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#!/usr/bin/env python
import unittest
import gemmi
from common import full_path
class TestAlignment(unittest.TestCase):
def test_string_align(self):
result = gemmi.align_string_sequences(list('AABCC'),
list('ABC'), [0])
self.assertEqual(result.score, 0)
self.assertEqual(result.cigar_str(), '1I3M1I')
self.assertEqual(result.add_gaps('AABCC', 1), 'AABCC')
self.assertEqual(result.add_gaps('ABC', 2), '-ABC-')
self.assertEqual(result.calculate_identity(), 100.)
self.assertEqual(result.calculate_identity(1), 60.)
self.assertEqual(result.calculate_identity(2), 100.)
self.assertEqual(result.match_string, ' ||| ')
result = gemmi.align_string_sequences(list('SIMILARITY'),
list('PILLAR'), [])
self.assertEqual(result.match_count, 4)
self.assertEqual(result.cigar_str(), '3M1I3M3I')
def test_hemoglobin_alignment(self):
# based on example from
# http://biopython.org/DIST/docs/tutorial/Tutorial.html
hba_human = ("MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQ"
"VKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTL"
"AAHLPAEFTPAVHASLDKFLASVSTVLTSKYR")
hbb_human = ("MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAV"
"MGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNV"
"LVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH")
AA = gemmi.ResidueKind.AA
hba_seq = gemmi.expand_one_letter_sequence(hba_human, AA)
hbb_seq = gemmi.expand_one_letter_sequence(hbb_human, AA)
id_score = gemmi.AlignmentScoring()
id_score.match = 1
id_score.mismatch = 0
id_score.gapo = 0
id_score.gape = 0
result = gemmi.align_string_sequences(hba_seq, hbb_seq, [], id_score)
# "80 different alignments with the score 72"
self.assertEqual(result.score, 72)
blosum62 = gemmi.AlignmentScoring('b')
blosum62.gapo = -9
result = gemmi.align_string_sequences(hba_seq, hbb_seq, [], blosum62)
# BioPython equivalent is:
# pairwise2.align.globalds(seq1.seq, seq2.seq, blosum62, -10, -1)
self.assertEqual(result.score, 290)
def test_assign_best_sequences(self):
st = gemmi.read_structure(full_path('1lzh.pdb.gz'))
st.setup_entities()
seq3 = st.entities[0].full_sequence
self.assertEqual(len(seq3), 129)
seq1 = gemmi.one_letter_code(seq3)
self.assertEqual(len(seq1), 129)
st.clear_sequences()
self.assertEqual(len(st.entities[0].full_sequence), 0)
st.assign_best_sequences([seq1+'A', seq1])
self.assertEqual(len(st.entities[0].full_sequence), 129)
self.assertEqual(st.entities[0].subchains, ['Axp', 'Bxp'])
def test_superposition(self):
model = gemmi.read_structure(full_path('4oz7.pdb'))[0]
poly1 = model['A'].get_polymer()
poly2 = model['B'].get_polymer()
ptype = poly1.check_polymer_type()
S = gemmi.SupSelect
s1 = gemmi.calculate_superposition(poly1, poly2, ptype, S.CaP)
s2 = gemmi.calculate_superposition(poly1, poly2, ptype, S.MainChain)
s3 = gemmi.calculate_superposition(poly1, poly2, ptype, S.All)
self.assertEqual(s1.count, 10)
self.assertEqual(s2.count, 39)
self.assertEqual(s3.count, 77)
self.assertAlmostEqual(s1.rmsd, 0.146, places=3)
self.assertAlmostEqual(s2.rmsd, 0.174, places=3)
self.assertAlmostEqual(s3.rmsd, 0.400, places=3)
for s in [s1, s2, s3]:
self.assertAlmostEqual(s.transform.vec.y, 17.0, places=1)
if __name__ == '__main__':
unittest.main()
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