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

Class PostLigPrepStage

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


This stage limits the number of steroisomers, removes states penalized by
Epik/Ionizer, and generates the variant codes.

PRESERVE_NJOBS
    whether to write out as many output files as there are inputs.
    Useful to create the same number of subjobs for QikProp as were
    used for LigPrep.

Instance Methods

[hide private]

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

getEnergy(self, st)
Returns the energy of the st

writeBestStereos(self, stereoisomers)
Given a list of Structure objects from the same ion/taut state, decices which structures (stereoisomers) need to be kept and which ones need to be removed.

nextOutFile(self)

operate(self)
Optionally limits the number of stereoisomers in the input_files to <maxstereo> keeping lowest energy isomers.

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)


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__

writeBestStereos(self, stereoisomers)

Given a list of Structure objects from the same ion/taut state, decices which structures (stereoisomers) need to be kept and which ones need to be removed. This is done by keeping MAXSTEREO lowest- energy stereoisomers.

The structures that are "kept" are then written to the output file.

operate(self)

Optionally limits the number of stereoisomers in the input_files to <maxstereo> keeping lowest energy isomers. Optionally filters on ionization penalty

Overrides: stage.Stage.operate

Class PostLigPrepStage

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

writeBestStereos(self, stereoisomers)

operate(self)

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