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