Package schrodinger :: Package pipeline :: Package stages :: Module filtering :: Class SubSetStage

Class SubSetStage

    UserDict.UserDict --+        
                        |        
UserDict.IterableUserDict --+    
                            |    
                  stage.Stage --+
                                |
                               SubSetStage


Stage for making a subset of the input files based on a list of
titles or other property.

The keywords specific to this stage are...
    
    PROPERTY       Property to filter on (default s_m_title)
    VALUE_FILE      File containing a list of values to keep (one per line)
                   if a FILTER_FILE is specified.

The stage takes one set of input structure files and generates one set
of corresponding output files.

NOTE: SMILES format files can only be filtered on the title.

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
See class docstring.

filterSmilesFile(self, ligfile, outfile)
Filter the file <ligfile> by title based on VALUE_FILE and add the output file to self.output_files list

filterFile(self, ligfile, outfile)
Filter the file <ligfile> based on PROPERTY & VALUE_FILE and add the output file to self.output_files list

readValueList(self)

operate(self)
Perform the filtering operation on the input files.

Inherited from stage.Stage: JobDJOptions, __getitem__, __getstate__, addExpectedInput, addExpectedOutput, addOutputFile, checkFile, checkFiles, checkInputs, checkParameters, checkProducts, debug, dump, error, exit, genFileName, genOutputFileName, getAdjustedNJobs, getCleanupRequested, getHostList, getHostStr, getInput, getInputNames, getJobDJ, getLocal, getMaxRetries, getNJobs, getName, getOutput, getOutputName, getOutputNames, getRuntimePath, getStageDirectory, getVerbosity, hasCompleted, hasStarted, info, iterInputs, log, lognoret, mainProduct, outputRequested, productsInstalled, reportParameters, requiredProduct, requiredProductRuntime, run, runJobDJ, setInput, setJobDJOptions, setJobOptions, setMainProduct, setOutput, setOutputName, updateJobdj, validateValues, waitForFileStatus, waitForFiles, warning

Inherited from stage.Stage (private): _adjustNJobs, _calcStsPerJob, _getNCpus, _inputCheck, _minVersionPresent, _readMessageFromDriver

Inherited from UserDict.IterableUserDict: __iter__

Inherited from UserDict.UserDict: __cmp__, __contains__, __delitem__, __len__, __repr__, __setitem__, clear, copy, get, has_key, items, iteritems, iterkeys, itervalues, keys, pop, popitem, setdefault, update, values

Class Methods

[hide private]

Inherited from UserDict.UserDict: fromkeys

Class Variables

[hide private]

Inherited from UserDict.UserDict: __hash__

Method Details

[hide private]

init(self, *args, **kwargs)
(Constructor)

See class docstring.

Overrides: UserDict.UserDict.__init__

operate(self)

Perform the filtering operation on the input files.

Overrides: stage.Stage.operate

Class SubSetStage

__init__(self, *args, **kwargs) (Constructor)

operate(self)

init(self, *args, **kwargs)
(Constructor)