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

Class LigFilterStage

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


Stage interface for the LigFilter utility.

The keywords specific to this stage are...

    FILTER_FILE    File name for a Ligfilter criteria file.

    CONDITIONS     String list of Ligfilter criteria. Ignored
                   if a FILTER_FILE is specified.

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

Instance Methods

[hide private]

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

setupJobs(self)
Sets up LigFilter jobs, which are distributed via JobDJ.

processJobOutputs(self)
Reports the number of structures that passed the stage.

operate(self)
Perform an 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__

setupJobs(self)

Sets up LigFilter jobs, which are distributed via JobDJ. There will be one Ligfilter job for each input file. This method clears the working directory of previous output and log files (if any). Raises a RuntimeError if there is no FILTER_FILE and no CONDITIONS.

processJobOutputs(self)

Reports the number of structures that passed the stage. Raises a RuntimeError if any Ligfilter .log file is missing the summary information.

operate(self)

Perform an operation on the input files. There are setup, running, and post-processing steps, and the stage records its current status so that it can be restarted in that step if there is a failure. Raises a RuntimeError if the JobDJ run() method fails, or if the stage finishes with an improper status.

Overrides: stage.Stage.operate

Class LigFilterStage

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

setupJobs(self)

processJobOutputs(self)

operate(self)

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