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import unittest
from ost import *
from ost import settings
from ost import testutils
from ost.seq.alg import SequenceIdentity
from ost.bindings import tmtools
from ost.bindings import WrappedTMAlign
class TestTMBindings(unittest.TestCase):
def setUp(self):
self.protein = io.LoadEntity("testfiles/testprotein.pdb")
def testTMAlign(self):
try:
cad_calc_path = settings.Locate('tmalign')
except:
print("Could not find tmalign executable: ignoring unit tests")
return
tm_result = tmtools.TMAlign(self.protein, self.protein)
# model and reference are the same, we expect pretty good results
self.assertEqual(tm_result.rmsd, 0.0)
self.assertEqual(tm_result.tm_score, 1.0)
self.assertEqual(tm_result.aligned_length, len(self.protein.chains[0].residues))
self.assertEqual(SequenceIdentity(tm_result.alignment), 100.0)
# transformation should be identity matrix (no transformation at all...)
identity = geom.Mat4(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1)
self.assertEqual(tm_result.transform, identity)
def testTMScore(self):
try:
cad_calc_path = settings.Locate('tmscore')
except:
print("Could not find tmalign executable: ignoring unit tests")
return
tm_result = tmtools.TMScore(self.protein, self.protein)
# model and reference are the same, we expect pretty good results
self.assertEqual(tm_result.rmsd_common, 0.0)
self.assertEqual(tm_result.tm_score, 1.0)
self.assertEqual(tm_result.max_sub, 1.0)
self.assertEqual(tm_result.gdt_ts, 1.0)
self.assertEqual(tm_result.gdt_ha, 1.0)
self.assertEqual(tm_result.rmsd_below_five, 0.0)
# transformation should be identity matrix (no transformation at all...)
identity = geom.Mat4(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1)
self.assertEqual(tm_result.transform, identity)
def testWrappedTMAlign(self):
tm_result = WrappedTMAlign(self.protein.CreateFullView().chains[0],
self.protein.CreateFullView().chains[0])
# model and reference are the same, we expect pretty good results
self.assertAlmostEqual(tm_result.rmsd, 0.0, places=4)
self.assertAlmostEqual(tm_result.tm_score, 1.0, places=4)
self.assertEqual(tm_result.aligned_length, len(self.protein.chains[0].residues))
self.assertEqual(SequenceIdentity(tm_result.alignment), 100.0)
# transformation should be identity matrix (no transformation at all...)
identity = geom.Mat4(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1)
for i in range(4):
for j in range(4):
self.assertAlmostEqual(tm_result.transform[i,j], identity[i,j])
if __name__ == "__main__":
testutils.RunTests()
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