openscience.cdk.exception.CDKException

Descriptor or block names expected

Parameters:

names -

Throws:

org.openscience.cdk.exception.CDKException

setDescriptors

public Object[] setDescriptors()

getHomeDir

protected String getHomeDir(File file)

Overrides:

getHomeDir in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

getHome

protected String getHome()
                  throws ShellException

Specified by:

getHome in class AbstractDescriptorShell

Throws:

ShellException

initialize

protected void initialize()
                   throws ShellException

Overrides:

initialize in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

transform_input

protected org.openscience.cdk.interfaces.IAtomContainer transform_input(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                 throws ShellException

Overrides:

transform_input in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

prepareInput

protected List<String> prepareInput(String path,
                                    org.openscience.cdk.interfaces.IAtomContainer mol)
                             throws ShellException

Description copied from class: CommandShell

Returns empty string, override with smth meaningfull

Overrides:

prepareInput in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Returns:

list of command line parameters (exe name excluded) to be passed to the executable

Throws:

ShellException

parseOutput

protected org.openscience.cdk.interfaces.IAtomContainer parseOutput(String path,
                                                                    org.openscience.cdk.interfaces.IAtomContainer mol)
                                                             throws ShellException

Description copied from class: CommandShell

Does nothing, override with smth meaningfull

Specified by:

parseOutput in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

toString

public String toString()

Overrides:

toString in class Object