def testCounts(self):
vals = [
((0, 1, 2), 4),
((0, 0, 0), 0),
((2, 2, 2), 9),
((1, 1, 2), 7),
((1, 2, 2), 8),
]
for combo, tgt in vals:
res = Utils.CountUpTo(3, 3, combo)
assert res == tgt, f'Bad res ({res}) for combo {str((combo, tgt))}'
def GetBitIdx(self, featIndices, dists, sortIndices=True):
""" returns the index for a pharmacophore described using a set of
feature indices and distances
**Arguments***
- featIndices: a sequence of feature indices
- dists: a sequence of distance between the features, only the
unique distances should be included, and they should be in the
order defined in Utils.
- sortIndices : sort the indices
**Returns**
the integer bit index
"""
nPoints = len(featIndices)
if nPoints > 3:
raise NotImplementedError('>3 points not supported')
if nPoints < self.minPointCount:
raise IndexError('bad number of points')
if nPoints > self.maxPointCount:
raise IndexError('bad number of points')
# this is the start of the nPoint-point pharmacophores
startIdx = self._starts[nPoints]
#
# now we need to map the pattern indices to an offset from startIdx
#
if sortIndices:
tmp = list(featIndices)
tmp.sort()
featIndices = tmp
if featIndices[0] < 0: raise IndexError('bad feature index')
if max(featIndices) >= self._nFeats:
raise IndexError('bad feature index')
if nPoints == 3:
featIndices, dists = Utils.OrderTriangle(featIndices, dists)
offset = Utils.CountUpTo(self._nFeats, nPoints, featIndices)
if _verbose:
print('offset for feature %s: %d' % (str(featIndices), offset))
offset *= len(self._scaffolds[len(dists)])
try:
if _verbose:
print('>>>>>>>>>>>>>>>>>>>>>>>')
print('\tScaffolds:', repr(self._scaffolds[len(dists)]),
type(self._scaffolds[len(dists)]))
print('\tDists:', repr(dists), type(dists))
print('\tbins:', repr(self._bins), type(self._bins))
bin = self._findBinIdx(dists, self._bins,
self._scaffolds[len(dists)])
except ValueError:
fams = self.GetFeatFamilies()
fams = [fams[x] for x in featIndices]
raise IndexError(
'distance bin not found: feats: %s; dists=%s; bins=%s; scaffolds: %s'
% (fams, dists, self._bins, self._scaffolds))
return startIdx + offset + bin