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

Class MergeStage

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


Stage for merging up to 100 Glide output files with 'glide_ensemble_merge'.
The input files can be either PV or LIB, and have to be sorted by
GlideScoreglide.  The output file will also be sorted, and the GlideScores
can be offset by a specified value for each input file.

The keywords specific to this stage are...

    NREPORT     Save only the top NREPORT poses.  The default is 0, which
                retains all poses.

    MAXPERLIG   Retain at most MAXPERLIG poses for each ligand
                (determined by the structure title).  The default is 1.
                Use 0 to retain all poses.

    UNIQUEFIELD Property to uniquely identify compounds by. Default is title.

    OFFSETS     List of GlideScore offsets (float) to be applied to the
                input structures. First item in the list is the offset
                for the first input, second is for second input, etc.
                If not specified, all are defaulted to 0.0.

    MARKERS     List of string lables for each receptor. Each ligand will
                be marked by this value depending on which input set it
                originated from.

The stage takes up to 100 input structure file sets (PV or LIB) and
generates a single output pose file.

Instance Methods

[hide private]

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

operate(self)
Run the 'glide_ensemble_merge' script on all the input files from all sets, optionally applying GlideScore offsets to some sets.

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, 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)

See class docstring.

Overrides: UserDict.UserDict.__init__

operate(self)

Run the 'glide_ensemble_merge' script on all the input files from all sets, optionally applying GlideScore offsets to some sets. Generates a single output pose file.

Overrides: stage.Stage.operate

Class MergeStage

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

operate(self)

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