ambit2.smi23d

Class ShellSmi2SDF

java.lang.Object

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

ambit2.core.external.ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer>

ambit2.smi23d.ShellSmi2SDF

All Implemented Interfaces:

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

public class ShellSmi2SDF
extends ShellSDFoutput<org.openscience.cdk.interfaces.IAtomContainer>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	dropHydrogens
protected org.openscience.cdk.smiles.SmilesGenerator	gen

Fields inherited from class ambit2.core.external.ShellSDFoutput

readOutput

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
ShellSmi2SDF()

Method Summary

Modifier and Type	Method and Description
protected boolean	exitCodeOK(int exitVal)
protected void	initialize()
boolean	isDropHydrogens()
boolean	isGenerateSmiles()
protected List<String>	prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol) Returns empty string, override with smth meaningfull
void	setDropHydrogens(boolean dropHydrogens)
void	setGenerateSmiles(boolean generateSmiles)
String	toString()
protected org.openscience.cdk.interfaces.IAtomContainer	transform(org.openscience.cdk.interfaces.IAtomContainer mol)

Methods inherited from class ambit2.core.external.ShellSDFoutput

isReadOutput, parseOutput, setReadOutput, writeInputSDF

Methods inherited from class ambit2.base.external.CommandShell

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

Methods inherited from class java.lang.Object

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

Field Detail

dropHydrogens

protected boolean dropHydrogens

gen

protected transient org.openscience.cdk.smiles.SmilesGenerator gen

Constructor Detail

ShellSmi2SDF

public ShellSmi2SDF()
             throws ShellException

Throws:

ShellException

Method Detail

isDropHydrogens

public boolean isDropHydrogens()

setDropHydrogens

public void setDropHydrogens(boolean dropHydrogens)

initialize

protected void initialize()
                   throws ShellException

Overrides:

initialize in class ShellSDFoutput<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

toString

public String toString()

Overrides:

toString in class Object

exitCodeOK

protected boolean exitCodeOK(int exitVal)

Overrides:

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

transform

protected org.openscience.cdk.interfaces.IAtomContainer transform(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

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

isGenerateSmiles

public boolean isGenerateSmiles()

setGenerateSmiles

public void setGenerateSmiles(boolean generateSmiles)