Package schrodinger :: Package pipeline :: Package stages :: Module qikprop :: Class QikPropStage

Class QikPropStage

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

Stage for running QikProp jobs. QikProp properties are added to the output structures.

There are no keywords specific to this stage.

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

The number of subjobs generated is equal to the number of input files.

Instance Methods

[hide private]

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

recombineInputLigands(self)
Read all input structures, and save each structure into a subjob input file.

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

processJobOutputs(self)
Checks for failure of any subjobs (by reading the .log file).

checkForCompletion(self, i, job, restarting)
Test whether output files exist for the given job, given the JobDJ's job object.

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, getNCpus, getNJobs, getName, getOutput, getOutputName, getOutputNames, getRuntimePath, getStageDirectory, getVerbosity, hasCompleted, hasStarted, info, iterInputs, log, lognoret, mainProduct, outputRequested, reportParameters, requiredProduct, requiredProductRuntime, run, runJobDJ, setInput, setJobDJOptions, setJobOptions, setMainProduct, setOutput, setOutputName, updateJobdj, validateValues, waitForFileStatus, waitForFiles, warning

Inherited from stage.Stage (private): _adjustNJobs, _calcStsPerJob, _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 the QikProp jobs, which are distributed via JobDJ. There will be one QikProp job for each input file.

processJobOutputs(self)

Checks for failure of any subjobs (by reading the .log file). Renames the QikProp output files. Raises a RuntimeError if any subjob failed.

checkForCompletion(self, i, job, restarting)

Test whether output files exist for the given job, given the JobDJ's job object. If not <restarting> then makr the job for restart if the files are missing. If <restarting> and the job files exit, mark the job as finished.

Return True if job files exist, False otherwise.

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 QikPropStage

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

setupJobs(self)

processJobOutputs(self)

checkForCompletion(self, i, job, restarting)

operate(self)

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