Package schrodinger :: Package pipeline :: Package stages :: Module rmsd :: Class RmsdStage

Class RmsdStage

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


Stage for calculating RMSDs for structures in two sets.
    First set - original structures
    Second set - new conformations

The keywords specific to this stage are...

    UNIQUEFIELD_REF     - Property in the reference set used to match
                          structures for comparison.  If unset, it defaults
                          to the UNIQUEFIELD property. The RMSD is
                          calculated for pairs in which the UNIQUEFIELD_REF
                          value in the reference ligand matches the
                          UNIQUEFIELD value in the modified ligand.


    UNIQUEFIELD         - Property in the modified set used to match
                          structures for comparison.

    RMSDFIELD           - Property to save RMSDs into in the output file

    RENUMBER_STRUCTURES - Should be False if atom numbering is the same
                          between same structure in two input sets

    IGNORE_STATES       - If True, ignore hydrogens and treat all bonds
                          as single order.

The stage takes two input structure file sets and generates one
output structure file set.

Instance Methods

[hide private]

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

operate(self)
Algorithm: Compare each structure in the original (first) ligands set to every structure in the modified (second) set.

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)

See class docstring.

Overrides: UserDict.UserDict.__init__

operate(self)

Algorithm: Compare each structure in the original (first) ligands set to every structure in the modified (second) set. If their corresponding UNIQUEFIELD_* properties are the same, calculate RMS for the structure, save it to RMSDFIELD, and write out the structure to the output file.

Overrides: stage.Stage.operate

Class RmsdStage

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

operate(self)

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