def check_ob223():
import openbabel
from chemfp import openbabel
assert openbabel._ob_version == "2.2.3", openbabel._ob_version
assert not support.can_skip("ob")
assert not support.can_skip("ob223")
def check_ob23svn1():
import openbabel
from chemfp import openbabel
assert openbabel._ob_version == "2.3.90", openbabel._ob_version
assert not support.can_skip("ob")
assert not support.can_skip("ob23svn1")
def check_x64():
assert sys.maxint == 9223372036854775807
assert not support.can_skip("x64")
def check_oe2011Oct():
from openeye.oechem import OEChemGetRelease
version = OEChemGetRelease()
assert version == "1.7.6", version
assert not support.can_skip("oe")
assert not support.can_skip("oe2011Oct")
def check_py27():
version = sys.version_info[:2]
assert version == (2,7), version
assert not support.can_skip("py27")
def check_x32():
assert sys.maxint == 2147483647
assert not support.can_skip("x32")
import unittest2
import sys
import os
from cStringIO import StringIO as SIO
import support
try:
from openeye import oechem # These tests require OEChem
has_oechem = True
skip_oechem = False
except ImportError:
has_oechem = False
skip_oechem = True
if not support.can_skip("oe"):
skip_oechem = False
from openeye import oechem
if has_oechem:
from chemfp.commandline import oe2fps
import chemfp.openeye
chemfp.openeye._USE_SELECT = False # Grrr. Needed to automate testing.
real_stdout = sys.stdout
real_stderr = sys.stderr
PUBCHEM_SDF = support.fullpath("pubchem.sdf")
PUBCHEM_SDF_GZ = support.fullpath("pubchem.sdf.gz")
PUBCHEM_ANOTHER_EXT = support.fullpath("pubchem.should_be_sdf_but_is_not")
oeerrs = oechem.oeosstream()
import sys
import unittest2
import support
try:
from openeye.oechem import OEGraphMol, OEParseSmiles
skip_oechem = False
except ImportError:
skip_oechem = support.can_skip("oe")
else:
from chemfp import openeye_patterns
import test_patterns
def parse_smiles(smiles):
mol = OEGraphMol()
OEParseSmiles(mol, smiles)
return mol
def _count(it):
return sum(1 for item in it)
class ReferenceMixin(object):
def test_reference_data_set(self):
largest = min(self.reference_limit,
max(v for (k, v) in self.reference_cases))
matcher = self.reference_class(largest)
import os
from cStringIO import StringIO as SIO
import support
try:
from openeye import oechem # These tests require OEChem
if not oechem.OEChemIsLicensed():
print >>sys.stderr, "oechem library available but not license found. Skipping its tests."
raise ImportError
has_oechem = True
skip_oechem = False
except ImportError:
has_oechem = False
skip_oechem = True
if not support.can_skip("oe"):
skip_oechem = False
from openeye import oechem
if has_oechem:
from chemfp.commandline import oe2fps
import chemfp.openeye
OEGRAPHSIM_API_VERSION = chemfp.openeye.OEGRAPHSIM_API_VERSION
chemfp.openeye._USE_SELECT = False # Grrr. Needed to automate testing.
real_stdout = sys.stdout
real_stderr = sys.stderr
PUBCHEM_SDF = support.fullpath("pubchem.sdf")
PUBCHEM_SDF_GZ = support.fullpath("pubchem.sdf.gz")
PUBCHEM_ANOTHER_EXT = support.fullpath("pubchem.should_be_sdf_but_is_not")
import os
import shutil
import tempfile
import unittest2
import support
try:
import openbabel
has_openbabel = True
skip_openbabel = False
except ImportError:
has_openbabel = False
skip_openbabel = True
if not support.can_skip("ob"):
skip_openbabel = False
import openbabel
if has_openbabel:
import chemfp.openbabel
from chemfp.commandline import ob2fps
VERSION = chemfp.openbabel._ob_version
runner = support.Runner(ob2fps.main)
run = runner.run
run_fps = runner.run_fps
run_split = runner.run_split
run_exit = runner.run_exit
HAS_MACCS = chemfp.openbabel.HAS_MACCS
import os
import shutil
import tempfile
import unittest2
import support
try:
import openbabel
has_openbabel = True
skip_openbabel = False
except ImportError:
has_openbabel = False
skip_openbabel = True
if not support.can_skip("ob"):
skip_openbabel = False
import openbabel
if has_openbabel:
import chemfp.openbabel
from chemfp.commandline import ob2fps
VERSION = chemfp.openbabel._ob_version
runner = support.Runner(ob2fps.main)
run = runner.run
run_fps = runner.run_fps
run_split = runner.run_split
run_exit = runner.run_exit
HAS_MACCS = chemfp.openbabel.HAS_MACCS
import shutil
import os
from cStringIO import StringIO
import tempfile
import support
try:
import chemfp.rdkit
has_rdkit = True
skip_rdkit = False
except ImportError:
has_rdkit = False
skip_rdkit = True
if not support.can_skip("rdkit"):
skip_rdkit = False
import rdkit
if has_rdkit:
from chemfp.commandline import rdkit2fps
runner = support.Runner(rdkit2fps.main)
else:
runner = None
MACCS_SMI = support.fullpath("maccs.smi")
TRP = open(support.fullpath("tryptophan.sdf")).read()
class TestMACCS(unittest2.TestCase):
def test_bitorder(self):
from __future__ import with_statement
import sys
import unittest2
import support
try:
from openeye.oechem import OEGraphMol, OEParseSmiles, OEChemIsLicensed
if not OEChemIsLicensed():
raise ImportError
skip_oechem = False
except ImportError:
skip_oechem = support.can_skip("oe")
if not skip_oechem:
from chemfp import openeye_patterns
from chemfp.openeye import OEGRAPHSIM_API_VERSION
import test_patterns
from chemfp import types
MACCS_SMI = support.fullpath("maccs.smi")
def parse_smiles(smiles):
mol = OEGraphMol()
OEParseSmiles(mol, smiles)
return mol
def _count(it):
return sum(1 for item in it)
class ReferenceMixin(object):