mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-05 22:04:27 +08:00
port over some changes made on Subshape branch (r179:218)
This commit is contained in:
Greg Landrum
411
Python/DataStructs/SparseIntVect.py
Executable file
411
Python/DataStructs/SparseIntVect.py
Executable file
@@ -0,0 +1,411 @@
|
||||
# $Id$
|
||||
#
|
||||
# Copyright (C) 2007 Greg Landrum
|
||||
# All Rights Reserved
|
||||
#
|
||||
|
||||
class SparseIntVect(object):
|
||||
size=0
|
||||
container={}
|
||||
def __init__(self,size):
|
||||
self.size=size
|
||||
self.container={}
|
||||
|
||||
def UpdateFromSequence(self,seq):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1.UpdateFromSequence((0,1,1,5))
|
||||
>>> [x for x in c1]
|
||||
[(0, 1), (1, 2), (5, 1)]
|
||||
>>> c1.UpdateFromSequence((0,3))
|
||||
>>> [x for x in c1]
|
||||
[(0, 2), (1, 2), (3, 1), (5, 1)]
|
||||
|
||||
"""
|
||||
for v in seq:
|
||||
self[v] += 1
|
||||
def InitFromSequence(self,seq):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1.InitFromSequence((0,1,1,5))
|
||||
>>> [x for x in c1]
|
||||
[(0, 1), (1, 2), (5, 1)]
|
||||
|
||||
"""
|
||||
self.container={}
|
||||
self.UpdateFromSequence(seq)
|
||||
|
||||
def Sum(self):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[2] = 2
|
||||
>>> c1[4] = 5
|
||||
>>> c1.Sum()
|
||||
10
|
||||
"""
|
||||
res=0
|
||||
for v in self.container.values():
|
||||
res+=v
|
||||
return res
|
||||
|
||||
|
||||
def __eq__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[2] = 2
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 3
|
||||
>>> c2[2] = 2
|
||||
>>> c1 == c2
|
||||
False
|
||||
>>> c1 == c1
|
||||
True
|
||||
"""
|
||||
if not isinstance(other,SparseIntVect):
|
||||
raise TypeError
|
||||
if self.size != other.size:
|
||||
return 0
|
||||
return self.container==other.container
|
||||
|
||||
|
||||
def __iand__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[2] = 2
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 2
|
||||
>>> c2[2] = -2
|
||||
>>> c2[5] = 6
|
||||
>>> c1 &= c2
|
||||
>>> [x for x in c1]
|
||||
[(0, 2), (2, -2)]
|
||||
|
||||
"""
|
||||
if not isinstance(other,SparseIntVect):
|
||||
raise TypeError
|
||||
if self.size != other.size:
|
||||
raise ValueError
|
||||
|
||||
newC = {}
|
||||
for idx,v in self.container.iteritems():
|
||||
ov = other.container.get(idx,0)
|
||||
if ov:
|
||||
if v<ov:
|
||||
newC[idx]=v
|
||||
else:
|
||||
newC[idx]=ov
|
||||
self.container=newC
|
||||
return self
|
||||
def __ior__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[2] = 2
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 2
|
||||
>>> c2[2] = -2
|
||||
>>> c2[5] = 6
|
||||
>>> c1 |= c2
|
||||
>>> [x for x in c1]
|
||||
[(0, 3), (2, 2), (4, 5), (5, 6)]
|
||||
|
||||
"""
|
||||
if not isinstance(other,SparseIntVect):
|
||||
raise TypeError
|
||||
if self.size != other.size:
|
||||
raise ValueError
|
||||
|
||||
newC = {}
|
||||
for idx,v in self.container.iteritems():
|
||||
ov = other.container.get(idx,0)
|
||||
if v<ov:
|
||||
newC[idx]=ov
|
||||
else:
|
||||
newC[idx]=v
|
||||
for k,v in other.container.iteritems():
|
||||
if not newC.has_key(k):
|
||||
newC[k]=v
|
||||
self.container=newC
|
||||
return self
|
||||
|
||||
def __iadd__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[2] = 2
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 2
|
||||
>>> c2[2] = -2
|
||||
>>> c2[5] = 6
|
||||
>>> c1 += c2
|
||||
>>> [x for x in c1]
|
||||
[(0, 5), (4, 5), (5, 6)]
|
||||
|
||||
"""
|
||||
if not isinstance(other,SparseIntVect):
|
||||
raise TypeError
|
||||
if self.size != other.size:
|
||||
raise ValueError
|
||||
seen={}
|
||||
for idx in self.container.keys():
|
||||
seen[idx]=1
|
||||
v = self.container[idx]+other[idx]
|
||||
if v:
|
||||
self.container[idx]=v
|
||||
else:
|
||||
del self.container[idx]
|
||||
for idx,v in other:
|
||||
if not seen.has_key(idx):
|
||||
self.container[idx]=v
|
||||
return self
|
||||
|
||||
def __isub__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[2] = 2
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 2
|
||||
>>> c2[2] = 2
|
||||
>>> c2[5] = 6
|
||||
>>> c1 -= c2
|
||||
>>> [x for x in c1]
|
||||
[(0, 1), (4, 5), (5, -6)]
|
||||
|
||||
"""
|
||||
if not isinstance(other,SparseIntVect):
|
||||
raise TypeError
|
||||
if self.size != other.size:
|
||||
raise ValueError
|
||||
seen={}
|
||||
for idx in self.container.keys():
|
||||
seen[idx]=1
|
||||
v = self.container[idx]-other[idx]
|
||||
if v:
|
||||
self.container[idx]=v
|
||||
else:
|
||||
del self.container[idx]
|
||||
for idx,v in other:
|
||||
if not seen.has_key(idx):
|
||||
self.container[idx]=-v
|
||||
return self
|
||||
|
||||
def __imul__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 2
|
||||
>>> c2[5] = 6
|
||||
>>> c1 *= c2
|
||||
>>> [x for x in c1]
|
||||
[(0, 6)]
|
||||
|
||||
"""
|
||||
if not isinstance(other,SparseIntVect):
|
||||
raise TypeError
|
||||
if self.size != other.size:
|
||||
raise ValueError
|
||||
for idx in self.container.keys():
|
||||
v = self.container[idx]*other[idx]
|
||||
if v:
|
||||
self.container[idx]=v
|
||||
else:
|
||||
del self.container[idx]
|
||||
return self
|
||||
|
||||
def __add__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 2
|
||||
>>> c2[5] = 6
|
||||
>>> c3 = c2+c1
|
||||
>>> [x for x in c3]
|
||||
[(0, 5), (4, 5), (5, 6)]
|
||||
|
||||
"""
|
||||
res = SparseIntVect(self.size)
|
||||
res.container = self.container
|
||||
res += other
|
||||
return res
|
||||
def __sub__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[2] = 2
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 2
|
||||
>>> c2[2] = 2
|
||||
>>> c2[5] = 6
|
||||
>>> c3 = c1-c2
|
||||
>>> [x for x in c1]
|
||||
[(0, 1), (4, 5), (5, -6)]
|
||||
|
||||
"""
|
||||
res = SparseIntVect(self.size)
|
||||
res.container = self.container
|
||||
res -= other
|
||||
return res
|
||||
def __mul__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 2
|
||||
>>> c2[5] = 6
|
||||
>>> c3 = c1*c2
|
||||
>>> [x for x in c3]
|
||||
[(0, 6)]
|
||||
|
||||
"""
|
||||
res = SparseIntVect(self.size)
|
||||
res.container = self.container
|
||||
res *= other
|
||||
return res
|
||||
def __and__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[2] = 2
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 2
|
||||
>>> c2[2] = -2
|
||||
>>> c2[5] = 6
|
||||
>>> c3 = c1 & c2
|
||||
>>> [x for x in c3]
|
||||
[(0, 2), (2, -2)]
|
||||
|
||||
"""
|
||||
res = SparseIntVect(self.size)
|
||||
res.container = self.container
|
||||
res &= other
|
||||
return res
|
||||
def __or__(self,other):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[2] = 2
|
||||
>>> c1[4] = 5
|
||||
>>> c2=SparseIntVect(10)
|
||||
>>> c2[0] = 2
|
||||
>>> c2[2] = -2
|
||||
>>> c2[5] = 6
|
||||
>>> c3 = c1 | c2
|
||||
>>> [x for x in c3]
|
||||
[(0, 3), (2, 2), (4, 5), (5, 6)]
|
||||
|
||||
"""
|
||||
res = SparseIntVect(self.size)
|
||||
res.container = self.container
|
||||
res |= other
|
||||
return res
|
||||
|
||||
|
||||
def __len__(self):
|
||||
return self.size
|
||||
def __getitem__(self,which):
|
||||
"""
|
||||
>>> c1=SparseIntVect(10)
|
||||
>>> c1[0] = 3
|
||||
>>> c1[4] = 5
|
||||
>>> c1[0]
|
||||
3
|
||||
>>> c1[1]
|
||||
0
|
||||
|
||||
"""
|
||||
if abs(which)>=self.size:
|
||||
raise IndexError,which
|
||||
if which<0:
|
||||
which = self.size-which
|
||||
return self.container.get(which,0)
|
||||
def __setitem__(self,which,val):
|
||||
if abs(which)>=self.size:
|
||||
raise IndexError,which
|
||||
val = int(val)
|
||||
if which<0:
|
||||
which = self.size-which
|
||||
self.container[which]=val
|
||||
def __iter__(self):
|
||||
"""
|
||||
>>> c=SparseIntVect(10)
|
||||
>>> c[0] = 3
|
||||
>>> c[4] = 5
|
||||
>>> c[7] = -1
|
||||
>>> for idx,v in c:
|
||||
... print idx,v
|
||||
0 3
|
||||
4 5
|
||||
7 -1
|
||||
|
||||
"""
|
||||
return self.container.iteritems()
|
||||
|
||||
|
||||
|
||||
def DiceSimilarity(v1,v2,bounds=None):
|
||||
""" Implements the DICE similarity metric.
|
||||
|
||||
>>> v1 = SparseIntVect(10)
|
||||
>>> v2 = SparseIntVect(10)
|
||||
>>> v1.InitFromSequence((1,2,3))
|
||||
>>> v2.InitFromSequence((1,2,3))
|
||||
>>> DiceSimilarity(v1,v2)
|
||||
1.0
|
||||
|
||||
>>> v2.InitFromSequence((5,6))
|
||||
>>> DiceSimilarity(v1,v2)
|
||||
0.0
|
||||
|
||||
>>> v1.InitFromSequence((1,2,3,4))
|
||||
>>> v2.InitFromSequence((1,3,5,7))
|
||||
>>> DiceSimilarity(v1,v2)
|
||||
0.5
|
||||
|
||||
>>> v1.InitFromSequence((1,2,3,4,5,6))
|
||||
>>> v2.InitFromSequence((1,3))
|
||||
>>> DiceSimilarity(v1,v2)
|
||||
0.5
|
||||
|
||||
"""
|
||||
denom = 1.0*(v1.Sum()+v2.Sum())
|
||||
if not denom:
|
||||
res = 0.0
|
||||
else:
|
||||
if bounds and (min(len(v1),len(v2))/denom) < bounds:
|
||||
numer = 0.0
|
||||
else:
|
||||
tv = v1&v2
|
||||
numer = 2.0*tv.Sum()
|
||||
res = numer/denom
|
||||
|
||||
return res
|
||||
|
||||
#------------------------------------
|
||||
#
|
||||
# doctest boilerplate
|
||||
#
|
||||
def _test():
|
||||
import doctest,sys
|
||||
return doctest.testmod(sys.modules["__main__"])
|
||||
|
||||
if __name__ == '__main__':
|
||||
import sys
|
||||
failed,tried = _test()
|
||||
sys.exit(failed)
|
||||
|
||||
Reference in New Issue
Block a user