Package schrodinger :: Package pipeline :: Package stages :: Module qsite :: Class QSiteStage

Class QSiteStage

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


Stage for running QSite jobs.

Input can be one of the following:

1. Complex maestro file
      QM region may be defined via molecule number or atom numbers

2. PV maestro file
      QM region will be set to the ligand

Instance Methods

[hide private]

addExpectedKeyword(self, fullname, qsname, type, default=None, doc=None)
Used by constructor.

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

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

setupQSiteJob(self, complex_st, qsite_jobname)
Setup the QSite job(s)

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

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]

addExpectedKeyword(self, fullname, qsname, type, default=None, doc=None)

Used by constructor. Saves "QSite name" for specified keyword and returns ConfigObj validation string for it.

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

See class docstring.

Overrides: UserDict.UserDict.__init__

processJobOutputs(self)

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

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 QSiteStage

addExpectedKeyword(self, fullname, qsname, type, default=None, doc=None)

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

processJobOutputs(self)

operate(self)

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