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

Class DockingStage

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

VSW stage for performing Glide docking

Instance Methods

[hide private]

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

checkInputs(self)
OVERWRITE: Return False if something is wrong with the input files or the parameter, otherwise return True.

recombineInputLigands(self)

setupJobs(self)
Docks the structures in ligfiles to the grid <gridprefix>.

processJobOutputs(self)

write_glide_input_file(self, ligfile, gridfile, nreport, glide_jobname)
Write Glide docking job input file

(str, int)

mergeGlideOutputs(self, input_files, num_comps_to_keep, best_by_compound)
Takes in a list of _lib.mae or _pv.mae files, and merges them together based on glidescore.

generateCsvFile(self, pre_csv_file, csv_props)

check_subjob_output(self, glide_jobname)
Will return the output file for the specified subjob.

_find_subjob_output(self, glide_jobname)

buildDockedLigandsMap(self)
Builds up a dict of self.docked_ligands from the job names in self.glide_jobnames.

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

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


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__

checkInputs(self)

OVERWRITE: Return False if something is wrong with the input files or the parameter, otherwise return True.

Overrides: stage.Stage.checkInputs: (inherited documentation)

mergeGlideOutputs(self, input_files, num_comps_to_keep, best_by_compound)

Takes in a list of _lib.mae or _pv.mae files, and merges them together based on glidescore. Assumes that the files have already been sorted with glide_sort (default in Glide). Stops merging when num_comps_to_keep number of compounds have been reached.

Parameters:

best_by_compound - whether to keep only the best scoring pose per compound (based on unique ID property).

Returns: (str, int)

Merged file path and number of structures in it (including rec). If none of the structures docked (SIP mode), will return (None, 0).

check_subjob_output(self, glide_jobname)

Will return the output file for the specified subjob. If no valid poses were produced, None is returned. Raises a descriptive RuntimeError if logfile and/or output file is incomplete.

buildDockedLigandsMap(self)

Builds up a dict of self.docked_ligands from the job names in self.glide_jobnames.

If self._force_jobs is False, the job fails in the event of subjob failure. Otherwise, the errors are logged and the job continues.

operate(self)

Perform an operation on the input files.

Overrides: stage.Stage.operate

Class DockingStage

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

checkInputs(self)

mergeGlideOutputs(self, input_files, num_comps_to_keep, best_by_compound)

check_subjob_output(self, glide_jobname)

buildDockedLigandsMap(self)

operate(self)

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