1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
|
#
# Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Created by Nadine Schneider, July 2016
from rdkit import Chem
from rdkit.Chem import AllChem
from collections import defaultdict
import copy
def transferAgentsToReactants(rxn):
for a in range(rxn.GetNumAgentTemplates()):
agent = rxn.GetAgentTemplate(a)
rxn.AddReactantTemplate(agent)
def removeAgentsAndTransferToReactants(rxn):
tmp=[]
rxn.RemoveAgentTemplates(tmp)
for a in tmp:
rxn.AddReactantTemplate(a)
def getNumPositiveCounts(fp):
count=0
for k,v in fp.GetNonzeroElements().items():
if v > 0:
count+=v
return count
def getNumNegativeCounts(fp):
count=0
for k,v in fp.GetNonzeroElements().items():
if v < 0:
count+=abs(v)
return count
def getNumPositiveBitCountsOfRadius0(fp,bitinfo):
count=0
bitsUnmappedAtoms=[]
for k in bitinfo:
if bitinfo[k][0][1] == 0:
v = fp[k]
if v>0:
count += 1
bitsUnmappedAtoms.append((k,v))
return count,bitsUnmappedAtoms
def getSumFps(fps):
summedFP = copy.deepcopy(fps[0])
for fp in fps[1:]:
summedFP += fp
return summedFP
def uniqueMolecules(mols):
smiles = [Chem.MolToSmiles(mol) for mol in mols]
uniqueMolecules=defaultdict(int)
for n,smi in enumerate(smiles):
uniqueMolecules[n]=smiles.index(smi)
return uniqueMolecules,smiles
|
