Package schrodinger :: Package pipeline :: Package stages :: Module glide :: Class GlideSortStage
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Class GlideSortStage

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


Stage for sorting Glide _pv/lib.mae files.  Currently, a sorted file is
produced for each input file; that is, the input files are merged and
sorted together.

The keywords specific to this stage are...

    BLOCK_SORT_BY_TITLE       Whether to block-sort the poses by title.  If
                              True (the default), all poses with the same
                              title are grouped and sorted by the
                              INTRATITLE_SORT_KEYS keys.  The blocks
                              themselves are sorted by applying the
                              SORT_KEYS to just the top pose in each block.

    INTRATITLE_SORT_KEYS      The sort key(s) within a title block.  The
                              default is 'r_i_glide_emodel' (appropriate
                              for Glide HTVS/SP results).  Multiple sort
                              keys must be whitespace-separated.

    SORT_KEYS                 The key(s) for sorting the pose file.  If
                              BLOCK_SORT_BY_TITLE is True, the blocks are
                              sorted by the values of their top pose's
                              SORT_KEYS properties.  Multiple sort keys
                              must be whitespace-separated.

    OUTPUT_POSES_PER_TITLE    The number of top poses per title to keep.
                              Applies only if BLOCK_SORT_BY_TITLE is true.
                              The default is 0, which means retain all
                              poses.

    INPUT_TYPE                Specify whether the receptor is ('pv') or is
                              not ('lib') in the file.  By default, 
                              the type will be determined from
                              the file name (i.e., _pv/lib.mae).

Instance Methods [hide private]
 
__init__(self, *args, **kwargs)
See class docstring.
 
operate(self)
Sort each input pose file using the application.glide.glideanalysis module.

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 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__

operate(self)

 

Sort each input pose file using the application.glide.glideanalysis module. Generates a sorted output pose file for each input pose file.

Overrides: stage.Stage.operate