Package CHEM :: Package CombiCDB :: Module BaseScreen :: Class BaseScreen

Class BaseScreen

Abstract base class for all screen classes. Screen classes are those that take an oemolistream (list of molecules) as input and outputs a subset of them, as an oemolostream, that passes some screening criteria, determined by the instantiating class.

Subclasses should primarily just define their own constructor that accepts as parameters anything necessary to define the screening function, and override the screenMolecule(...) method.

Once done, then client code just needs to create an instance, set the input and output sources and any screening parameters and call runScreen(...) to fill in the output stream.

Instance Methods

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setOEIS(self, oeis)

setOEOS(self, oeos)

setParameter(self, key, value)

getParameter(self, key)

clearParameters(self)

screenMolecule(self, mol)
Primary method for subclass to override.

screenSmiles(self, smiles)
Wrapper for primary screenMolecule method.

prepareParameters(self)
Another method for subclass to override.

runScreen(self)
Primary execution method to be called by client code.

runScreenByFilename(self, sourceFilename, screenFilename)
Alternative to runScreen(...) where filenames are specified to read / write instead of assuming the mOEIS and mOEOS attributes are set.

Class Variables

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mOEIS = <CHEM.DB.rdb.search.NameRxnPatternMatchingModel.Search...
Output oemolostream to send screened results to

mOEOS = <CHEM.DB.rdb.search.NameRxnPatternMatchingModel.Search...
Screening parameters as a dictionary.

mParameters = {}

Method Details

[hide private]

screenMolecule(self, mol)

Primary method for subclass to override. Given a molecule (OEMolBase), the method should just return True or False as to whether the molecule passes the screening criteria.

screenSmiles(self, smiles)

Wrapper for primary screenMolecule method. Creates a molecule object by parsing the SMILES string first.

prepareParameters(self)

Another method for subclass to override. Called before any screenMolecule(...) is done by the runScreen(...) method. This is important if say, the caller uses the setParameter(...) method after instantiation, then need to have a chance to prepare the parameters for usage, since can't count on it being done at construction time and don't want to have to do it each time screenMolecule(...) is called.

However, this also means, if the screenMolecule(...) method is called directly instead of runScreen(...), the caller must be responsible to call prepareParameters(...) first.

The again, if no extra parameter preparation is necessary, as in if simple calls to getParameter(...) can be used by the screenMolecule(...) method, then not much to do here.

runScreen(self)

Primary execution method to be called by client code. After setting the input and output streams and any screening parameters, just iterate through the input stream and pass all molecules that pass the screenMolecule(...) method to the output stream.

Class Variable Details

[hide private]

mOEIS

Output oemolostream to send screened results to

Value:

None

mOEOS

Screening parameters as a dictionary. Better to have these all set by the instantiating subclass's constructor, but have it here to provide option to specify or change after instantiation, while still only using base class methods.

Value:

None