43 lines
1.7 KiB
Python
43 lines
1.7 KiB
Python
'''
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missing residues
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'''
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from pymol import cmd, CmdException, testing, stored
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@testing.requires_version('1.8.1.0')
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class TestPYMOL2727(testing.PyMOLTestCase):
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def _get_seq(self, selection):
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from pymol.exporting import _resn_to_aa as one_letter
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prev_resi = [None]
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seq = []
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def callback(resi, resn):
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if resi == prev_resi[0]:
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return
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prev_resi[0] = resi
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seq.append(one_letter[resn])
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cmd.iterate(selection, 'callback(resi, resn)', space=locals())
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return ''.join(seq)
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@testing.foreach.product(
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(0, 1),
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('1hbb_pdbx_seq_one_letter_code.cif', '1hbb_entity_poly_seq.cif'),
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)
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def testMissingRes(self, use_auth, filename):
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cmd.set('cif_use_auth', use_auth)
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cmd.load(self.datafile(filename), '1hbb')
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seq = self._get_seq('segi A')
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self.assertEqual(seq, 'VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR')
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seq = self._get_seq('segi B')
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self.assertEqual(seq, 'VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH')
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@testing.requires_version('2.4')
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def testMissingResIns(self):
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# label_seq_id 10-19 can't be inserted (without insertion codes)
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cmd.load(self.datafile('1hbb_pdbx_seq_one_letter_code-ins.cif'), '1hbb')
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seq = self._get_seq('segi A')
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self.assertEqual(seq, 'VLSPADKTNHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR')
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