Package schrodinger :: Package pipeline :: Package stages :: Module prime :: Class MMGBSAStage

Class MMGBSAStage

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

Stage for running Prime MM-GBSA on input structures. First structure in the input set is assumed to be the receptor.

There are no keywords specific to the stage.

The stage takes one input structure file set and generates one set of corresponding output structure files (also in PV format).

Instance Methods

[hide private]

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

mainProduct(self)
Product string identifying the job type.

setupJobs(self)
Sets up Prime MM-GBSA jobs, which are distributed via JobDJ.

processJobOutputs(self)
Process the MMGBSA output.

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, outputRequested, 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__

mainProduct(self)

Product string identifying the job type. Used for running different job types with different host sets.

Overrides: stage.Stage.mainProduct

setupJobs(self)

Sets up Prime MM-GBSA jobs, which are distributed via JobDJ. There will be one MMGBSA job for each input PV file. This method clears the working directory of previous input file symlinks, output files, and log files (if any).

processJobOutputs(self)

Process the MMGBSA output. Returns with an error if any of the output files are missing.

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 MMGBSAStage

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

mainProduct(self)

setupJobs(self)

processJobOutputs(self)

operate(self)

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