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# $Id$
#
# Created by Greg Landrum, July 2008
#
from __future__ import print_function
from rdkit import RDConfig
import os, sys
import unittest
from rdkit import DataStructs, Chem
from rdkit.Avalon import pyAvalonTools
struchk_conf_path = os.path.join(RDConfig.RDDataDir, 'struchk', '')
struchk_log_path = ''
STRUCHK_INIT = '''-tm
-ta %(struchk_conf_path)scheckfgs.trn
-tm
-or
-ca %(struchk_conf_path)scheckfgs.chk
-cc
-cl 3
-cs
-cn 999
-l %(struchk_log_path)sstruchk.log''' % locals()
STRUCHK_INIT_IN_MEMORY_LOGGING = '''-tm
-ta %(struchk_conf_path)scheckfgs.trn
-tm
-or
-ca %(struchk_conf_path)scheckfgs.chk
-cc
-cl 3
-cs
-cn 999''' % locals()
#
# PubChem test molecule converted from the RCSB
# mondo errors here.
atom_clash = """2FV9_002_B_2
RCSB PDB01151502013D
Coordinates from PDB:2FV9:B:2 Model:1 without hydrogens
32 32 0 0 0 0 999 V2000
46.8220 28.7360 39.6060 C 0 0 0 0 0 0 0 0 0 0 0 0
47.3620 28.0340 38.3430 C 0 0 0 0 0 0 0 0 0 0 0 0
47.5920 29.0540 37.2270 C 0 0 0 0 0 0 0 0 0 0 0 0
48.4130 28.4900 36.0770 C 0 0 0 0 0 0 0 0 0 0 0 0
47.1640 31.0380 40.1700 C 0 0 0 0 0 0 0 0 0 0 0 0
46.6160 27.6990 40.7140 C 0 0 0 0 0 0 0 0 0 0 0 0
45.0330 26.1340 41.6460 C 0 0 0 0 0 0 0 0 0 0 0 0
44.1100 26.4530 42.8300 C 0 0 0 0 0 0 0 0 0 0 0 0
49.2550 34.1450 39.3140 C 0 0 0 0 0 0 0 0 0 0 0 0
48.2670 33.0140 39.1740 C 0 0 0 0 0 0 0 0 0 0 0 0
44.3710 25.0810 40.7680 C 0 0 0 0 0 0 0 0 0 0 0 0
46.3620 26.9550 37.9090 C 0 0 0 0 0 0 0 0 0 0 0 0
47.7210 29.8260 39.9930 N 0 0 0 0 0 0 0 0 0 0 0 0
47.5720 27.2580 41.3530 O 0 0 0 0 0 0 0 0 0 0 0 0
44.7760 23.9020 40.8430 O 0 0 0 0 0 0 0 0 0 0 0 0
49.7640 36.2780 39.7670 O 0 0 0 0 0 0 0 0 0 0 0 0
44.8290 27.0700 44.0370 C 0 0 0 0 0 0 0 0 0 0 0 0
46.0700 26.2600 44.4160 C 0 0 0 0 0 0 0 0 0 0 0 0
43.8840 27.1450 45.2400 C 0 0 0 0 0 0 0 0 0 0 0 0
48.7580 35.3740 39.5170 N 0 0 0 0 0 0 0 0 0 0 0 0
50.4620 33.9280 39.2410 O 0 0 0 0 0 0 0 0 0 0 0 0
48.1640 32.1600 40.4390 C 0 0 0 0 0 0 0 0 0 0 0 0
47.7340 32.9890 41.6620 C 0 0 0 0 0 0 0 0 0 0 0 0
45.9630 31.2790 40.1090 O 0 0 0 0 0 0 0 0 0 0 0 0
45.3280 27.3570 40.9080 N 0 0 0 0 0 0 0 0 0 0 0 0
43.4500 25.4420 40.0020 O 0 0 0 0 0 0 0 0 0 0 0 0
47.8720 32.1800 42.9370 C 0 0 0 0 0 0 0 0 0 0 0 0
49.0780 32.2360 43.6910 C 0 0 0 0 0 0 0 0 0 0 0 0
49.1970 31.5090 44.9110 C 0 0 0 0 0 0 0 0 0 0 0 0
48.1080 30.7170 45.3760 C 0 0 0 0 0 0 0 0 0 0 0 0
46.9120 30.6330 44.6100 C 0 0 0 0 0 0 0 0 0 0 0 0
46.7920 31.3650 43.3900 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 6 1 0 0 0 0
1 13 1 0 0 0 0
2 3 1 0 0 0 0
2 12 1 0 0 0 0
3 4 1 0 0 0 0
5 13 1 0 0 0 0
5 22 1 0 0 0 0
5 24 2 0 0 0 0
6 14 2 0 0 0 0
6 25 1 0 0 0 0
7 8 1 0 0 0 0
7 11 1 0 0 0 0
7 25 1 0 0 0 0
8 17 1 0 0 0 0
9 10 1 0 0 0 0
9 20 1 0 0 0 0
9 21 2 0 0 0 0
10 22 1 0 0 0 0
11 15 2 0 0 0 0
11 26 1 0 0 0 0
16 20 1 0 0 0 0
17 18 1 0 0 0 0
17 19 1 0 0 0 0
22 23 1 0 0 0 0
23 27 1 0 0 0 0
27 28 2 0 0 0 0
27 32 1 0 0 0 0
28 29 1 0 0 0 0
29 30 2 0 0 0 0
30 31 1 0 0 0 0
31 32 2 0 0 0 0
M END
> <InstanceId>
2FV9_002_B_2
> <ChemCompId>
002
> <PdbId>
2FV9
> <ChainId>
B
> <ResidueNumber>
2
> <InsertionCode>
> <Model>
1
> <AltIds>
> <MissingHeavyAtoms>
0
> <ObservedFormula>
C23 N3 O6
> <Name>
N-[(2R)-2-BENZYL-4-(HYDROXYAMINO)-4-OXOBUTANOYL]-L-ISOLEUCYL-L-LEUCINE
> <SystematicName>
(2S)-2-[[(2S,3S)-2-[[(2R)-4-(hydroxyamino)-4-oxo-2-(phenylmethyl)butanoyl]amino]-3-methyl-pentanoyl]amino]-4-methyl-pentanoic acid
> <Synonyms>
> <Type>
NON-POLYMER
> <Formula>
C23 H35 N3 O6
> <MolecularWeight>
449.541
> <ModifiedDate>
2011-06-04
> <Parent>
> <OneLetterCode>
> <SubcomponentList>
> <AmbiguousFlag>
> <InChI>
InChI=1S/C23H35N3O6/c1-5-15(4)20(22(29)24-18(23(30)31)11-14(2)3)25-21(28)17(13-19(27)26-32)12-16-9-7-6-8-10-16/h6-10,14-15,17-18,20,32H,5,11-13H2,1-4H3,(H,24,29)(H,25,28)(H,26,27)(H,30,31)/t15-,17+,18-,20-/m0/s1
> <InChIKey>
MWZOULASPWUGJJ-NFBUACBFSA-N
> <SMILES>
CC[C@H](C)[C@@H](C(=O)N[C@@H](CC(C)C)C(=O)O)NC(=O)[C@H](Cc1ccccc1)CC(=O)NO
$$$$
"""
def feq(v1, v2, tol=1e-4):
return abs(v1 - v2) < tol
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test1(self):
m1 = Chem.MolFromSmiles('c1cccnc1')
smi = pyAvalonTools.GetCanonSmiles(m1)
self.assertTrue(smi == 'c1ccncc1')
smi = pyAvalonTools.GetCanonSmiles('c1cccnc1', True)
self.assertTrue(smi == 'c1ccncc1')
def test2(self):
tgts = ['CC1=CC(=O)C=CC1=O', 'c2ccc1SC(=Nc1c2)SSC4=Nc3ccccc3S4',
'[O-][N+](=O)c1cc(Cl)c(O)c(c1)[N+]([O-])=O', 'N=C1NC=C(S1)[N+]([O-])=O',
'Nc3ccc2C(=O)c1ccccc1C(=O)c2c3', 'OC(=O)c1ccccc1C3=C2C=CC(=O)C(Br)=C2Oc4c3ccc(O)c4Br',
'CN(C)C2C(=O)c1ccccc1C(=O)C=2Cl', 'Cc3ccc2C(=O)c1ccccc1C(=O)c2c3[N+]([O-])=O',
r'C/C(=N\O)/C(/C)=N/O', 'c1ccc(cc1)P(c2ccccc2)c3ccccc3']
with open(os.path.join(RDConfig.RDDataDir, 'NCI', 'first_200.props.sdf'), 'r') as f:
d = f.read()
mbs = d.split('$$$$\n')[:10]
smis = [pyAvalonTools.GetCanonSmiles(mb, False) for mb in mbs]
self.assertTrue(smis == tgts)
smis = [pyAvalonTools.GetCanonSmiles(smi, True) for smi in smis]
self.assertTrue(smis == tgts)
def test3(self):
bv = pyAvalonTools.GetAvalonFP(Chem.MolFromSmiles('c1ccccn1'))
self.assertEqual(len(bv), 512)
self.assertEqual(bv.GetNumOnBits(), 20)
bv = pyAvalonTools.GetAvalonFP(Chem.MolFromSmiles('c1ccccc1'))
self.assertEqual(bv.GetNumOnBits(), 8)
bv = pyAvalonTools.GetAvalonFP(Chem.MolFromSmiles('c1nnccc1'))
self.assertEqual(bv.GetNumOnBits(), 30)
bv = pyAvalonTools.GetAvalonFP(Chem.MolFromSmiles('c1ncncc1'))
self.assertEqual(bv.GetNumOnBits(), 27)
bv = pyAvalonTools.GetAvalonFP(Chem.MolFromSmiles('c1ncncc1'), nBits=1024)
self.assertEqual(len(bv), 1024)
self.assertTrue(bv.GetNumOnBits() > 27)
def test4(self):
bv = pyAvalonTools.GetAvalonFP('c1ccccn1', True)
self.assertEqual(bv.GetNumOnBits(), 20)
bv = pyAvalonTools.GetAvalonFP('c1ccccc1', True)
self.assertEqual(bv.GetNumOnBits(), 8)
bv = pyAvalonTools.GetAvalonFP('c1nnccc1', True)
self.assertEqual(bv.GetNumOnBits(), 30)
bv = pyAvalonTools.GetAvalonFP('c1ncncc1', True)
self.assertEqual(bv.GetNumOnBits(), 27)
bv = pyAvalonTools.GetAvalonFP('c1ncncc1', True, nBits=1024)
self.assertEqual(len(bv), 1024)
self.assertTrue(bv.GetNumOnBits() > 27)
bv = pyAvalonTools.GetAvalonFP(Chem.MolToMolBlock(Chem.MolFromSmiles('c1ccccn1')), False)
self.assertEqual(len(bv), 512)
self.assertEqual(bv.GetNumOnBits(), 20)
bv = pyAvalonTools.GetAvalonFP(Chem.MolToMolBlock(Chem.MolFromSmiles('c1ccccc1')), False)
self.assertEqual(bv.GetNumOnBits(), 8)
def test4b(self):
words = pyAvalonTools.GetAvalonFPAsWords(Chem.MolFromSmiles('c1ccccn1'))
words2 = pyAvalonTools.GetAvalonFPAsWords(Chem.MolFromSmiles('Cc1ccccn1'))
self.assertEqual(len(words), len(words2))
for i, word in enumerate(words):
self.assertEqual(word & words2[i], word)
def test5(self):
m = Chem.MolFromSmiles('c1ccccc1C1(CC1)N')
pyAvalonTools.Generate2DCoords(m)
self.assertEqual(m.GetNumConformers(), 1)
self.assertTrue(m.GetConformer(0).Is3D() == False)
def test6(self):
mb = pyAvalonTools.Generate2DCoords('c1ccccc1C1(CC1)N', True)
m = Chem.MolFromMolBlock(mb)
self.assertEqual(m.GetNumConformers(), 1)
self.assertTrue(m.GetConformer(0).Is3D() == False)
def testRDK151(self):
smi = "C[C@H](F)Cl"
m = Chem.MolFromSmiles(smi)
temp = pyAvalonTools.GetCanonSmiles(smi, True)
self.assertEqual(temp, smi)
temp = pyAvalonTools.GetCanonSmiles(m)
self.assertEqual(temp, smi)
def testStruChk(self):
smi_good = 'c1ccccc1C1(CC-C(C)C1)C'
smi_bad = 'c1c(R)cccc1C1(CC-C(C)C1)C'
r = pyAvalonTools.InitializeCheckMol(STRUCHK_INIT)
self.assertEqual(r, 0)
(err, fixed_mol) = pyAvalonTools.CheckMolecule(smi_good, True)
self.assertEqual(err, 0)
mol = Chem.MolFromSmiles(smi_good)
(err, fixed_mol) = pyAvalonTools.CheckMolecule(mol)
self.assertEqual(err, 0)
(err, fixed_mol) = pyAvalonTools.CheckMoleculeString(smi_good, True)
self.assertEqual(err, 0)
self.assertNotEqual(fixed_mol, "")
self.assertTrue(fixed_mol.find('M END') > 0)
(err, fixed_mol) = pyAvalonTools.CheckMolecule(smi_bad, False)
self.assertNotEqual(err, 0)
self.assertFalse(fixed_mol)
(err, fixed_mol) = pyAvalonTools.CheckMoleculeString(smi_bad, False)
self.assertNotEqual(err, 0)
self.assertFalse(fixed_mol)
pyAvalonTools.CloseCheckMolFiles()
def testStruChkInMemoryLog(self):
r = pyAvalonTools.InitializeCheckMol(STRUCHK_INIT_IN_MEMORY_LOGGING)
try:
(err, fixed_mol) = pyAvalonTools.CheckMoleculeString(atom_clash, False)
log = pyAvalonTools.GetCheckMolLog()
self.assertTrue("of average bond length from bond" in log)
# make sure that the log is cleared for the next molecule
(err, fixed_mol) = pyAvalonTools.CheckMoleculeString("c1ccccc1", True)
log = pyAvalonTools.GetCheckMolLog()
self.assertFalse(log)
finally:
pyAvalonTools.CloseCheckMolFiles()
# def testIsotopeBug(self):
# mb="""D isotope problem.mol
# Mrv0541 08141217122D
# 4 3 0 0 0 0 999 V2000
# -3.2705 0.5304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
# -2.5561 0.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
# -1.8416 0.5304 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
# -2.5561 1.7679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
# 1 2 1 0 0 0 0
# 2 3 1 0 0 0 0
# 2 4 1 0 0 0 0
# M ISO 1 3 2
# M END
# """
# csmi = pyAvalonTools.GetCanonSmiles(mb,False)
# self.assertEqual(csmi,'[2H]C(C)C')
# mb="""D isotope problem.mol
# Mrv0541 08141217122D
# 4 3 0 0 0 0 999 V2000
# -3.2705 0.5304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
# -2.5561 0.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
# -1.8416 0.5304 0.0000 H 2 0 0 0 0 0 0 0 0 0 0 0
# -2.5561 1.7679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
# 1 2 1 0 0 0 0
# 2 3 1 0 0 0 0
# 2 4 1 0 0 0 0
# M ISO 1 3 2
# M END
# """
# csmi = pyAvalonTools.GetCanonSmiles(mb,False)
# self.assertEqual(csmi,'[2H]C(C)C')
# mb="""D isotope problem.mol
# Mrv0541 08141217122D
# 4 3 0 0 0 0 999 V2000
# -3.2705 0.5304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
# -2.5561 0.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
# -1.8416 0.5304 0.0000 D 0 0 0 0 0 0 0 0 0 0 0 0
# -2.5561 1.7679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
# 1 2 1 0 0 0 0
# 2 3 1 0 0 0 0
# 2 4 1 0 0 0 0
# M END
# """
# csmi = pyAvalonTools.GetCanonSmiles(mb,False)
# self.assertEqual(csmi,'[2H]C(C)C')
# def testChiralPBug(self):
# mb="""Untitled Document-1
# Mrv0541 08161213182D
# 5 4 0 0 0 0 999 V2000
# -1.1196 1.1491 0.0000 P 0 0 2 0 0 0 0 0 0 0 0 0
# -0.4052 1.5616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
# -1.9446 1.1491 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
# -1.3332 1.9460 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
# -0.7071 0.4346 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
# 1 2 1 0 0 0 0
# 1 3 1 0 0 0 0
# 1 4 2 0 0 0 0
# 1 5 1 1 0 0 0
# M END
# """
# r = pyAvalonTools.InitializeCheckMol(STRUCHK_INIT)
# self.assertEqual(r, 0)
# (err, fixed_mol) = pyAvalonTools.CheckMolecule(mb, False)
# self.assertEqual(err, 0)
# self.assertTrue(fixed_mol)
# self.assertNotEqual(fixed_mol.GetAtomWithIdx(0).GetChiralTag(),Chem.rdchem.ChiralType.CHI_UNSPECIFIED)
def testAvalonCountFPs(self):
# need to go to longer bit counts to avoid collions:
cv1 = pyAvalonTools.GetAvalonCountFP('c1ccccc1', True, nBits=6000)
cv2 = pyAvalonTools.GetAvalonCountFP('c1ccccc1.c1ccccc1', True, nBits=6000)
for idx, v in cv1.GetNonzeroElements().items():
self.assertEqual(2 * v, cv2[idx])
cv1 = pyAvalonTools.GetAvalonCountFP(Chem.MolFromSmiles('c1ccccc1'), nBits=6000)
cv2 = pyAvalonTools.GetAvalonCountFP(Chem.MolFromSmiles('c1ccccc1.c1ccccc1'), nBits=6000)
for idx, v in cv1.GetNonzeroElements().items():
self.assertEqual(2 * v, cv2[idx])
if __name__ == '__main__':
unittest.main()
|
