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
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
|
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
#
# $Id: testDepictor.py 2112 2012-07-02 09:47:45Z glandrum $
#
#pylint:disable=E1101,C0111,C0103,R0904
from __future__ import division, print_function
import unittest
import os, sys
import numpy as np
from rdkit import Chem
from rdkit.Chem import rdDepictor
from rdkit import Geometry
from rdkit import RDConfig
from rdkit.Chem.ChemUtils import AlignDepict
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 getDistMat(mol):
conf = mol.GetConformer()
nat = mol.GetNumAtoms()
nl = nat * (nat - 1) // 2
res = np.zeros(nl, np.float)
for i in range(1, nat):
pi = conf.GetAtomPosition(i)
idx = i * (i - 1) // 2
for j in range(i):
pj = conf.GetAtomPosition(j)
pj -= pi
res[idx + j] = pj.Length()
return res
def compareCoords(m, molFile):
mo = Chem.MolFromMolFile(molFile)
co = mo.GetConformer()
ci = m.GetConformer()
nat = m.GetNumAtoms()
if (nat != mo.GetNumAtoms()):
return 0
for i in range(nat):
pos = ci.GetAtomPosition(i)
opos = co.GetAtomPosition(i)
if not ptEq(pos, opos):
return 0
return 1
def compareWithOld(smilesFile, sdFile):
smiSup = Chem.SmilesMolSupplier(smilesFile, ",", 0, -1)
sdsup = Chem.SDMolSupplier(sdFile)
im = 0
for mol in smiSup:
omol = sdsup[im]
rdDepictor.Compute2DCoords(mol, canonOrient=False)
conf = mol.GetConformer()
oconf = omol.GetConformer()
nat = mol.GetNumAtoms()
for i in range(nat):
pos = conf.GetAtomPosition(i)
opos = oconf.GetAtomPosition(i)
if not ptEq(pos, opos):
print(Chem.MolToMolBlock(omol), file=sys.stderr)
print('> <Failed>\n%d\n' % i, file=sys.stderr)
print("$$$$", file=sys.stderr)
print(Chem.MolToMolBlock(mol), file=sys.stderr)
print('> <Failed>\n%d\n' % i, file=sys.stderr)
print("$$$$", file=sys.stderr)
return 0
im += 1
return 1
def stereoCompare(smilesFile):
smiSup = Chem.SmilesMolSupplier(smilesFile, ",", 0, -1)
for mol in smiSup:
rdDepictor.Compute2DCoords(mol, canonOrient=False)
mb = Chem.MolToMolBlock(mol)
nmol = Chem.MolFromMolBlock(mb)
matches = nmol.GetSubstructMatches(mol, False)
dbnds = [x for x in mol.GetBonds() if (x.GetBondType() == Chem.BondType.DOUBLE and \
x.GetStereo() > Chem.BondStereo.STEREOANY) ]
ok = True
for match in matches:
for bnd in dbnds:
obnd = nmol.GetBondBetweenAtoms(match[bnd.GetBeginAtomIdx()], match[bnd.GetEndAtomIdx()])
assert (obnd.GetBondType() == Chem.BondType.DOUBLE)
if ok:
break
if not ok:
print(Chem.MolToMolBlock(mol), file=sys.stderr)
print("$$$$", file=sys.stderr)
return 0
return 1
class TestCase(unittest.TestCase):
def _test0First200(self):
# this test is disabled because it's not particularly useful and
# causes problems every time anything changes.
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Depictor', 'test_data',
'first_200.tpsa.csv')
#smiSup = Chem.SmilesMolSupplier(fileN, ",", 0, -1)
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Depictor', 'test_data',
'first_200.python.sdf')
self.assertTrue(compareWithOld(fileN, ofile))
def test1CisTrans(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Depictor', 'test_data',
"cis_trans_cases.csv")
self.assertTrue(stereoCompare(fileN))
def test2Coords(self):
m1 = Chem.MolFromSmiles('C1CCC1CC')
coordMap = {0: Geometry.Point2D(0, 0),
1: Geometry.Point2D(1.5, 0),
2: Geometry.Point2D(1.5, 1.5),
3: Geometry.Point2D(0, 1.5)}
rdDepictor.Compute2DCoords(m1, coordMap=coordMap)
conf = m1.GetConformer(0)
for i in range(4):
self.assertTrue(
ptEq(conf.GetAtomPosition(i), Geometry.Point3D(coordMap[i].x, coordMap[i].y, 0.0)))
m1 = Chem.MolFromSmiles('CCC')
try:
rdDepictor.Compute2DCoords(m1, coordMap=coordMap)
ok = 0
except ValueError:
ok = 1
self.assertTrue(ok)
def test3IssueSF1526844(self):
t = Chem.MolFromSmiles('c1nc(N)ccc1')
rdDepictor.Compute2DCoords(t, canonOrient=False)
m2 = Chem.MolFromSmiles('c1nc(NC=O)ccc1')
AlignDepict.AlignDepict(m2, t)
expected = [Geometry.Point3D(1.5, 0.0, 0.0), Geometry.Point3D(0.75, -1.299, 0.0),
Geometry.Point3D(-0.75, -1.299, 0.0), Geometry.Point3D(-1.5, -2.5981, 0.0),
Geometry.Point3D(-3.0, -2.5981, 0.0), Geometry.Point3D(-3.75, -3.8971, 0.0),
Geometry.Point3D(-1.5, 0.0, 0.0), Geometry.Point3D(-0.75, 1.2990, 0.0),
Geometry.Point3D(0.75, 1.2990, 0.0)]
nat = m2.GetNumAtoms()
conf = m2.GetConformer()
for i in range(nat):
pos = conf.GetAtomPosition(i)
self.assertTrue(ptEq(pos, expected[i], 0.001))
def test4SamplingSpread(self):
mol = Chem.MolFromMolFile(
os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor', 'test_data/7UPJ_xtal.mol'))
# default mode
rdDepictor.Compute2DCoords(mol, canonOrient=False)
self.assertTrue(
compareCoords(mol, os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor',
'test_data/7UPJ_default.mol')))
# spread the structure as much as possible by sampling
rdDepictor.Compute2DCoords(mol, canonOrient=False, nFlipsPerSample=3, nSample=100,
sampleSeed=100, permuteDeg4Nodes=1)
self.assertTrue(
compareCoords(mol, os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor',
'test_data/7UPJ_spread.mol')))
def test5SamplingMimic3D(self):
mol = Chem.MolFromMolFile(
os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor', 'test_data/7UPJ_xtal.mol'))
dmat3D = getDistMat(mol)
# now mimic the coordinate with a very small weight
rdDepictor.Compute2DCoordsMimicDistmat(mol, dmat3D, weightDistMat=0.001)
self.assertTrue(
compareCoords(mol, os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor',
'test_data/7UPJ_mimic3D_1.mol')))
# now mimic the coordinate with a very small weight
rdDepictor.Compute2DCoordsMimicDistmat(mol, dmat3D, weightDistMat=0.003)
self.assertTrue(
compareCoords(mol, os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor',
'test_data/7UPJ_mimic3D_2.mol')))
#mb = Chem.MolToMolBlock(mol)
#ofile = open('../test_data/7UPJ_mimic3D_2.mol', 'w')
#ofile.write(mb)
#ofile.close()
def test6ChangeBondLength(self):
m = Chem.MolFromSmiles('CC')
rdDepictor.Compute2DCoords(m)
conf = m.GetConformer()
self.assertAlmostEqual(conf.GetAtomPosition(0).x, -0.750, 3)
self.assertAlmostEqual(conf.GetAtomPosition(1).x, 0.750, 3)
rdDepictor.Compute2DCoords(m, bondLength=1.0)
conf = m.GetConformer()
self.assertAlmostEqual(conf.GetAtomPosition(0).x, -0.500, 3)
self.assertAlmostEqual(conf.GetAtomPosition(1).x, 0.500, 3)
rdDepictor.Compute2DCoords(m)
conf = m.GetConformer()
self.assertAlmostEqual(conf.GetAtomPosition(0).x, -0.750, 3)
self.assertAlmostEqual(conf.GetAtomPosition(1).x, 0.750, 3)
def testConstrainedCoords(self) :
templ = Chem.MolFromSmiles( 'c1nccc2n1ccc2' )
rdDepictor.Compute2DCoords( templ )
m1 = Chem.MolFromSmiles( 'c1cccc2ncn3cccc3c21' )
rdDepictor.GenerateDepictionMatching2DStructure(m1,templ)
m2 = Chem.MolFromSmiles( 'c1cc(Cl)cc2ncn3cccc3c21' )
rdDepictor.Compute2DCoords(m2)
refPatt1 = Chem.MolFromSmarts( '*1****2*1***2' )
rdDepictor.GenerateDepictionMatching2DStructure( m2 , templ , -1 , refPatt1 )
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Depictor', 'test_data',
'1XP0_ligand.sdf')
xp0_lig = Chem.MolFromMolFile( fileN )
xp0_lig_2d = Chem.Mol( xp0_lig )
rdDepictor.GenerateDepictionMatching3DStructure( xp0_lig_2d , xp0_lig )
xp0_ref = Chem.MolFromSmarts( '[#6]1~[#7][#6]~[#6]2[#6](=[#8])[#7]~[#6](c3ccccc3)[#7][#7]12' )
rdDepictor.GenerateDepictionMatching3DStructure( xp0_lig_2d , xp0_lig , -1 , xp0_ref )
if __name__ == '__main__':
rdDepictor.SetPreferCoordGen(False);
unittest.main()
|
