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import unittest
from ost import *
from ost import settings
from ost.bindings import msms
class TestMSMSBindings(unittest.TestCase):
def setUp(self):
self.protein = io.LoadEntity("testfiles/testprotein.pdb")
self.num_tri=111546
self.num_vert=55762
self.ases=20051.928
self.asas=21574.324
self.volume=60229.848
def testCalculateSurface(self):
surf=msms.CalculateSurface(self.protein,
msms_env='MSMSSERVER',
density=3,
radius=1.4,
attach_asa="asa",
attach_esa="esa")[0]
self.assertEqual(self.num_vert, len(surf.GetVertexIDList()))
self.assertEqual(self.num_tri, len(surf.GetTriIDList()))
def testCalculateSurfaceArea(self):
(msms_ases, msms_asas)=msms.CalculateSurfaceArea(self.protein, \
msms_env='MSMSSERVER',
density=3,
radius=1.4)
self.assertAlmostEqual(self.ases, msms_ases[0], 1)
self.assertAlmostEqual(self.asas, msms_asas[0], 1)
def testCalculateSurfaceVolume(self):
volume=msms.CalculateSurfaceVolume(self.protein, \
msms_env='MSMSSERVER',
density=3,
radius=1.4)
self.assertAlmostEqual(self.volume, volume, 1)
if __name__ == "__main__":
# test if msms package is available on system, otherwise ignore tests
VERSION_REQUIRED = '2.6.1'
try:
msms._GetExecutable(msms_exe=None, msms_env='MSMSSERVER')
except(settings.FileNotFound):
print("Could not find msms executable: ignoring unit tests")
exit(0)
version = msms.GetVersion(msms_exe=None, msms_env='MSMSSERVER')
if version!=VERSION_REQUIRED:
print("MSMS version (%s) does not match required version %s: ignoring unit tests"%(version, VERSION_REQUIRED))
from ost import testutils
testutils.RunTests()
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