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Package CHEM :: Package Structure :: Module RMSDvsCorina :: Class RMSDvsCorina
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Class RMSDvsCorina



Given a list of molecules, presumably with 3D coordinates, run each through Corina to generate predicted 3D coordinates. Then compare the original 3D coordinates with those predicted by RMSD calculation and record the results.

Instance Methods [hide private]
 
__init__(self)
Constructor.
 
run(self, moleculeOEIS, rmsdFile)
Primary method to do everything, from Corina coordinate prediction, output of molecules to the simple format readable by the RMSD program, to the actual run of the RMSD program and recording of its results.
 
runCorina(self, inputFilename, outputFilename, inputFormat=None, outputFormat=None)
Reads from the named inputFile as an oemolistream and run Corina on these molecules to generate predicted coordinates.
Method Details [hide private]

__init__(self)
(Constructor)

  
Constructor.  Just setup default parameter values.

- outputFlushPeriod: Number of records to process before flushing output.
- inputStart: Only start processing from this record in the input stream (0-based)
- inputEnd: Stop processing before reaching this record in the input stream (0-based).
            Set to -1 to process until end of input.

The following are all boolean values
- delSmallFrags: Whether to delete everything except the first 
                largest component for multi-component molecules before 
                attempting any structure comparison.

The following are OERMSD parameters.  See OEChem API documentation for more info
- automorphism: Account for symmetry related transformations.  Useful, but can cause memory leak / crash for complicated mols
- heavyOnly: Only consider non-hydrogen atoms
- overlay: Rotate / translate molecules to find smallest RMSD

runCorina(self, inputFilename, outputFilename, inputFormat=None, outputFormat=None)

 

Reads from the named inputFile as an oemolistream and run Corina on these molecules to generate predicted coordinates. Writes the generated molecules as an oemolostream object to the named outputFile.

Must indicate the input / output formats of the molecule files as strings recognizable by Corina's -i/o t option. If omitted, will just use the extension string of the filenames.

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