Package schrodinger :: Package pipeline :: Package stages :: Module ligprep :: Class LigPrepStage

Class LigPrepStage

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

Pipeline stage for running LigPrep on the input structures

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
This is the Stage class.

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

setupJobs(self)
Setup LigPrep subjobs by building up a command to submit, and passing that command to JobDJ via addJob().

missingOutput(self, logfile)
Returns True if logfile is present and shows that no structures where returned by LigPrep.

processJobOutputs(self)
After all LigPrep subjobs are complete, read each output file and combined them into one file, or a few files with up to 100K structures in each file.

checkProducts(self)
Overrides the checkProducts() method of Stage class.

operate(self)
Run the stage on the input structure file set.

Inherited from stage.Stage: JobDJOptions, __getitem__, __getstate__, addExpectedInput, addExpectedOutput, addOutputFile, checkFile, checkFiles, checkInputs, checkParameters, 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)


This is the Stage class. Derive your own class from it.
  stagename - full name for this stage (<jobname>-<stagename>)
  specs - ConfigObj specification for the supported keywords
  allow_extra_keywords - Whether to allow keywords that are not in the specification.
  cleanup - Whether to remove intermediate files
  inpipeline - Whether the state is running within a Python Pipeline.
               If the stage is manually created, do NOT set this flag.
               Python Pipeline will set it as needed.

Overrides: UserDict.UserDict.__init__

recombineInputLigands(self)

Read all input structures, while optionally skipping bad structures, and save each structure into a subjob input file. Optionally structures may be retitled where the compound ID of a structure is determined either from UNIQUEFIELD property, or each structure is assumed to be its own compound (no variants).

Structures can also be mixed within subjobs in order to make subjob lengths more uniform, if MIXLIGS is set to True.

processJobOutputs(self)

After all LigPrep subjobs are complete, read each output file and combined them into one file, or a few files with up to 100K structures in each file. Structures are NOT combined if COMBINEOUTS is set to False. Instead each file is renamed in order to have a Pipeline-compliant name.

checkProducts(self)

Overrides the checkProducts() method of Stage class. If USE_EPIK is True, adds 'epik' as required prodct before the actual check is performed. Will get called after the instance of this stage is created.

Overrides: stage.Stage.checkProducts

operate(self)

Run the stage on the input structure file set.

Overrides: stage.Stage.operate

Class LigPrepStage

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

recombineInputLigands(self)

processJobOutputs(self)

checkProducts(self)

operate(self)

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