def testRSMItoRINCHI(self):
data = [
("C>N>O", "RInChI=1.00.1S/CH4/h1H4<>H2O/h1H2<>H3N/h1H3/d+"),
("O>N>C", "RInChI=1.00.1S/CH4/h1H4<>H2O/h1H2<>H3N/h1H3/d-"),
("O>>C", "RInChI=1.00.1S/CH4/h1H4<>H2O/h1H2/d-"),
# The following is assumed to be d+ by analogy with
# the empty reaction which is d+
("O>>O", "RInChI=1.00.1S/H2O/h1H2<>H2O/h1H2/d+"),
# Example: esterification of acetic acid
("OCC.CC(=O)O>S(=O)(=O)(O)O>CC(=O)OCC.O", "RInChI=1.00.1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)!C2H6O/c1-2-3/h3H,2H2,1H3<>C4H8O2/c1-3-6-4(2)5/h3H2,1-2H3!H2O/h1H2<>H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/d+"),
# Example: alkaline ring opening
("CC[C@]1(C)O[C@H]1C.[OH-]>>CC[C@](C)(O)[C@@H](C)O", "RInChI=1.00.1S/C6H12O/c1-4-6(3)5(2)7-6/h5H,4H2,1-3H3/t5-,6-/m0/s1!H2O/h1H2/p-1<>C6H14O2/c1-4-6(3,8)5(2)7/h5,7-8H,4H2,1-3H3/t5-,6+/m1/s1/d+"),
# Partial reactions
(">>C1CC=C(O)CC1", "RInChI=1.00.1S/<>C6H10O/c7-6-4-2-1-3-5-6/h4,7H,1-3,5H2/d+"),
("C1CC=C(O)CC1>>", "RInChI=1.00.1S/<>C6H10O/c7-6-4-2-1-3-5-6/h4,7H,1-3,5H2/d-"),
# The empty reaction
(">>", "RInChI=1.00.1S//d+"),
# Test 'no-structure'
("c1ccccc1C=C>>*", "RInChI=1.00.1S/<>C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2/d-/u1-0-0"),
("*>>C1CC=C(O)CC1", "RInChI=1.00.1S/<>C6H10O/c7-6-4-2-1-3-5-6/h4,7H,1-3,5H2/d+/u1-0-0"),
("O>*>C", "RInChI=1.00.1S/CH4/h1H4<>H2O/h1H2/d-/u0-0-1"),
("*.O>>C", "RInChI=1.00.1S/CH4/h1H4<>H2O/h1H2/d-/u0-1-0"),
# Empty except for 'no-structures' (assumed)
("*>*>*", "RInChI=1.00.1S//d+/u1-1-1"),
]
for eqm in [False, True]:
for rsmi, rinchi in data:
if eqm:
output, error = run_exec('obabel -:%s -ismi -orinchi -xe' % rsmi)
ans = rinchi.replace("/d-", "/d=").replace("/d+", "/d=")
self.assertEqual(output.rstrip(), ans)
else:
output, error = run_exec('obabel -:%s -ismi -orinchi' % rsmi)
self.assertEqual(output.rstrip(), rinchi)
def testSMILESto3DMDL(self):
"""Test interconversion between SMILES and 3D MDL"""
data = [
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 3]), # 'ClC=CF'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0]), # 'Cl/C=C/F'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0]), # 'Cl/C=C\\F'
# The bond parities are irrelevant/meaningless for the next two
([0, 0, 0, 0, 1], []), # 'Cl[C@@](Br)(F)I'
([0, 0, 0, 0, 2], []), # 'Cl[C@](Br)(F)I'
([0, 0, 0, 0, 3], [0, 0, 0, 4]), # 'ClC(Br)(F)I'
([0, 0, 0, 1], []), # 'O=[S@@](Cl)I),
([0, 0, 0, 2], []), # 'O=[S@](Cl)I),
([0, 0, 0, 3], []), # 'O=S(Cl)I),
([0]*9, [0]*8 + [3]), # "IC=C1NC1"
([0]*9, [0]*9), # r"I/C=C\1/NC1"
([0]*9, [0]*9), # r"I/C=C/1\NC1"
]
for i, (atompar, bondstereo) in enumerate(data):
smiles, can = self.data[i][0:2]
output, error = run_exec(smiles, "babel -ismi -osdf --gen3d")
atoms, bonds = self.parseMDL(output)
parities = [atom['parity'] for atom in atoms]
parities.sort()
stereos = [bond['stereo'] for bond in bonds]
stereos.sort()
self.assertEqual(atompar, parities)
if bondstereo:
self.assertEqual(bondstereo, stereos)
output, error = run_exec(output, "babel -isdf -ocan")
self.assertEqual(output.rstrip(), can)
def testSMILESto3DMDL(self):
"""Test interconversion between SMILES and 3D MDL"""
data = [
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 3]), # 'ClC=CF'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 3]), # 'ClC=CF'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0]), # 'Cl/C=C/F'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0]), # 'Cl/C=C\\F'
# The bond parities are irrelevant/meaningless for the next two
([0, 0, 0, 0, 1], []), # 'Cl[C@@](Br)(F)I'
([0, 0, 0, 0, 2], []), # 'Cl[C@](Br)(F)I'
([0, 0, 0, 0, 3], [0, 0, 0, 0]), # 'ClC(Br)(F)I'
([0, 0, 0, 1], []), # 'O=[S@@](Cl)I),
([0, 0, 0, 2], []), # 'O=[S@](Cl)I),
([0, 0, 0, 3], []), # 'O=S(Cl)I),
([0] * 9, [0] * 8 + [3]), # "IC=C1NC1"
([0] * 9, [0] * 9), # r"I/C=C\1/NC1"
([0] * 9, [0] * 9), # r"I/C=C/1\NC1"
]
for i, (atompar, bondstereo) in enumerate(data):
smiles, can = self.data[i][0:2]
output, error = run_exec(smiles, "babel -ismi -osdf --gen3d")
atoms, bonds = self.parseMDL(output)
parities = [atom['parity'] for atom in atoms]
parities.sort()
stereos = [bond['stereo'] for bond in bonds]
stereos.sort()
self.assertEqual(atompar, parities)
if bondstereo:
self.assertEqual(bondstereo, stereos)
output, error = run_exec(output, "obabel -isdf -as -ocan")
# "-as" is necessary to identify the unknown stereo
self.assertEqual(output.rstrip(), can)
def testSMILESto0DMDL(self):
"""Test interconversion between SMILES and 0D MDL"""
data = [
([0, 0, 0, 0, 1], [0, 0, 0, 0]), # 'Cl[C@@](Br)(F)I'
([0, 0, 0, 0, 2], [0, 0, 0, 0]), # 'Cl[C@](Br)(F)I'
([0, 0, 0, 0, 0], [0, 0, 0, 0]), # 'ClC(Br)(F)I'
([0, 0, 0, 0, 3], [0, 0, 0,
0]) # 'ClC(Br)(F)I' option 'S' when reading
]
for i, (atompar, bondstereo) in enumerate(data):
if i == 3:
smiles, can = self.data[6][0:2]
output, error = run_exec(smiles, "babel -ismi -osdf -aS")
else:
smiles, can = self.data[i + 4][0:2]
output, error = run_exec(smiles, "babel -ismi -osdf")
atoms, bonds = self.parseMDL(output)
parities = [atom['parity'] for atom in atoms]
parities.sort()
stereos = [bond['stereo'] for bond in bonds]
stereos.sort()
self.assertEqual(atompar, parities)
self.assertEqual(bondstereo, stereos)
output, error = run_exec(output, "babel -isdf -as -ocan")
self.assertEqual(output.rstrip(), can)
def testSMIthruXML(self):
"""Verify that roundtripping through CML preserves stereo"""
output, error = run_exec("\n".join(self.smiles), "babel -ismi -ocml tmp.cml")
output, error = run_exec(output.rstrip(), "babel -icml tmp.cml -ocan")
output = "\n".join([x.rstrip() for x in output.split("\n")])
self.assertEqual(output.rstrip(), "\n".join([self.cansmi] * len(self.smiles)))
os.remove("tmp.cml")
def testSMItoSMI(self):
"""
Some initial tests based on previous geometry stereo bugs
(i.e., OBBuilder can't handle correctly)
"""
self.canFindExecutable("obabel")
# A series of aromatic strings, which should convert to themselves
self.smiles = [
'c1ccccc1', # benzene
'C/C=C\\C', # Z-butene
'C/C=C/C', # E-butene
'N[C@](Br)(O)C',
#'CCC[C@@H]([C@H](CC(C)C)C)C',
#'C1CC[C@H]2[C@@H](C1)CCCC2', # cis-decalin
#'C1CC[C@@H]2[C@@H](C1)CCCC2', # trans-decalin
#'CCCNC1=C(C)C(=O)C2=C(C1=O)[C@@H](COC(=O)N)[C@]1(N2C[C@H]2[C@H]1N2)OC',
#'CN([C@H]1C(=O)C(=C([C@]2([C@@H]1C[C@@H]1Cc3c(C(=C1C2=O)O)c(O)ccc3N(C)C)O)O)C(=O)N)C',
#'CN([C@@H]1C(=O)C(=C([C@@]2([C@H]1C[C@@H]1C(=C(O)c3c([C@@]1(C)O)c(Cl)ccc3O)C2=O)O)O)C(=O)N)C',
#'C[C@@H](CC(=O)OC[C@@]12CC[C@H]3[C@@]([C@@H]2C[C@@H](O1)C1=CC(=O)O[C@H]1O)(C)CC[C@@H]1[C@]3(C)CCCC1(C)C)O',
#'CC(=O)OC[C@@]12CC[C@H]3[C@@]([C@@H]2C[C@H](O1)C1=CC(=O)O[C@H]1O)(C)CC[C@@H]1[C@]3(C)CCCC1(C)C'
]
for smi in self.smiles:
# generate a canonical SMILES in case the ordering changes
canSMI, error = run_exec(smi, "obabel -ismi -ocan")
# generate a mol2 (any 3D format without implicit hydrogens)
mol2, error = run_exec(smi, "obabel -ismi -osdf --gen3d dg")
# now check if it matches the previous canonical SMILES
output, error = run_exec(mol2, "obabel -isdf -ocan")
self.assertEqual(output.split('\t')[0].rstrip(), canSMI.rstrip())
def testSingleHit(self):
"""PR#2955101 - Difficulty reading from a fastsearch index"""
smiles = """C12(C(N(C(=O)C)c3c2cccc3)=O)Nc2c(ccc(c2N1)OCCCC)OCCCC
n1c([nH]c(cc1c1ccccc1)=O)c1ccc(cc1)Br
n1c(nc2c(c1N(C)C)cccc2)c1c(O)cccc1
C1(/[CH]2[CH]3\C(=C4/CC(C)(C)NC(C4)(C)C)C=C[CH]3[CH]1C=C2)=C1/CC(C)(C)NC(C1)(C)C
n1c(c2ccc(C(=O)O)cc2)ccc(c1)CCCCC
N1(C(CN(CC1=O)C(=O)C1CCCCC1)=O)CCc1ccccc1
S(N1[CH](c2ccccc2C=C1)C#N)(c1ccc(cc1)C)(=O)=O
c12c(c(OC)c3c(c1OC)occ3)ccc(o2)=O
c12c(O[CH](C1=O)C(C)C)cc1c(c2)ccc(=O)o1
c12[C]3([C@H]4([N@@](CCc1c1ccccc1[nH]2)C[C@H](C=C4CC)C3))C(=O)OC"""
outputfile = open("ten.smi", "w")
outputfile.write(smiles)
outputfile.close()
output, error = run_exec("babel ten.smi ten.fs")
self.canFindFile("ten.fs")
self.assertConverted(error, 10)
query = "Nc2nc(c1ccccc1)nc3ccccc23"
output, error = run_exec("babel ten.fs -ifs -s %s -osmi" % query)
self.assertConverted(error, 1)
output, error = run_exec("babel ten.fs -ifs -s %s -at 0.5 -aa -osmi" %
query)
self.assertConverted(error, 1)
def testSingleHit(self):
"""PR#2955101 - Difficulty reading from a fastsearch index"""
smiles = """C12(C(N(C(=O)C)c3c2cccc3)=O)Nc2c(ccc(c2N1)OCCCC)OCCCC
n1c([nH]c(cc1c1ccccc1)=O)c1ccc(cc1)Br
n1c(nc2c(c1N(C)C)cccc2)c1c(O)cccc1
C1(/[CH]2[CH]3\C(=C4/CC(C)(C)NC(C4)(C)C)C=C[CH]3[CH]1C=C2)=C1/CC(C)(C)NC(C1)(C)C
n1c(c2ccc(C(=O)O)cc2)ccc(c1)CCCCC
N1(C(CN(CC1=O)C(=O)C1CCCCC1)=O)CCc1ccccc1
S(N1[CH](c2ccccc2C=C1)C#N)(c1ccc(cc1)C)(=O)=O
c12c(c(OC)c3c(c1OC)occ3)ccc(o2)=O
c12c(O[CH](C1=O)C(C)C)cc1c(c2)ccc(=O)o1
c12[C]3([C@H]4([N@@](CCc1c1ccccc1[nH]2)C[C@H](C=C4CC)C3))C(=O)OC"""
outputfile = open("ten.smi", "w")
outputfile.write(smiles)
outputfile.close()
output, error = run_exec("babel ten.smi ten.fs")
self.canFindFile("ten.fs")
self.assertConverted(error, 10)
query = "Nc2nc(c1ccccc1)nc3ccccc23"
output, error = run_exec("babel ten.fs -ifs -s %s -osmi" % query)
self.assertConverted(error, 1)
def testSMILEStoInChI(self):
# Tests interconversions between the SMILES on the left versus
# the InChI on the right.
# The canonical smiles (in the middle) were derived from the SMILES.
for smiles, can, inchi in self.data:
output, error = run_exec(smiles, "babel -ismi -oinchi")
self.assertEqual(output.rstrip(), inchi)
output, error = run_exec(inchi, "babel -iinchi -ocan")
self.assertEqual(output.rstrip(), can)
def testInChIToSMILES_Bug(self):
"""PR#2101034- InChI <-> SMILES conv misrepresents stereo"""
test_inchi = 'InChI=1S/C10H10/c1-2-3-7-10-8-5-4-6-9-10/h2-9H,1H2/b7-3+'
output, error = run_exec(test_inchi, "babel -iinchi -osmi")
self.assertEqual(output.rstrip(), "C=C/C=C/c1ccccc1")
test_smiles = "C=C\C=C/c1ccccc1"
output, error = run_exec(test_smiles, "babel -ismi -oinchi")
self.assertEqual(output.rstrip(), "InChI=1S/C10H10/c1-2-3-7-10-8-5-4-6-9-10/h2-9H,1H2/b7-3-")
def testSMILEStoInChI(self):
# Tests interconversions between the SMILES on the left versus
# the InChI on the right.
# The canonical smiles (in the middle) were derived from the SMILES.
for smiles, can, inchi in self.data:
output, error = run_exec(smiles, "babel -ismi -oinchi")
self.assertEqual(output.rstrip(), inchi)
output, error = run_exec(inchi, "babel -iinchi -ocan")
self.assertEqual(output.rstrip(), can)
def testSMIthruXML(self):
"""Verify that roundtripping through CML preserves stereo"""
output, error = run_exec("\n".join(self.smiles),
"babel -ismi -ocml tmp.cml")
output, error = run_exec(output.rstrip(), "babel -icml tmp.cml -ocan")
output = "\n".join([x.rstrip() for x in output.split("\n")])
self.assertEqual(output.rstrip(),
"\n".join([self.cansmi] * len(self.smiles)))
os.remove("tmp.cml")
def testInChIToSMILES_Bug(self):
"""PR#2101034- InChI <-> SMILES conv misrepresents stereo"""
test_inchi = 'InChI=1S/C10H10/c1-2-3-7-10-8-5-4-6-9-10/h2-9H,1H2/b7-3+'
output, error = run_exec(test_inchi, "babel -iinchi -osmi")
self.assertEqual(output.rstrip(), "C=C/C=C/c1ccccc1")
test_smiles = "C=C\C=C/c1ccccc1"
output, error = run_exec(test_smiles, "babel -ismi -oinchi")
self.assertEqual(
output.rstrip(),
"InChI=1S/C10H10/c1-2-3-7-10-8-5-4-6-9-10/h2-9H,1H2/b7-3-")
def test2DMDLto0D(self):
"""Test conversion for 2D MDL to CAN and InChI"""
# The following file was created using RDKit starting from
# the SMILES strings in data[x][0] below.
filename = self.getTestFile("testsym_2Dtests.sdf")
output, error = run_exec("babel -isdf %s -ocan" % filename)
for i, smiles in enumerate(output.rstrip().split("\n")):
self.assertEqual(smiles.rstrip(), self.data[i][1])
output, error = run_exec("babel -isdf %s -oinchi" % filename)
for i, inchi in enumerate(output.rstrip().split("\n")):
self.assertEqual(inchi.rstrip(), self.data[i][2])
def test2DMDLto0D(self):
"""Test conversion for 2D MDL to CAN and InChI"""
# The following file was created using RDKit starting from
# the SMILES strings in data[x][0] below.
filename = self.getTestFile("testsym_2Dtests.sdf")
output, error = run_exec("babel -isdf %s -ocan" % filename)
for i, smiles in enumerate(output.rstrip().split("\n")):
self.assertEqual(smiles.rstrip(), self.data[i][1])
output, error = run_exec("babel -isdf %s -oinchi" % filename)
for i, inchi in enumerate(output.rstrip().split("\n")):
self.assertEqual(inchi.rstrip(), self.data[i][2])
def testChiralToLonePair(self):
"""PR#3058701 - Handle stereochemistry at lone pair on S"""
# Note to self: Need to ensure that roundtripping through the various
# 2D and 3D formats works. In the meanwhile, this test at least ensures
# that SMILES reading and writing works fine.
can = '[S@@](=O)(Cl)C'
smiles = [can, '[S@](Cl)(=O)C', 'O=[S@](Cl)C']
for smile in smiles:
output, error = run_exec(smile, "babel -ismi -ocan")
self.assertEqual(output.rstrip(), can)
# Check that regular chiral S still work fine
smi = "[S@](=O)(=N)(C)O"
output, error = run_exec(smi, "babel -ismi -osmi")
self.assertEqual(output.rstrip(), smi)
def testChiralToLonePair(self):
"""PR#3058701 - Handle stereochemistry at lone pair on S"""
# Note to self: Need to ensure that roundtripping through the various
# 2D and 3D formats works. In the meanwhile, this test at least ensures
# that SMILES reading and writing works fine.
can = 'C[S@](=O)Cl'
smiles = [can, '[S@](Cl)(=O)C', 'O=[S@](Cl)C']
for smile in smiles:
output, error = run_exec(smile, "babel -ismi -ocan")
self.assertEqual(output.rstrip(), can)
# Check that regular chiral S still work fine
smi = "[S@](=O)(=N)(C)O"
output, error = run_exec(smi, "babel -ismi -osmi")
self.assertEqual(output.rstrip(), smi)
def test2DMDLto2DMDL(self):
"""Make sure that stereo is preserved when writing wedge bonds"""
filenames = [self.getTestFile(x) for x in
["testsym_2Dtests_more.sdf",
"testsym_2Dtests_threeligands.sdf"]]
# The test files have the correct canonical SMILES string
# stored in the data field "smiles"
output, error = run_exec("obabel -isdf %s %s -osdf --append smiles" %
(filenames[0], filenames[1]))
finaloutput, error = run_exec(output, "obabel -isdf -ocan")
for line in finaloutput.rstrip().split("\n"):
result, correct_answer = line.split()
self.assertEqual(result, correct_answer)
def test2DMDLto2DMDL(self):
"""Make sure that stereo is preserved when writing wedge bonds"""
filenames = [
self.getTestFile(x) for x in
["testsym_2Dtests_more.sdf", "testsym_2Dtests_threeligands.sdf"]
]
# The test files have the correct canonical SMILES string
# stored in the data field "smiles"
output, error = run_exec("obabel -isdf %s %s -osdf --append smiles" %
(filenames[0], filenames[1]))
finaloutput, error = run_exec(output, "obabel -isdf -ocan")
for line in finaloutput.rstrip().split("\n"):
result, correct_answer = line.split()
self.assertEqual(result, correct_answer)
def fastcheckmatch(query, molecules):
"""May fail where Open Babel does not output the input query, e.g.
[C@@]([H])(Br)(Cl)I is output as [C@@H](Br)(Cl)I"""
output, error = run_exec("\n".join(molecules), "obabel -ismi -s%s -osmi" % query)
converted = [x.rstrip() for x in output.split("\n")]
results = [smi in converted for smi in molecules]
return results
def testRInChIOfficialExamples(self):
"""These test RXN to RInChI using the examples in the RInChI distrib"""
for rxnfile in glob.glob(os.path.join(here, "rinchi", "*.rxn")):
dirname, fname = os.path.split(rxnfile)
output, error = run_exec('obabel %s -orinchi' % rxnfile)
ans = open(os.path.join(dirname, fname.split(".")[0]+".txt")).readlines()[0]
self.assertEqual(output.rstrip(), ans.rstrip())
def testSMItoInChI(self):
"""Verify that all molecules give the same InChI"""
output, error = run_exec("\n".join(self.smiles),
"obabel -ismi -oinchi")
output = "\n".join([x.rstrip() for x in output.split("\n")])
self.assertEqual(output.rstrip(),
"\n".join([self.inchi] * len(self.smiles)))
def testSMItoCAN(self):
"""PR#1842055- bad isotope canonicalization"""
self.canFindExecutable("babel")
# A series of isotopamers, and their canonical forms
self.smiles = [
'c1ccccc1',
'c1[14cH]cccc1',
'[14cH]1[14cH]cccc1',
'[14cH]1[14cH]ccc[14cH]1',
'[14cH]1[14cH]cc[14cH][14cH]1',
'[14cH]1[14cH]c[14cH][14cH][14cH]1',
'[14cH]1[14cH][14cH][14cH][14cH][14cH]1',
]
self.cansmis = [
'c1ccccc1',
'[14cH]1ccccc1',
'[14cH]1[14cH]cccc1',
'[14cH]1[14cH]ccc[14cH]1',
'[14cH]1[14cH][14cH]cc[14cH]1',
'[14cH]1[14cH][14cH]c[14cH][14cH]1',
'[14cH]1[14cH][14cH][14cH][14cH][14cH]1',
]
for i in range(0, len(self.smiles)):
output, error = run_exec(self.smiles[i], "babel -ismi -ocan")
self.assertEqual(output.rstrip(), self.cansmis[i])
def testSMItoSMI(self):
"""
PR#2705497 aromatic - kekule conversion issue
PR#1445453 SMILES aromaticity fails on 4-valent N+ atoms
PR#1814248 Aromaticity munged by SMILES input
PR#1761638 Error in Aromaticity / Kekulize
PR#2948661 Trunk fails aromaticity
"""
self.canFindExecutable("babel")
# A series of aromatic strings, which should convert to themselves
self.smiles = [
'c12c3c(cc(N)cc3)Cc1cccc2', 'c1(=O)n(c2c(c(=O)o1)cccc2)CC(=O)OCC',
'c1n[nH]c(=S)[nH]1', 'O=c1[nH]ccc2nc3oc4ccccc4c(=O)c3cc12',
'c1nc2sccn2c1', 'c1[n+]cnc2[nH]cnc12', 'c1onc(c2ccccc2Cl)c1',
'c1ccc2[nH]c3ccc4cc[n+]cc4c3c2c1',
'[nH]1c2ccccc2c2c3C(=O)NCc3c3c4ccccc4[nH]c3c12',
'c1c(C)c2C=c3[n-]c(=Cc4[nH]c(C=c5[n-]c(=Cc1[nH]2)c(C)c5C=C)c(C)c4CCC(=O)O)c(CCC(=O)O)c3',
'C1=C2CCC(=Cc3ccc([nH]3)C=c3ccc(=Cc4ccc1[nH]4)[nH]3)N2',
'c1(NC(=O)C2CC2)nc2c3c(cccc3)CCc2cn1',
'O=C1N(CCCC)C(=O)NC2C1C1N(N2)CCN1', 'Cn1cccnc1=O',
'O=c1n(C)c(=O)nc2c1c1n([nH]2)cc[nH]1',
'Cn1ccn2c1nc1c2c(=O)n(C)c(=O)n1C'
]
for i in range(0, len(self.smiles)):
output, error = run_exec(self.smiles[i], "babel -ismi -osmi")
self.assertEqual(output.rstrip(), self.smiles[i])
def testSMItoCAN(self):
"""PR#1842055- bad isotope canonicalization"""
self.canFindExecutable("babel")
# A series of isotopamers, and their canonical forms
self.smiles = [
'c1ccccc1',
'c1[14cH]cccc1',
'c1[14cH][14cH]ccc1',
'c1[14cH][14cH][14cH]cc1',
'c1[14cH][14cH][14cH][14cH]c1',
'c1[14cH][14cH][14cH][14cH][14cH]1',
'[14cH]1[14cH][14cH][14cH][14cH][14cH]1',
]
self.cansmis = [
'c1ccccc1',
'[14cH]1ccccc1',
'[14cH]1[14cH]cccc1',
'[14cH]1[14cH]ccc[14cH]1',
'[14cH]1[14cH][14cH]cc[14cH]1',
'[14cH]1[14cH][14cH]c[14cH][14cH]1',
'[14cH]1[14cH][14cH][14cH][14cH][14cH]1',
'[14cH]1[14cH][14cH][14cH][14cH][14cH]1',
]
for i in range(0, len(self.smiles)):
output, error = run_exec(self.smiles[i], "babel -ismi -ocan")
self.assertEqual(output.rstrip(), self.cansmis[i])
def testSMItoSMI(self):
"""
PR#2705497 aromatic - kekule conversion issue
PR#1445453 SMILES aromaticity fails on 4-valent N+ atoms
PR#1814248 Aromaticity munged by SMILES input
PR#1761638 Error in Aromaticity / Kekulize
PR#2948661 Trunk fails aromaticity
"""
self.canFindExecutable("babel")
# A series of aromatic strings, which should convert to themselves
self.smiles = [
'c12-c3c(cc(N)cc3)Cc1cccc2',
'c1(=O)n(c2c(c(=O)o1)cccc2)CC(=O)OCC',
'c1n[nH]c(=S)[nH]1',
'O=c1[nH]ccc2nc3oc4ccccc4c(=O)c3cc12',
'c1nc2sccn2c1',
'c1[nH+]cnc2[nH]cnc12',
'c1onc(c2ccccc2Cl)c1',
'c1ccc2[nH]c3ccc4cc[nH+]cc4c3c2c1',
'[nH]1c2ccccc2c2c3C(=O)NCc3c3c4ccccc4[nH]c3c12',
'c1c(C)c2C=c3[n-]c(=Cc4[nH]c(C=c5[n-]c(=Cc1[nH]2)c(C)c5C=C)c(C)c4CCC(=O)O)c(CCC(=O)O)c3',
'C1=C2CCC(=Cc3ccc([nH]3)C=c3ccc(=Cc4ccc1[nH]4)[nH]3)N2',
'c1(NC(=O)C2CC2)nc2-c3c(cccc3)CCc2cn1',
'O=C1N(CCCC)C(=O)NC2C1C1N(N2)CCN1',
'Cn1cccnc1=O',
'O=c1n(C)c(=O)nc2-c1c1n([nH]2)cc[nH]1',
'Cn1ccn2c1nc1c2c(=O)n(C)c(=O)n1C'
]
for i in range(0, len(self.smiles)):
output, error = run_exec(self.smiles[i], "babel -ismi -osmi")
self.assertEqual(output.rstrip(), self.smiles[i])
def testSMILEStoInChI(self):
# Tests interconversions between the SMILES on the left versus
# the InChI on the right.
# The canonical smiles (in the middle) were derived from the SMILES.
data = [
('ClC=CF', 'FC=CCl', 'InChI=1S/C2H2ClF/c3-1-2-4/h1-2H'),
('Cl/C=C/F', 'F/C=C/Cl', 'InChI=1S/C2H2ClF/c3-1-2-4/h1-2H/b2-1+'),
('Cl/C=C\\F', 'F/C=C\\Cl', 'InChI=1S/C2H2ClF/c3-1-2-4/h1-2H/b2-1-'),
('Cl[C@@](Br)(F)I', 'F[C@@](Cl)(Br)I', 'InChI=1S/CBrClFI/c2-1(3,4)5/t1-/m0/s1'),
('Cl[C@](Br)(F)I', 'F[C@](Cl)(Br)I', 'InChI=1S/CBrClFI/c2-1(3,4)5/t1-/m1/s1'),
('ClC(Br)(F)I', 'FC(Cl)(Br)I', 'InChI=1S/CBrClFI/c2-1(3,4)5')]
for smiles, can, inchi in data:
output, error = run_exec(smiles, "babel -ismi -oinchi")
self.assertEqual(output.rstrip(), inchi)
output, error = run_exec(inchi, "babel -iinchi -ocan")
self.assertEqual(output.rstrip(), can)
def testSMItoSMI(self):
"""
Some initial tests based on previous geometry stereo bugs
(i.e., OBBuilder can't handle correctly)
"""
self.canFindExecutable("obabel")
# A series of aromatic strings, which should convert to themselves
self.smiles = [
'c1ccccc1', # benzene
'C#C', # triple bond
'CC=CC', # butene unspecified
'C/C=C\\C', # Z-butene
'C/C=C/C', # E-butene
'NC(Br)(O)C',
'N[C@](Br)(O)C',
'N[C@@](Br)(O)C',
'CCC[C@@H]([C@H](CC(C)C)C)C',
'C1CC[C@H]2[C@@H](C1)CCCC2', # cis-decalin
'C1CC[C@@H]2[C@@H](C1)CCCC2', # trans-decalin
'[C@H]1(NC[C@H]2[C@H]1N2)OC',
'Clc1cccc(Cl)c1\\C=N\\NC(=O)c1cccs1',
'O=C1NC(=S)S\\C1=C/c1ccco1',
'S=C1NC(=O)/C(=C/c2ccco2)/S1',
'O=C1NC(=S)N\\C1=C\\c1ccncc1',
'S=C1NC(=O)C(=C)N1',
'CC(=O)N\\N=C\\c1ccncc1',
'N/N=c/1\\sc2c(n1C)cccc2',
'OCCN/C=C\\1/C(=NN(C1=O)c1ccccc1)C',
'Cc1ccc(o1)/C=C/C=O',
# disabled to make test run faster:
#'CCCNC1=C(C)C(=O)C2=C(C1=O)[C@@H](COC(=O)N)[C@]1(N2C[C@H]2[C@H]1N2)OC',
#'CN([C@H]1C(=O)C(=C([C@]2([C@@H]1C[C@@H]1Cc3c(C(=C1C2=O)O)c(O)ccc3N(C)C)O)O)C(=O)N)C',
#'CN([C@@H]1C(=O)C(=C([C@@]2([C@H]1C[C@@H]1C(=C(O)c3c([C@@]1(C)O)c(Cl)ccc3O)C2=O)O)O)C(=O)N)C',
#'C[C@@H](CC(=O)OC[C@@]12CC[C@H]3[C@@]([C@@H]2C[C@@H](O1)C1=CC(=O)O[C@H]1O)(C)CC[C@@H]1[C@]3(C)CCCC1(C)C)O',
#'CC(=O)OC[C@@]12CC[C@H]3[C@@]([C@@H]2C[C@H](O1)C1=CC(=O)O[C@H]1O)(C)CC[C@@H]1[C@]3(C)CCCC1(C)C'
]
for smi in self.smiles:
# generate a canonical SMILES in case the ordering changes
canSMI, error = run_exec(smi, "obabel -ismi -ocan")
# generate a mol2 (any 3D format without implicit hydrogens)
mol2, error = run_exec(smi, "obabel -ismi -osdf --gen3d dg")
# now check if it matches the previous canonical SMILES
output, error = run_exec(mol2, "obabel -isdf -ocan")
self.assertEqual(output.split('\t')[0].rstrip(), canSMI.rstrip())
def fastcheckmatch(query, molecules):
"""May fail where Open Babel does not output the input query, e.g.
[C@@]([H])(Br)(Cl)I is output as [C@@H](Br)(Cl)I"""
output, error = run_exec("\n".join(molecules),
"obabel -ismi -s%s -osmi" % query)
converted = [x.rstrip() for x in output.split("\n")]
results = [smi in converted for smi in molecules]
return results
def testRSMItoRINCHI(self):
data = [
("C>N>O", "RInChI=1.00.1S/CH4/h1H4<>H2O/h1H2<>H3N/h1H3/d+"),
("O>N>C", "RInChI=1.00.1S/CH4/h1H4<>H2O/h1H2<>H3N/h1H3/d-"),
("O>>C", "RInChI=1.00.1S/CH4/h1H4<>H2O/h1H2/d-"),
# The following is assumed to be d+ by analogy with
# the empty reaction which is d+
("O>>O", "RInChI=1.00.1S/H2O/h1H2<>H2O/h1H2/d+"),
# Example: esterification of acetic acid
("OCC.CC(=O)O>S(=O)(=O)(O)O>CC(=O)OCC.O",
"RInChI=1.00.1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)!C2H6O/c1-2-3/h3H,2H2,1H3<>C4H8O2/c1-3-6-4(2)5/h3H2,1-2H3!H2O/h1H2<>H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/d+"
),
# Example: alkaline ring opening
("CC[C@]1(C)O[C@H]1C.[OH-]>>CC[C@](C)(O)[C@@H](C)O",
"RInChI=1.00.1S/C6H12O/c1-4-6(3)5(2)7-6/h5H,4H2,1-3H3/t5-,6-/m0/s1!H2O/h1H2/p-1<>C6H14O2/c1-4-6(3,8)5(2)7/h5,7-8H,4H2,1-3H3/t5-,6+/m1/s1/d+"
),
# Partial reactions
(">>C1CC=C(O)CC1",
"RInChI=1.00.1S/<>C6H10O/c7-6-4-2-1-3-5-6/h4,7H,1-3,5H2/d+"),
("C1CC=C(O)CC1>>",
"RInChI=1.00.1S/<>C6H10O/c7-6-4-2-1-3-5-6/h4,7H,1-3,5H2/d-"),
# The empty reaction
(">>", "RInChI=1.00.1S//d+"),
# Test 'no-structure'
("c1ccccc1C=C>>*",
"RInChI=1.00.1S/<>C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2/d-/u1-0-0"),
("*>>C1CC=C(O)CC1",
"RInChI=1.00.1S/<>C6H10O/c7-6-4-2-1-3-5-6/h4,7H,1-3,5H2/d+/u1-0-0"
),
("O>*>C", "RInChI=1.00.1S/CH4/h1H4<>H2O/h1H2/d-/u0-0-1"),
("*.O>>C", "RInChI=1.00.1S/CH4/h1H4<>H2O/h1H2/d-/u0-1-0"),
# Empty except for 'no-structures' (assumed)
("*>*>*", "RInChI=1.00.1S//d+/u1-1-1"),
]
for eqm in [False, True]:
for rsmi, rinchi in data:
if eqm:
output, error = run_exec(
'obabel -:%s -irsmi -orinchi -xe' % rsmi)
ans = rinchi.replace("/d-", "/d=").replace("/d+", "/d=")
self.assertEqual(output.rstrip(), ans)
else:
output, error = run_exec('obabel -:%s -irsmi -orinchi' %
rsmi)
self.assertEqual(output.rstrip(), rinchi)
def testRInChIOfficialExamples(self):
"""These test RXN to RInChI using the examples in the RInChI distrib"""
for rxnfile in glob.glob(os.path.join(here, "rinchi", "*.rxn")):
dirname, fname = os.path.split(rxnfile)
output, error = run_exec('obabel %s -orinchi' % rxnfile)
ans = open(os.path.join(dirname,
fname.split(".")[0] +
".txt")).readlines()[0]
self.assertEqual(output.rstrip(), ans.rstrip())
def testSMILESto0DMDL(self):
"""Test interconversion between SMILES and 0D MDL"""
data = [
([0, 0, 0, 0, 1], [0, 0, 0, 0]), # 'Cl[C@@](Br)(F)I'
([0, 0, 0, 0, 2], [0, 0, 0, 0]), # 'Cl[C@](Br)(F)I'
([0, 0, 0, 0, 3], [0, 0, 0, 0]) # 'ClC(Br)(F)I'
]
for i, (atompar, bondstereo) in enumerate(data):
smiles, can = self.data[i + 3][0:2]
output, error = run_exec(smiles, "babel -ismi -osdf")
atoms, bonds = self.parseMDL(output)
parities = [atom['parity'] for atom in atoms]
parities.sort()
stereos = [bond['stereo'] for bond in bonds]
stereos.sort()
self.assertEqual(atompar, parities)
self.assertEqual(bondstereo, stereos)
output, error = run_exec(output, "babel -isdf -as -ocan")
self.assertEqual(output.rstrip(), can)
def test2DMDLto0D(self):
"""Test conversion for 2D MDL to CAN and InChI"""
# The following file was created using RDKit starting from
# the SMILES strings in data[x][0] below.
filename = self.getTestFile("testsym_2Dtests.sdf")
data = [
('ClC=CF', 'FC=CCl', 'InChI=1S/C2H2ClF/c3-1-2-4/h1-2H'),
('Cl/C=C/F', 'F/C=C/Cl', 'InChI=1S/C2H2ClF/c3-1-2-4/h1-2H/b2-1+'),
('Cl/C=C\\F', 'F/C=C\\Cl', 'InChI=1S/C2H2ClF/c3-1-2-4/h1-2H/b2-1-'),
('Cl[C@@](Br)(F)I', 'F[C@@](Cl)(Br)I', 'InChI=1S/CBrClFI/c2-1(3,4)5/t1-/m0/s1'),
('Cl[C@](Br)(F)I', 'F[C@](Cl)(Br)I', 'InChI=1S/CBrClFI/c2-1(3,4)5/t1-/m1/s1'),
('ClC(Br)(F)I', 'FC(Cl)(Br)I', 'InChI=1S/CBrClFI/c2-1(3,4)5')]
output, error = run_exec("babel -isdf %s -ocan" % filename)
for i, smiles in enumerate(output.rstrip().split("\n")):
self.assertEqual(smiles.rstrip(), data[i][1])
output, error = run_exec("babel -isdf %s -oinchi" % filename)
for i, inchi in enumerate(output.rstrip().split("\n")):
self.assertEqual(inchi.rstrip(), data[i][2])
def testFindDups(self):
"""Look for duplicates using --unique"""
params = [("", 13), ("/formula", 5), ("/connect", 6), ("/nostereo", 9),
("/nosp3", 11), ("/noEZ", 11), ("/nochg", 12),
("/noiso", 11), ("cansmi", 13), ("cansmiNS", 7)]
for param in params:
output, error = run_exec(
self.smiles, "babel -ismi -osmi --unique %s" % param[0])
self.assertConverted(error, param[1])
def testSelfMatch(self):
"""Verify that a molecule matches itself"""
data = [
'[C@@](F)(Br)(Cl)I', '[C@](F)(Br)(Cl)I', 'F[C@](Br)(Cl)I',
'[C@H](Br)(Cl)I', 'Br[C@H](Cl)I', '[C@]1(Br)(Cl)NC1',
'[C@@]1(Br)(Cl)NC1', 'Br[C@]1(Cl)NC1', 'C1N[C@]1(Cl)Br',
'F[C@]1(Br)N[C@]1(Br)Cl', '[C@H]1(Cl)NC1'
]
for smi in data:
output, error = run_exec("obabel -:%s -s%s -osmi" % (smi, smi))
self.assertEqual(output.rstrip(), smi)
def testSMILESto3DMDL(self):
"""Test interconversion between SMILES and 3D MDL"""
data = [
('ClC=CF', 'FC=CCl', [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 3]),
('Cl/C=C/F', 'F/C=C/Cl', [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0]),
('Cl/C=C\\F', 'F/C=C\\Cl', [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0]),
('Cl[C@@](Br)(F)I', 'F[C@@](Cl)(Br)I', [0, 0, 0, 0, 1], [0, 0, 0, 1]),
('Cl[C@](Br)(F)I', 'F[C@](Cl)(Br)I', [0, 0, 0, 0, 2], [0, 0, 0, 6]),
('ClC(Br)(F)I', 'FC(Cl)(Br)I', [0, 0, 0, 0, 3], [0, 0, 0, 4])
]
for smiles, can, atompar, bondstereo in data:
output, error = run_exec(smiles, "babel -ismi -osdf --gen3d")
atoms, bonds = self.parseMDL(output)
parities = [atom['parity'] for atom in atoms]
parities.sort()
stereos = [bond['stereo'] for bond in bonds]
stereos.sort()
self.assertEqual(atompar, parities)
self.assertEqual(bondstereo, stereos)
output, error = run_exec(output, "babel -isdf -ocan")
self.assertEqual(output.rstrip(), can)
def testXYZtoSMILESand3DMDL(self):
"""Test conversion from XYZ to SMILES and 3D MDL"""
# Since the XYZ format does not trigger stereo perception,
# this test makes sure that the SMILES and 3D MDL formats
# perceive stereo themselves.
data = [
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 3]), # 'ClC=CF'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 3]), # 'ClC=CF'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0]), # 'Cl/C=C/F'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0]), # 'Cl/C=C\\F'
# The bond parities are irrelevant/meaningless for the next two
([0, 0, 0, 0, 1], []), # 'Cl[C@@](Br)(F)I'
([0, 0, 0, 0, 2], []), # 'Cl[C@](Br)(F)I'
([0, 0, 0, 0, 3], [0, 0, 0, 4]), # 'ClC(Br)(F)I'
([0, 0, 0, 1], []), # 'O=[S@@](Cl)I),
([0, 0, 0, 2], []), # 'O=[S@](Cl)I),
([0, 0, 0, 3], []), # 'O=S(Cl)I),
([0] * 9, [0] * 8 + [3]), # "IC=C1NC1"
([0] * 9, [0] * 9), # r"I/C=C\1/NC1"
([0] * 9, [0] * 9), # r"I/C=C/1\NC1"
]
for i, (atompar, bondstereo) in enumerate(data):
if i in [0, 1, 6, 10]: continue # ambiguous stereo is lost in XYZ
if i in [7, 8, 9]: continue # perception of S=O from XYZ fails
smiles, can = self.data[i][0:2]
output, error = run_exec(smiles, "babel -ismi -oxyz --gen3d")
canoutput, error = run_exec(output, "babel -ixyz -ocan")
self.assertEqual(canoutput.rstrip(), can)
sdfoutput, error = run_exec(output, "babel -ixyz -osdf")
atoms, bonds = self.parseMDL(sdfoutput)
parities = [atom['parity'] for atom in atoms]
parities.sort()
stereos = [bond['stereo'] for bond in bonds]
stereos.sort()
self.assertEqual(atompar, parities)
if bondstereo:
self.assertEqual(bondstereo, stereos)
def testXYZtoSMILESand3DMDL(self):
"""Test conversion from XYZ to SMILES and 3D MDL"""
# Since the XYZ format does not trigger stereo perception,
# this test makes sure that the SMILES and 3D MDL formats
# perceive stereo themselves.
data = [
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 3]), # 'ClC=CF'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 3]), # 'ClC=CF'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0]), # 'Cl/C=C/F'
([0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0]), # 'Cl/C=C\\F'
# The bond parities are irrelevant/meaningless for the next two
([0, 0, 0, 0, 1], []), # 'Cl[C@@](Br)(F)I'
([0, 0, 0, 0, 2], []), # 'Cl[C@](Br)(F)I'
([0, 0, 0, 0, 3], [0, 0, 0, 4]), # 'ClC(Br)(F)I'
([0, 0, 0, 1], []), # 'O=[S@@](Cl)I),
([0, 0, 0, 2], []), # 'O=[S@](Cl)I),
([0, 0, 0, 3], []), # 'O=S(Cl)I),
([0]*9, [0]*8 + [3]), # "IC=C1NC1"
([0]*9, [0]*9), # r"I/C=C\1/NC1"
([0]*9, [0]*9), # r"I/C=C/1\NC1"
]
for i, (atompar, bondstereo) in enumerate(data):
if i in [0, 1, 6, 10]: continue # ambiguous stereo is lost in XYZ
if i in [7, 8, 9]: continue # perception of S=O from XYZ fails
smiles, can = self.data[i][0:2]
output, error = run_exec(smiles, "babel -ismi -oxyz --gen3d")
canoutput, error = run_exec(output, "babel -ixyz -ocan")
self.assertEqual(canoutput.rstrip(), can)
sdfoutput, error = run_exec(output, "babel -ixyz -osdf")
atoms, bonds = self.parseMDL(sdfoutput)
parities = [atom['parity'] for atom in atoms]
parities.sort()
stereos = [bond['stereo'] for bond in bonds]
stereos.sort()
self.assertEqual(atompar, parities)
if bondstereo:
self.assertEqual(bondstereo, stereos)
def test2DMDLto0D_more(self):
"""Test various combinations of stereobonds in 2D perception"""
filenames = [self.getTestFile(x) for x in
["testsym_2Dtests_more.sdf",
"testsym_2Dtests_threeligands.sdf"]]
# The test files have the correct canonical SMILES string
# stored in the data field "smiles"
output, error = run_exec("obabel -isdf %s %s -ocan --append smiles" %
(filenames[0], filenames[1]))
for line in output.rstrip().split("\n"):
result, correct_answer = line.split()
self.assertEqual(result, correct_answer)
def testFindDups(self):
"""Look for duplicates using --unique"""
params = [("", 13), ("/formula", 5),
("/connect", 6), ("/nostereo", 9),
("/nosp3", 11), ("/noEZ", 11),
("/nochg", 12), ("/noiso", 11),
("cansmi", 13), ("cansmiNS", 7)]
for param in params:
output, error = run_exec(self.smiles,
"babel -ismi -osmi --unique %s" % param[0])
self.assertConverted(error, param[1])
def test2DMDLto0D_more(self):
"""Test various combinations of stereobonds in 2D perception"""
filenames = [
self.getTestFile(x) for x in
["testsym_2Dtests_more.sdf", "testsym_2Dtests_threeligands.sdf"]
]
# The test files have the correct canonical SMILES string
# stored in the data field "smiles"
output, error = run_exec("obabel -isdf %s %s -ocan --append smiles" %
(filenames[0], filenames[1]))
for line in output.rstrip().split("\n"):
result, correct_answer = line.split()
self.assertEqual(result, correct_answer)
def testXYZtoXYZ(self):
"""PR#2956135- crash in kekulize"""
self.canFindExecutable("babel")
# A series of isotopamers, and their canonical forms
self.xyz = """39
crash.gamout
C -0.31501 -0.05904 0.00332
C 0.47846 1.04480 0.28483
N 1.83248 1.00566 0.38129
C 2.42024 -0.19701 0.19943
C 1.71953 -1.35983 -0.07408
C 0.33143 -1.28624 -0.17253
H -0.24386 -2.18519 -0.38442
H 2.23907 -2.30258 -0.20635
H 3.50341 -0.20251 0.28526
H 0.06258 2.02989 0.46235
C -1.79310 -0.00135 -0.09779
O -2.46156 -1.02575 -0.18756
N -2.41033 1.21816 -0.10797
H -1.94649 2.11169 -0.16198
H -3.41687 1.20930 -0.22381
C 0.26924 0.47947 -3.35313
C -0.44373 -0.03140 -4.37204
H -0.48212 0.45752 -5.34214
H -1.00864 -0.95087 -4.26294
C 1.00998 1.73774 -3.59280
O 1.09874 2.34143 -4.64607
O 1.61155 2.19132 -2.48091
H 2.04906 3.01525 -2.77997
C 0.34525 -0.16868 -2.00668
H -0.05656 0.49552 -1.23462
H 1.38253 -0.41344 -1.75510
H -0.22965 -1.10058 -1.97049
C 0.26203 0.28311 3.26498
C 1.38529 0.78393 2.72190
H 1.56449 0.74957 1.65029
H 2.15564 1.24022 3.33413
C -0.73494 -0.32012 2.35309
O -0.68045 -0.35957 1.13769
O -1.76945 -0.85942 3.01857
H -2.33520 -1.21968 2.30453
C -0.01692 0.31604 4.73465
H -0.11977 -0.69915 5.13149
H -0.93979 0.86887 4.93917
H 0.78936 0.80651 5.29109
"""
output, error = run_exec(self.xyz, "babel -ixyz -oxyz")
self.assertConverted(error, 1)
def testXYZtoXYZ(self):
"""PR#2956135- crash in kekulize"""
self.canFindExecutable("babel")
# A series of isotopamers, and their canonical forms
self.xyz = """39
crash.gamout
C -0.31501 -0.05904 0.00332
C 0.47846 1.04480 0.28483
N 1.83248 1.00566 0.38129
C 2.42024 -0.19701 0.19943
C 1.71953 -1.35983 -0.07408
C 0.33143 -1.28624 -0.17253
H -0.24386 -2.18519 -0.38442
H 2.23907 -2.30258 -0.20635
H 3.50341 -0.20251 0.28526
H 0.06258 2.02989 0.46235
C -1.79310 -0.00135 -0.09779
O -2.46156 -1.02575 -0.18756
N -2.41033 1.21816 -0.10797
H -1.94649 2.11169 -0.16198
H -3.41687 1.20930 -0.22381
C 0.26924 0.47947 -3.35313
C -0.44373 -0.03140 -4.37204
H -0.48212 0.45752 -5.34214
H -1.00864 -0.95087 -4.26294
C 1.00998 1.73774 -3.59280
O 1.09874 2.34143 -4.64607
O 1.61155 2.19132 -2.48091
H 2.04906 3.01525 -2.77997
C 0.34525 -0.16868 -2.00668
H -0.05656 0.49552 -1.23462
H 1.38253 -0.41344 -1.75510
H -0.22965 -1.10058 -1.97049
C 0.26203 0.28311 3.26498
C 1.38529 0.78393 2.72190
H 1.56449 0.74957 1.65029
H 2.15564 1.24022 3.33413
C -0.73494 -0.32012 2.35309
O -0.68045 -0.35957 1.13769
O -1.76945 -0.85942 3.01857
H -2.33520 -1.21968 2.30453
C -0.01692 0.31604 4.73465
H -0.11977 -0.69915 5.13149
H -0.93979 0.86887 4.93917
H 0.78936 0.80651 5.29109
"""
output, error = run_exec(self.xyz, "babel -ixyz -oxyz")
self.assertConverted(error, 1)
def testSelfMatch(self):
"""Verify that a molecule matches itself"""
data = [
'[C@@](F)(Br)(Cl)I',
'[C@](F)(Br)(Cl)I',
'F[C@](Br)(Cl)I',
'[C@H](Br)(Cl)I',
'Br[C@H](Cl)I',
'[C@]1(Br)(Cl)NC1',
'[C@@]1(Br)(Cl)NC1',
'Br[C@]1(Cl)NC1',
'C1N[C@]1(Cl)Br',
'F[C@]1(Br)N[C@]1(Br)Cl',
'[C@H]1(Cl)NC1'
]
for smi in data:
output, error = run_exec("obabel -:%s -s%s -osmi" % (smi, smi))
self.assertEqual(output.rstrip(), smi)
def testInChItoSMI(self):
"""Verify that the InChI is read correctly"""
output, error = run_exec(self.inchi, "babel -iinchi -ocan")
self.assertEqual(output.rstrip(), self.cansmi)
def checkmatch(query, molecules):
result = []
for smi in molecules:
output, error = run_exec("obabel -:%s -s%s -osmi" % (smi, query))
result.append(output.strip() != "")
return result
def testInsertionCodes(self):
"""
Testing a PDB entry with insertion codes to distinguish residues
upon conversion to FASTA.
"""
self.canFindExecutable("babel")
self.entryPDBwithInsertioncodes = """ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
ATOM 407 CA VAL L 29 57.124 18.088 47.170 1.00 0.00 C
ATOM 408 C VAL L 29 55.739 17.571 47.538 1.00 0.00 C
ATOM 409 O VAL L 29 55.535 16.362 47.550 1.00 0.00 O
ATOM 410 CB VAL L 29 57.580 17.456 45.842 1.00 0.00 C
ATOM 411 CG1 VAL L 29 56.571 17.743 44.741 1.00 0.00 C
ATOM 412 CG2 VAL L 29 58.957 17.973 45.450 1.00 0.00 C
ATOM 413 H VAL L 29 58.603 16.959 48.212 1.00 0.00 H
ATOM 414 HA VAL L 29 57.012 19.163 47.024 1.00 0.00 H
ATOM 415 HB VAL L 29 57.674 16.378 45.977 1.00 0.00 H
ATOM 416 1HG1 VAL L 29 56.909 17.289 43.809 1.00 0.00 H
ATOM 417 2HG1 VAL L 29 55.603 17.327 45.016 1.00 0.00 H
ATOM 418 3HG1 VAL L 29 56.479 18.821 44.604 1.00 0.00 H
ATOM 419 1HG2 VAL L 29 59.263 17.515 44.510 1.00 0.00 H
ATOM 420 2HG2 VAL L 29 58.917 19.055 45.331 1.00 0.00 H
ATOM 421 3HG2 VAL L 29 59.676 17.719 46.229 1.00 0.00 H
ATOM 422 N SER L 30 54.838 18.500 47.837 1.00 0.00 N
ATOM 423 CA SER L 30 53.494 18.162 48.273 1.00 0.00 C
ATOM 424 C SER L 30 52.725 17.364 47.221 1.00 0.00 C
ATOM 425 O SER L 30 52.723 17.697 46.056 1.00 0.00 O
ATOM 426 CB SER L 30 52.734 19.429 48.610 1.00 0.00 C
ATOM 427 OG SER L 30 51.403 19.143 48.941 1.00 0.00 O
ATOM 428 H SER L 30 55.100 19.472 47.757 1.00 0.00 H
ATOM 429 HA SER L 30 53.471 17.585 49.199 1.00 0.00 H
ATOM 430 1HB SER L 30 53.219 19.934 49.445 1.00 0.00 H
ATOM 431 2HB SER L 30 52.761 20.107 47.758 1.00 0.00 H
ATOM 432 HG SER L 30 50.919 19.965 48.828 1.00 0.00 H
ATOM 433 N SER L 30A 52.170 16.303 47.698 1.00 0.00 N
ATOM 434 CA SER L 30A 51.329 15.409 46.920 1.00 0.00 C
ATOM 435 C SER L 30A 52.015 14.812 45.685 1.00 0.00 C
ATOM 436 O SER L 30A 51.350 14.366 44.764 1.00 0.00 O
ATOM 437 CB SER L 30A 50.082 16.156 46.488 1.00 0.00 C
ATOM 438 OG SER L 30A 49.348 16.592 47.599 1.00 0.00 O
ATOM 439 H SER L 30A 52.421 16.046 48.642 1.00 0.00 H
ATOM 440 HA SER L 30A 50.943 14.567 47.497 1.00 0.00 H
ATOM 441 1HB SER L 30A 50.364 17.013 45.876 1.00 0.00 H
ATOM 442 2HB SER L 30A 49.463 15.505 45.873 1.00 0.00 H
ATOM 443 HG SER L 30A 49.931 17.176 48.090 1.00 0.00 H
ATOM 444 N SER L 31 53.347 14.792 45.683 1.00 0.00 N
ATOM 445 CA SER L 31 54.094 14.259 44.549 1.00 0.00 C
ATOM 446 C SER L 31 53.734 14.959 43.242 1.00 0.00 C
ATOM 447 O SER L 31 53.703 14.356 42.179 1.00 0.00 O
ATOM 448 CB SER L 31 53.835 12.771 44.418 1.00 0.00 C
ATOM 449 OG SER L 31 54.240 12.087 45.572 1.00 0.00 O
ATOM 450 H SER L 31 53.852 15.150 46.480 1.00 0.00 H
ATOM 451 HA SER L 31 55.175 14.292 44.689 1.00 0.00 H
ATOM 452 1HB SER L 31 52.774 12.600 44.243 1.00 0.00 H
ATOM 453 2HB SER L 31 54.375 12.383 43.555 1.00 0.00 H
ATOM 454 HG SER L 31 53.773 11.248 45.560 1.00 0.00 H
ATOM 455 N TYR L 32 53.460 16.259 43.402 1.00 0.00 N
ATOM 456 CA TYR L 32 53.176 17.161 42.301 1.00 0.00 C
ATOM 457 C TYR L 32 54.489 17.641 41.668 1.00 0.00 C
ATOM 458 O TYR L 32 54.910 18.762 41.892 1.00 0.00 O
ATOM 459 CB TYR L 32 52.342 18.352 42.780 1.00 0.00 C
ATOM 460 CG TYR L 32 50.880 18.031 42.990 1.00 0.00 C
ATOM 461 CD1 TYR L 32 50.294 16.936 42.371 1.00 0.00 C
ATOM 462 CD2 TYR L 32 50.089 18.824 43.807 1.00 0.00 C
ATOM 463 CE1 TYR L 32 48.958 16.639 42.559 1.00 0.00 C
ATOM 464 CE2 TYR L 32 48.751 18.535 44.002 1.00 0.00 C
ATOM 465 CZ TYR L 32 48.190 17.441 43.376 1.00 0.00 C
ATOM 466 OH TYR L 32 46.859 17.150 43.569 1.00 0.00 O
ATOM 467 H TYR L 32 53.456 16.618 44.347 1.00 0.00 H
ATOM 468 HA TYR L 32 52.651 16.625 41.509 1.00 0.00 H
ATOM 469 1HB TYR L 32 52.778 18.693 43.721 1.00 0.00 H
ATOM 470 2HB TYR L 32 52.439 19.136 42.030 1.00 0.00 H
ATOM 471 HD1 TYR L 32 50.908 16.305 41.727 1.00 0.00 H
ATOM 472 HD2 TYR L 32 50.537 19.687 44.299 1.00 0.00 H
ATOM 473 HE1 TYR L 32 48.512 15.775 42.066 1.00 0.00 H
ATOM 474 HE2 TYR L 32 48.145 19.172 44.648 1.00 0.00 H
ATOM 475 HH TYR L 32 46.462 17.658 44.280 1.00 0.00 H
"""
output, error = run_exec(self.entryPDBwithInsertioncodes,
"babel -ipdb -ofasta")
self.assertEqual(output.rstrip().rsplit("\n", 1)[1], "VSSSY")
def checkmatch(query, molecules):
result = []
for smi in molecules:
output, error = run_exec("obabel -:%s -s%s -osmi" % (smi, query))
result.append(output.strip() != "")
return result
def testSMILESto2D(self):
"""Test gen2d for some basic cases"""
for smi, can, inchi in self.data:
output, error = run_exec(smi, "obabel -ismi --gen2d -omdl")
output, error = run_exec(output.rstrip(), "obabel -imdl -ocan")
self.assertEqual(can, output.rstrip())
def testSMItoCAN(self):
"""Verify that all molecules give the same cansmi"""
output, error = run_exec("\n".join(self.smiles), "babel -ismi -ocan")
output = "\n".join([x.rstrip() for x in output.split("\n")])
self.assertEqual(output.rstrip(), "\n".join([self.cansmi] * len(self.smiles)))
def testInsertionCodes(self):
"""
Testing a PDB entry with insertion codes to distinguish residues
upon conversion to FASTA.
"""
self.canFindExecutable("babel")
self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
ATOM 407 CA VAL L 29 57.124 18.088 47.170 1.00 0.00 C
ATOM 408 C VAL L 29 55.739 17.571 47.538 1.00 0.00 C
ATOM 409 O VAL L 29 55.535 16.362 47.550 1.00 0.00 O
ATOM 410 CB VAL L 29 57.580 17.456 45.842 1.00 0.00 C
ATOM 411 CG1 VAL L 29 56.571 17.743 44.741 1.00 0.00 C
ATOM 412 CG2 VAL L 29 58.957 17.973 45.450 1.00 0.00 C
ATOM 413 H VAL L 29 58.603 16.959 48.212 1.00 0.00 H
ATOM 414 HA VAL L 29 57.012 19.163 47.024 1.00 0.00 H
ATOM 415 HB VAL L 29 57.674 16.378 45.977 1.00 0.00 H
ATOM 416 1HG1 VAL L 29 56.909 17.289 43.809 1.00 0.00 H
ATOM 417 2HG1 VAL L 29 55.603 17.327 45.016 1.00 0.00 H
ATOM 418 3HG1 VAL L 29 56.479 18.821 44.604 1.00 0.00 H
ATOM 419 1HG2 VAL L 29 59.263 17.515 44.510 1.00 0.00 H
ATOM 420 2HG2 VAL L 29 58.917 19.055 45.331 1.00 0.00 H
ATOM 421 3HG2 VAL L 29 59.676 17.719 46.229 1.00 0.00 H
ATOM 422 N SER L 30 54.838 18.500 47.837 1.00 0.00 N
ATOM 423 CA SER L 30 53.494 18.162 48.273 1.00 0.00 C
ATOM 424 C SER L 30 52.725 17.364 47.221 1.00 0.00 C
ATOM 425 O SER L 30 52.723 17.697 46.056 1.00 0.00 O
ATOM 426 CB SER L 30 52.734 19.429 48.610 1.00 0.00 C
ATOM 427 OG SER L 30 51.403 19.143 48.941 1.00 0.00 O
ATOM 428 H SER L 30 55.100 19.472 47.757 1.00 0.00 H
ATOM 429 HA SER L 30 53.471 17.585 49.199 1.00 0.00 H
ATOM 430 1HB SER L 30 53.219 19.934 49.445 1.00 0.00 H
ATOM 431 2HB SER L 30 52.761 20.107 47.758 1.00 0.00 H
ATOM 432 HG SER L 30 50.919 19.965 48.828 1.00 0.00 H
ATOM 433 N SER L 30A 52.170 16.303 47.698 1.00 0.00 N
ATOM 434 CA SER L 30A 51.329 15.409 46.920 1.00 0.00 C
ATOM 435 C SER L 30A 52.015 14.812 45.685 1.00 0.00 C
ATOM 436 O SER L 30A 51.350 14.366 44.764 1.00 0.00 O
ATOM 437 CB SER L 30A 50.082 16.156 46.488 1.00 0.00 C
ATOM 438 OG SER L 30A 49.348 16.592 47.599 1.00 0.00 O
ATOM 439 H SER L 30A 52.421 16.046 48.642 1.00 0.00 H
ATOM 440 HA SER L 30A 50.943 14.567 47.497 1.00 0.00 H
ATOM 441 1HB SER L 30A 50.364 17.013 45.876 1.00 0.00 H
ATOM 442 2HB SER L 30A 49.463 15.505 45.873 1.00 0.00 H
ATOM 443 HG SER L 30A 49.931 17.176 48.090 1.00 0.00 H
ATOM 444 N SER L 31 53.347 14.792 45.683 1.00 0.00 N
ATOM 445 CA SER L 31 54.094 14.259 44.549 1.00 0.00 C
ATOM 446 C SER L 31 53.734 14.959 43.242 1.00 0.00 C
ATOM 447 O SER L 31 53.703 14.356 42.179 1.00 0.00 O
ATOM 448 CB SER L 31 53.835 12.771 44.418 1.00 0.00 C
ATOM 449 OG SER L 31 54.240 12.087 45.572 1.00 0.00 O
ATOM 450 H SER L 31 53.852 15.150 46.480 1.00 0.00 H
ATOM 451 HA SER L 31 55.175 14.292 44.689 1.00 0.00 H
ATOM 452 1HB SER L 31 52.774 12.600 44.243 1.00 0.00 H
ATOM 453 2HB SER L 31 54.375 12.383 43.555 1.00 0.00 H
ATOM 454 HG SER L 31 53.773 11.248 45.560 1.00 0.00 H
ATOM 455 N TYR L 32 53.460 16.259 43.402 1.00 0.00 N
ATOM 456 CA TYR L 32 53.176 17.161 42.301 1.00 0.00 C
ATOM 457 C TYR L 32 54.489 17.641 41.668 1.00 0.00 C
ATOM 458 O TYR L 32 54.910 18.762 41.892 1.00 0.00 O
ATOM 459 CB TYR L 32 52.342 18.352 42.780 1.00 0.00 C
ATOM 460 CG TYR L 32 50.880 18.031 42.990 1.00 0.00 C
ATOM 461 CD1 TYR L 32 50.294 16.936 42.371 1.00 0.00 C
ATOM 462 CD2 TYR L 32 50.089 18.824 43.807 1.00 0.00 C
ATOM 463 CE1 TYR L 32 48.958 16.639 42.559 1.00 0.00 C
ATOM 464 CE2 TYR L 32 48.751 18.535 44.002 1.00 0.00 C
ATOM 465 CZ TYR L 32 48.190 17.441 43.376 1.00 0.00 C
ATOM 466 OH TYR L 32 46.859 17.150 43.569 1.00 0.00 O
ATOM 467 H TYR L 32 53.456 16.618 44.347 1.00 0.00 H
ATOM 468 HA TYR L 32 52.651 16.625 41.509 1.00 0.00 H
ATOM 469 1HB TYR L 32 52.778 18.693 43.721 1.00 0.00 H
ATOM 470 2HB TYR L 32 52.439 19.136 42.030 1.00 0.00 H
ATOM 471 HD1 TYR L 32 50.908 16.305 41.727 1.00 0.00 H
ATOM 472 HD2 TYR L 32 50.537 19.687 44.299 1.00 0.00 H
ATOM 473 HE1 TYR L 32 48.512 15.775 42.066 1.00 0.00 H
ATOM 474 HE2 TYR L 32 48.145 19.172 44.648 1.00 0.00 H
ATOM 475 HH TYR L 32 46.462 17.658 44.280 1.00 0.00 H
"""
output, error = run_exec(self.entryPDBwithInsertioncodes,
"babel -ipdb -ofasta")
self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
def testSMILESto2D(self):
"""Test gen2d for some basic cases"""
for smi, can, inchi in self.data:
output, error = run_exec(smi, "obabel -ismi --gen2d -omdl")
output, error = run_exec(output.rstrip(), "obabel -imdl -ocan")
self.assertEqual(can, output.rstrip())
def testSMItoCAN(self):
"""Verify that all molecules give the same cansmi"""
output, error = run_exec("\n".join(self.smiles), "babel -ismi -ocan")
output = "\n".join([x.rstrip() for x in output.split("\n")])
self.assertEqual(output.rstrip(),
"\n".join([self.cansmi] * len(self.smiles)))
def testInChItoSMI(self):
"""Verify that the InChI is read correctly"""
output, error = run_exec(self.inchi, "babel -iinchi -ocan")
self.assertEqual(output.rstrip(), self.cansmi)
