pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-05 22:04:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
1f2aff8a3b0d18e01d45b5ef21647527796baefb
rdkit/Python/DataStructs/SparseIntVect.py

420 lines
8.8 KiB
Python
Executable File
Raw Blame History

# $Id$
#
# Copyright (C) 2007 Greg Landrum
# All Rights Reserved
#
import copy
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 = copy.deepcopy(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 c3]
[(0, 1), (4, 5), (5, -6)]
>>> [x for x in c1]
[(0, 3), (2, 2), (4, 5)]
"""
res = SparseIntVect(self.size)
res.container = copy.deepcopy(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)]
>>> [x for x in c1]
[(0, 3), (4, 5)]
"""
res = SparseIntVect(self.size)
res.container = copy.deepcopy(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)]
>>> [x for x in c1]
[(0, 3), (2, 2), (4, 5)]
"""
res = SparseIntVect(self.size)
res.container = copy.deepcopy(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)]
>>> [x for x in c1]
[(0, 3), (2, 2), (4, 5)]
"""
res = SparseIntVect(self.size)
res.container = copy.deepcopy(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 View Git Blame Copy Permalink