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
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
|
# $Id: testConformer.py 997 2009-02-25 06:12:43Z glandrum $
#
# Copyright (C) 2004 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import RDConfig
import os,sys
import unittest
from rdkit import Chem
from rdkit.Geometry import Point3D
def feq(v1,v2,tol2=1e-4):
return abs(v1-v2)<=tol2
def ptEq(pt1, pt2, tol=1e-4):
return feq(pt1.x,pt2.x,tol) and feq(pt1.y,pt2.y,tol) and feq(pt1.z,pt2.z,tol)
def addConf(mol):
conf = Chem.Conformer(mol.GetNumAtoms())
for i in range(mol.GetNumAtoms()):
conf.SetAtomPosition(i,(0.,0.,0.))
mol.AddConformer(conf)
mb = Chem.MolToMolBlock(mol)
mb = Chem.MolToMolBlock(mol)
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test0Conformers(self) :
"""Test the conformer data structure"""
mol = Chem.MolFromSmiles("CC")
conf = Chem.Conformer(2)
conf.SetAtomPosition(0, (-0.5, 0.0, 0.0))
conf.SetAtomPosition(1, (1.0, 0.0, 0.0))
conf.SetId(0)
cid = mol.AddConformer(conf)
self.failUnless(cid == 0)
conf2 = mol.GetConformer(0)
self.failUnless(conf2.GetId() == cid)
pt1 = conf2.GetAtomPosition(0)
self.failUnless(ptEq(pt1, Point3D(-0.5, 0.0, 0.0)))
pt2 = conf2.GetAtomPosition(1)
self.failUnless(ptEq(pt2, Point3D(1.0, 0.0, 0.0)))
#changing conf should not change conf2 - related to issue 217
conf.SetAtomPosition(1, Point3D(2.0, 0.0, 0.0))
pt2 = conf2.GetAtomPosition(1)
self.failUnless(feq(pt2[0], 1.0))
conf = Chem.Conformer(2)
conf.SetAtomPosition(0, Point3D(-0.5, 0.0, 0.0))
conf.SetAtomPosition(1, Point3D(1.0, 0.0, 0.0))
conf.SetId(2)
cid = mol.AddConformer(conf, 0)
self.failUnless(cid == 2)
conf3 = mol.GetConformer(2)
def test0AddHds(self) :
mol = Chem.MolFromSmiles("CC")
conf = Chem.Conformer(1)
conf.SetAtomPosition(0, Point3D(-0.5, 0.0, 0.0))
conf.SetAtomPosition(1, Point3D(1.0, 0.0, 0.0))
cid = mol.AddConformer(conf)
conf2 = mol.GetConformer()
self.failUnless(conf2.GetNumAtoms() == 2)
nmol = Chem.AddHs(mol, 0,1)
conf3 = nmol.GetConformer()
self.failUnless(conf3.GetNumAtoms() == 8)
self.failUnless(conf2.GetNumAtoms() == 2)
targetCoords = [[-0.5, 0.0, 0.0],
[1.0, 0.0, 0.0],
[-0.8667, 0.0, 1.03709],
[-0.8667, 0.8981, -0.5185],
[-0.8667, -0.8981, -0.5185],
[1.3667, 0.0, -1.0371],
[1.36667, 0.8981, 0.5185],
[1.36667, -0.8981, 0.5185]]
for i in range(8) :
pt = conf3.GetAtomPosition(i)
self.failUnless(ptEq(pt, apply(Point3D,tuple(targetCoords[i]))))
def test2Issue217(self) :
smi = 'c1ccccc1'
m = Chem.MolFromSmiles(smi)
addConf(m)
self.failUnless(m.GetNumConformers()==1);
mb2 = Chem.MolToMolBlock(m)
def test3Exceptions(self) :
smi = 'c1ccccc1'
m = Chem.MolFromSmiles(smi)
addConf(m)
self.failUnless(m.GetNumConformers()==1)
self.failUnlessRaises(ValueError,lambda:m.GetConformer(2))
def test4ConfTuple(self):
smi = 'c1ccccc1'
m = Chem.MolFromSmiles(smi)
for i in range(10):
addConf(m)
confs = m.GetConformers()
self.failUnless(len(confs) == 10)
for conf in confs:
for i in range(6):
pt = conf.GetAtomPosition(i)
self.failUnless(ptEq(pt, Point3D(0.0, 0.0, 0.0)))
m.RemoveAllConformers()
self.failUnless(m.GetNumConformers() == 0)
confs = m.GetConformers()
self.failUnless(confs == ())
if __name__ == '__main__':
unittest.main()
|
