Package CHEM :: Package DB :: Module DBPopulator2 :: Class DBPopulator

Class DBPopulator

BaseDBPopulator.BaseDBPopulator --+
                                  |
                                 DBPopulator

Script to read SDF or other molecule files and insert into the ChemDB non-redundantly.

The core structure is in the run method, leaving most of the details to independent processor and iterator preparer objects for each table. Standard ones are included in this module, but additional processors can be created and added to this DBPopulator object to accumulate the steps done for molecule curation / processing.

Instance Methods

[hide private]

__init__(self)
Constructor.

optparse(self, parser)

setoptions(self, options)
Load any relevant options from the command-line parser

run(self)
Primary method that traverses through the database schema, populating it with the input data as it goes.

__mainIteration(self, source, chemicalmix)
Primary execution code done once per iteration

Inherited from BaseDBPopulator.BaseDBPopulator: addProcessor, clearProcessors, loadOptions, prepareIterator, processObject, setIteratorPreparer

Class Variables

[hide private]

skipErrors = False

startIndex = <CHEM.DB.rdb.search.NameRxnPatternMatchingModel.S...

endIndex = <CHEM.DB.rdb.search.NameRxnPatternMatchingModel.Sea...

Inherited from BaseDBPopulator.BaseDBPopulator: preparerDict, processorsDict

Method Details

[hide private]

init(self)
(Constructor)

Constructor. Initialize processor object dictionaries to empty, and expected processor lists to empty lists.

Overrides: BaseDBPopulator.BaseDBPopulator.__init__

run(self)

Primary method that traverses through the database schema, populating it with the input data as it goes. High level function. Details are left to independent processor objects.

Overrides: BaseDBPopulator.BaseDBPopulator.run

Class Variable Details

[hide private]

startIndex

Value:

None

endIndex

Value:

None

Class DBPopulator

__init__(self) (Constructor)

run(self)

startIndex

endIndex

init(self)
(Constructor)