rdkit.Chem.Fingerprints.DbFpSupplier module

Supplies a class for working with fingerprints from databases #DOC

class rdkit.Chem.Fingerprints.DbFpSupplier.DbFpSupplier(dbResults, fpColName='AutoFragmentFp', usePickles=True)

Bases: VLibNode

new fps come back with all additional fields from the database set in a “_fieldsFromDb” data member

DbResults should be a subclass of Dbase.DbResultSet.DbResultBase

GetColumnNames()

next()

part of the iterator interface

raises StopIteration on failure

class rdkit.Chem.Fingerprints.DbFpSupplier.ForwardDbFpSupplier(*args, **kwargs)

Bases: DbFpSupplier

DbFp supplier supporting only forward iteration

>>> from rdkit import RDConfig
>>> from rdkit.Dbase.DbConnection import DbConnect
>>> fName = RDConfig.RDTestDatabase
>>> conn = DbConnect(fName,'simple_combined')
>>> suppl = ForwardDbFpSupplier(conn.GetData())

we can loop over the supplied fingerprints:

>>> fps = []
>>> for fp in suppl:
...   fps.append(fp)
>>> len(fps)
12

DbResults should be a subclass of Dbase.DbResultSet.DbResultBase

NextItem()

NOTE: this has side effects

reset()

resets our iteration state

class rdkit.Chem.Fingerprints.DbFpSupplier.RandomAccessDbFpSupplier(*args, **kwargs)

Bases: DbFpSupplier

DbFp supplier supporting random access:

>>> import os.path
>>> from rdkit import RDConfig
>>> from rdkit.Dbase.DbConnection import DbConnect
>>> fName = RDConfig.RDTestDatabase
>>> conn = DbConnect(fName,'simple_combined')
>>> suppl = RandomAccessDbFpSupplier(conn.GetData())
>>> len(suppl)
12

we can pull individual fingerprints:

>>> fp = suppl[5]
>>> fp.GetNumBits()
128
>>> fp.GetNumOnBits()
54

a standard loop over the fingerprints:

>>> fps = []
>>> for fp in suppl:
...   fps.append(fp)
>>> len(fps)
12

or we can use an indexed loop:

>>> fps = [None] * len(suppl)
>>> for i in range(len(suppl)):
...   fps[i] = suppl[i]
>>> len(fps)
12

DbResults should be a subclass of Dbase.DbResultSet.DbResultBase

NextItem()

reset()

resets our iteration state