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# $Id$
#
# Created by Greg Landrum, July 2008
#
from rdkit import RDConfig
import os
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 = '''-ta %(struchk_conf_path)scheckfgs.trn
-or
-ca %(struchk_conf_path)scheckfgs.chk
-cc
-cl 3
-cs
-cn 999
-l %(struchk_log_path)sstruchk.log'''%locals()
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.failUnless(smi=='c1ccncc1')
smi = pyAvalonTools.GetCanonSmiles('c1cccnc1',True)
self.failUnless(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']
d= file(os.path.join(RDConfig.RDDataDir,'NCI','first_200.props.sdf'),'r').read()
mbs = d.split('$$$$\n')[:10]
smis = [pyAvalonTools.GetCanonSmiles(mb,False) for mb in mbs]
self.failUnless(smis==tgts)
smis = [pyAvalonTools.GetCanonSmiles(smi,True) for smi in smis]
self.failUnless(smis==tgts)
def test3(self):
bv = pyAvalonTools.GetAvalonFP(Chem.MolFromSmiles('c1ccccn1'))
self.failUnlessEqual(len(bv),512)
self.failUnlessEqual(bv.GetNumOnBits(),20)
bv = pyAvalonTools.GetAvalonFP(Chem.MolFromSmiles('c1ccccc1'))
self.failUnlessEqual(bv.GetNumOnBits(),8)
bv = pyAvalonTools.GetAvalonFP(Chem.MolFromSmiles('c1nnccc1'))
self.failUnlessEqual(bv.GetNumOnBits(),30)
bv = pyAvalonTools.GetAvalonFP(Chem.MolFromSmiles('c1ncncc1'))
self.failUnlessEqual(bv.GetNumOnBits(),27)
bv = pyAvalonTools.GetAvalonFP(Chem.MolFromSmiles('c1ncncc1'),nBits=1024)
self.failUnlessEqual(len(bv),1024)
self.failUnless(bv.GetNumOnBits()>27)
def test4(self):
bv = pyAvalonTools.GetAvalonFP('c1ccccn1',True)
self.failUnlessEqual(bv.GetNumOnBits(),20)
bv = pyAvalonTools.GetAvalonFP('c1ccccc1',True)
self.failUnlessEqual(bv.GetNumOnBits(),8)
bv = pyAvalonTools.GetAvalonFP('c1nnccc1',True)
self.failUnlessEqual(bv.GetNumOnBits(),30)
bv = pyAvalonTools.GetAvalonFP('c1ncncc1',True)
self.failUnlessEqual(bv.GetNumOnBits(),27)
bv = pyAvalonTools.GetAvalonFP('c1ncncc1',True,nBits=1024)
self.failUnlessEqual(len(bv),1024)
self.failUnless(bv.GetNumOnBits()>27)
bv = pyAvalonTools.GetAvalonFP(Chem.MolToMolBlock(Chem.MolFromSmiles('c1ccccn1')),False)
self.failUnlessEqual(len(bv),512)
self.failUnlessEqual(bv.GetNumOnBits(),20)
bv = pyAvalonTools.GetAvalonFP(Chem.MolToMolBlock(Chem.MolFromSmiles('c1ccccc1')),False)
self.failUnlessEqual(bv.GetNumOnBits(),8)
def test4b(self):
words = pyAvalonTools.GetAvalonFPAsWords(Chem.MolFromSmiles('c1ccccn1'))
words2 = pyAvalonTools.GetAvalonFPAsWords(Chem.MolFromSmiles('Cc1ccccn1'))
self.failUnlessEqual(len(words),len(words2))
for i,word in enumerate(words):
self.failUnlessEqual(word&words2[i],word)
def test5(self):
m = Chem.MolFromSmiles('c1ccccc1C1(CC1)N')
pyAvalonTools.Generate2DCoords(m)
self.failUnlessEqual(m.GetNumConformers(),1)
self.failUnless(m.GetConformer(0).Is3D()==False)
def test6(self):
mb=pyAvalonTools.Generate2DCoords('c1ccccc1C1(CC1)N',True)
m = Chem.MolFromMolBlock(mb)
self.failUnlessEqual(m.GetNumConformers(),1)
self.failUnless(m.GetConformer(0).Is3D()==False)
def testRDK151(self):
smi="C[C@H](F)Cl"
m = Chem.MolFromSmiles(smi)
temp = pyAvalonTools.GetCanonSmiles(smi,True)
self.failUnlessEqual(temp,smi)
temp = pyAvalonTools.GetCanonSmiles(m)
self.failUnlessEqual(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.failUnlessEqual(r, 0)
(err, fixed_mol) = pyAvalonTools.CheckMolecule(smi_good, True)
self.failUnlessEqual(err, 0)
mol = Chem.MolFromSmiles(smi_good)
(err, fixed_mol)=pyAvalonTools.CheckMolecule(mol)
self.failUnlessEqual(err, 0)
(err, fixed_mol)=pyAvalonTools.CheckMoleculeString(smi_good,True)
self.failUnlessEqual(err, 0)
self.failIfEqual(fixed_mol,"")
self.failUnless(fixed_mol.find('M END')>0)
(err, fixed_mol)=pyAvalonTools.CheckMolecule(smi_bad, False)
self.failIfEqual(err, 0)
self.failIf(fixed_mol)
(err, fixed_mol)=pyAvalonTools.CheckMoleculeString(smi_bad, False)
self.failIfEqual(err, 0)
self.failIf(fixed_mol)
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.failUnlessEqual(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.failUnlessEqual(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.failUnlessEqual(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.failUnlessEqual(r, 0)
# (err, fixed_mol) = pyAvalonTools.CheckMolecule(mb, False)
# self.failUnlessEqual(err, 0)
# self.failUnless(fixed_mol)
# self.failIfEqual(fixed_mol.GetAtomWithIdx(0).GetChiralTag(),Chem.rdchem.ChiralType.CHI_UNSPECIFIED)
if __name__ == '__main__':
unittest.main()
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