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|
#
# Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Supplies a class for working with fingerprints from databases
#DOC
"""
from rdkit import DataStructs
from rdkit.VLib.Node import VLibNode
import pickle
class DbFpSupplier(VLibNode):
"""
new fps come back with all additional fields from the
database set in a "_fieldsFromDb" data member
"""
def __init__(self, dbResults, fpColName='AutoFragmentFp', usePickles=True):
"""
DbResults should be a subclass of Dbase.DbResultSet.DbResultBase
"""
VLibNode.__init__(self)
self._usePickles = usePickles
self._data = dbResults
self._fpColName = fpColName.upper()
self._colNames = [x.upper() for x in self._data.GetColumnNames()]
if self._fpColName not in self._colNames:
raise ValueError('fp column name "%s" not found in result set: %s' %
(self._fpColName, str(self._colNames)))
self.fpCol = self._colNames.index(self._fpColName)
del self._colNames[self.fpCol]
self._colNames = tuple(self._colNames)
self._numProcessed = 0
def GetColumnNames(self):
return self._colNames
def _BuildFp(self, data):
data = list(data)
pkl = bytes(data[self.fpCol], encoding='Latin1')
del data[self.fpCol]
self._numProcessed += 1
try:
if self._usePickles:
newFp = pickle.loads(pkl, encoding='bytes')
else:
newFp = DataStructs.ExplicitBitVect(pkl)
except Exception:
import traceback
traceback.print_exc()
newFp = None
if newFp:
newFp._fieldsFromDb = data
return newFp
def next(self):
itm = self.NextItem()
if itm is None:
raise StopIteration
return itm
__next__ = next # py3
class ForwardDbFpSupplier(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
"""
def __init__(self, *args, **kwargs):
DbFpSupplier.__init__(self, *args, **kwargs)
self.reset()
def reset(self):
DbFpSupplier.reset(self)
self._dataIter = iter(self._data)
def NextItem(self):
"""
NOTE: this has side effects
"""
try:
d = next(self._dataIter)
except StopIteration:
d = None
if d is not None:
newFp = self._BuildFp(d)
else:
newFp = None
return newFp
class RandomAccessDbFpSupplier(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
"""
def __init__(self, *args, **kwargs):
DbFpSupplier.__init__(self, *args, **kwargs)
self.reset()
def __len__(self):
return len(self._data)
def __getitem__(self, idx):
newD = self._data[idx]
return self._BuildFp(newD)
def reset(self):
self._pos = -1
def NextItem(self):
self._pos += 1
res = None
if self._pos < len(self):
res = self[self._pos]
return res
# ------------------------------------
#
# doctest boilerplate
#
def _runDoctests(verbose=None): # pragma: nocover
import sys
import doctest
failed, _ = doctest.testmod(optionflags=doctest.ELLIPSIS, verbose=verbose)
sys.exit(failed)
if __name__ == '__main__': # pragma: nocover
_runDoctests()
|
