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import unittest
import ost
from ost import seq, io, mol
class TestAlignToSeqRes(unittest.TestCase):
def testAlignWorking(self):
ent, seqres = io.LoadMMCIF("testfiles/align_to_seqres.mmcif", seqres = True)
chain = ent.FindChain("A")
sequence = seqres.FindSequence(chain.GetName());
seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first=False)
self.assertEqual(str(sequence), "MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEV"+
"LIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK")
self.assertEqual(str(seqres_aln.sequences[1]), "----SDFVVIKALEDGVNVIGLTR--"+
"-TRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGK-")
seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first=True)
self.assertEqual(str(seqres_aln.sequences[1]), "----SDFVVIKALEDGVNVIGLTR--"+
"-TRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGK-")
def testAlignFail(self):
ent, seqres = io.LoadMMCIF("testfiles/align_to_seqres_valueerror.mmcif",
seqres = True)
chain = ent.FindChain("A")
sequence = seqres.FindSequence(chain.GetName());
ost.PushVerbosityLevel(0)
self.assertRaises(ValueError, seq.alg.AlignToSEQRES, chain, sequence, True)
ost.PopVerbosityLevel()
def testValidateWorking(self):
ent, seqres = io.LoadMMCIF("testfiles/align_to_seqres.mmcif", seqres = True)
chain = ent.FindChain("A")
sequence = seqres.FindSequence(chain.GetName());
seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first=False)
self.assertEqual(seq.alg.ValidateSEQRESAlignment(seqres_aln, chain), True)
def testValidateWorkingOnAttachedView(self):
ent, seqres = io.LoadMMCIF("testfiles/align_to_seqres.mmcif", seqres = True)
chain = ent.FindChain("A")
sequence = seqres.FindSequence(chain.GetName());
seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first=False)
seqres_aln.AttachView(1, chain.Select(''))
self.assertEqual(seq.alg.ValidateSEQRESAlignment(seqres_aln), True)
def testValidateEmptySequenceWorking(self):
alignment = seq.CreateAlignment(seq.CreateSequence('SEQRES', ''),
seq.CreateSequence('atoms', ''))
chain = mol.ChainHandle()
self.assertEqual(seq.alg.ValidateSEQRESAlignment(alignment, chain), True)
def testValidateStrandBreakageFail(self):
ent, seqres = io.LoadMMCIF("testfiles/validate_segres_aln_breakage.mmcif",
seqres = True)
chain = ent.FindChain("A")
sequence = seqres.FindSequence(chain.GetName());
seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first = True,
validate = False)
self.assertEqual(seq.alg.ValidateSEQRESAlignment(seqres_aln, chain), False)
def testValidateGapConnectedFail(self):
ent, seqres = io.LoadMMCIF("testfiles/validate_seqres_aln_connected.mmcif",
seqres = True,)
chain = ent.FindChain("A")
sequence = seqres.FindSequence(chain.GetName());
seqres_aln = seq.alg.AlignToSEQRES(chain, sequence, try_resnum_first = True,
validate = False)
self.assertEqual(seq.alg.ValidateSEQRESAlignment(seqres_aln, chain), False)
if __name__ == "__main__":
from ost import testutils
if testutils.DefaultCompoundLibIsSet():
testutils.RunTests()
else:
print('No compound library available. Ignoring test_aligntoseqres.py tests.')
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