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

Class ChargeFilterStage

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

Stage-based class for filtering a set of structure files by total charge.

MIN_CHARGE and MAX_CHARGE are the two keywords specific to this stage. If a structure has a total charge within [MIN_CHARGE,MAX_CHARGE] (inclusive), it is retained; otherwise, the structure is filtered out.

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

Instance Methods

[hide private]

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

operate(self)
Read all the structures in 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)

Read all the structures in the input files. If a structure's total charge is between MIN_CHARGE and MAX_CHARGE, write it to a the corresponding output file. Raises an IOError if there is a problem reading an input file or writing an output file, and raises a SystemExit if there are no output structures.

Overrides: stage.Stage.operate

Class ChargeFilterStage

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

operate(self)

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