Package schrodinger :: Package pipeline :: Package stages :: Module filtering :: Class DrugLikeSplitStage

Class DrugLikeSplitStage

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

Stage for splitting the input ligand structures into 3 groups:

Drug-like ligands: *-dl.maegz Course ligands: *-co.maegz Left-over ligands: *-lo.maegz

Based on the specified criteria.

If at least one variant of a root matches all criteria for a drug-like ligand, then all variants of that root are included in the dl.maegz output file.

If none match, then if at least one variant matches all criteria for coarse ligand, then all variants are included in the co.maegz file.

Otherwise all variants are included in the lo.maegz file.

All variants for the same root must be listed in blocks (next to each other) in the input file and have the same title.

Also labels variants by setting s_vsw_variant field to <title>-# Where # is a variant number (1 to n).

Instance Methods

[hide private]

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

operate(self)
Perform an operation on the input files.

qualify(self, st)
Returns module constant classification for the structure: Drug-like, coarse, etc.

writeRoot(self, root_sts, current_root, current_root_qualification)

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, mainProduct, outputRequested, productsInstalled, 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)


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__

operate(self)

Perform an operation on the input files.

Overrides: stage.Stage.operate

Class DrugLikeSplitStage

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

operate(self)

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