def test_fill_doublegap(self):
"""Should insert fragments into correct sites."""
# prepare model
t = Template(DOUBLEGAP, 'file', 'A')
m = RnaModel()
for r in t:
m.copy_residue(r)
# insert first fragment
struc = ModernaStructure('file', FRAGMENT1)
f1 = ModernaFragment53(struc, anchor5=m['20'], anchor3=m['24'], \
new_sequence=Sequence('AUA'), keep=keep_first_last)
m.insert_fragment(f1)
resids = [r.identifier for r in m]
expected_resids1 = [
'18', '19', '20', '21', '21A', '23', '24', '27', '28', '29', '30',
'31', '32', '33', '34', '35'
]
self.assertEqual(resids, expected_resids1)
# insert second fragment
struc = ModernaStructure('file', FRAGMENT2)
f2 = ModernaFragment53(struc, anchor5=m['23'], anchor3=m['28'], \
new_sequence=Sequence('AUUA'), keep=keep_first_last)
m.insert_fragment(f2)
resids = [r.identifier for r in m]
expected_resids2 = [
'18', '19', '20', '21', '21A', '23', '24', '24A', '24B', '27',
'28', '29', '30', '31', '32', '33', '34', '35'
]
self.assertEqual(resids, expected_resids2)
class ModernaFragment5Tests(TestCase):
"""fragment attached at 3' end of model"""
def setUp(self):
self.m = RnaModel(data_type='file',
data=MINI_TEMPLATE,
seq=Sequence("GCGGAUUUALCUCAG"))
self.s1 = ModernaStructure('file',
SMALL_FRAGMENT,
seq=Sequence("GCGG"))
self.s2 = ModernaStructure('file',
SMALL_FRAGMENT,
seq=Sequence("GCGG"))
def test_attributes(self):
five = ModernaFragment5(self.s1, anchor5=self.m['15'])
self.assertEqual(len(five.anchor_residues), 1)
self.assertEqual(len(five.nonanchor_residues), 3)
self.assertTrue(str(five))
def test_add_on_3_end(self):
"""Model sequence should change accordingly."""
five = ModernaFragment5(self.s1, anchor5=self.m['15'])
self.m.insert_fragment(five)
self.assertEqual(self.m.get_sequence(), Sequence("GCGGAUUUALCUCAGCGG"))
self.assertTrue(five.rmsd <= 1.00)
def test_add_on_3_end_replace(self):
"""Model sequence should change accordingly."""
five_overwrite = ModernaFragment5(self.s2, anchor5=self.m['9'])
self.m.insert_fragment(five_overwrite)
self.assertEqual(self.m.get_sequence(), Sequence("GCGGAUUUACGG"))
self.assertTrue(five_overwrite.rmsd <= 1.00, 0)
def test_insert_eliminate(self):
"""Inserts a 2D fragment into a model."""
helix = load_model(HELIX, 'A')
helix = RnaModel(None, None, 'A', 'residues',
helix['1':'8'] + helix['73':'80'])
mf = ModernaFragment2D(self.motif, \
anchor5=helix['7'], anchor3=helix['74'], \
anchor5_upper=helix['8'], anchor3_upper=helix['73'], \
frag5_upper=self.motif['196'], frag3_upper=self.motif['217'], \
new_sequence=Sequence('C'), \
model=helix)
helix.insert_fragment(mf)
self.assertEqual(helix.get_sequence(), Sequence('AAAAAAAA_UCUUUUUUU'))
self.assertEqual(helix.get_secstruc(), '(((((((().)))))))')
def test_fill_gap_numbering(self):
"""Should insert fragment with correct numbering."""
t = Template(DOUBLEGAP, 'file', 'A')
m = RnaModel()
for r in t:
m.copy_residue(r)
struc = ModernaStructure('file', FRAGMENT1)
f1 = ModernaFragment53(struc,
anchor5=m['20'],
anchor3=m['24'],
new_sequence=Sequence('AUA'))
m.insert_fragment(f1)
resids = [r.identifier for r in m]
expected_resids1 = [
'18', '19', '20', '20A', '20B', '20C', '24', '27', '28', '29',
'30', '31', '32', '33', '34', '35'
]
self.assertEqual(resids, expected_resids1)
class ModernaFragment3Tests(TestCase):
def setUp(self):
"""
fragment attached at 5' end of model.
"""
self.m = RnaModel(data_type='file',
data=MINI_TEMPLATE,
seq=Sequence("GCGGAUUUALCUCAG"))
self.s1 = ModernaStructure('file',
SMALL_FRAGMENT,
seq=Sequence("GCGG"))
self.s2 = ModernaStructure('file',
SMALL_FRAGMENT,
seq=Sequence("GCGG"))
def test_attributes(self):
"""Attributes of fragment are accessible."""
three = ModernaFragment3(self.s1, anchor3=self.m['1'])
self.assertEqual(len(three.anchor_residues), 1)
self.assertEqual(len(three.nonanchor_residues), 3)
self.assertTrue(str(three))
def test_add_on_5_end(self):
"""Model sequence should change accordingly."""
three = ModernaFragment3(self.s1, anchor3=self.m['1'])
self.m.insert_fragment(three)
self.assertEqual(self.m.get_sequence(), Sequence("GCGGCGGAUUUALCUCAG"))
self.assertTrue(three.rmsd <= 1.00)
def test_add_on_5_end_exact(self):
"""Model sequence should change accordingly."""
# exactly fitting example replacing original residues.
three_overwrite = ModernaFragment3(self.s2, anchor3=self.m['6'])
self.m.insert_fragment(three_overwrite)
self.assertEqual(self.m.get_sequence(), Sequence("GCGUUUALCUCAG"))
self.assertTrue(three_overwrite.rmsd <= 1.00)
def test_add_discontinuous(self):
"""Tries to add a helix to an end."""
helix = ModernaStructure('file', 'test_data/rna_structures/helix.pdb')
helix_frag = ModernaFragment3(helix, anchor3=self.m['1'], strict=False)
self.m.insert_fragment(helix_frag)
self.assertEqual(self.m.get_sequence(),
Sequence('CCGACCUUCGGCC_GGUGGCCGAAGGGCGGAUUUALCUCAG'))
class ModernaFragment53Tests(TestCase):
"""
Checks basic functionality of the ModernaFragment class.
"""
def setUp(self):
self.m = RnaModel(data_type='file',
data=MINI_TEMPLATE,
seq=Sequence("GCGGAUUUALCUCAG"))
self.s1 = ModernaStructure('file',
SMALL_FRAGMENT,
seq=Sequence("GCGG"))
self.s2 = ModernaStructure('file',
SMALL_FRAGMENT,
seq=Sequence("GCGG"))
self.s3 = ModernaStructure('file',
MINI_TEMPLATE,
seq=Sequence("GCGGAUUUALCUCAG"))
def test_attributes(self):
"""object attributes are set up correctly."""
f1 = ModernaFragment53(self.s1,
anchor5=self.m['10'],
anchor3=self.m['13'])
self.assertEqual(len(f1.struc), 4)
self.assertEqual(f1.anchor5.fixed_resi, self.m['10'])
self.assertEqual(f1.anchor3.fixed_resi, self.m['13'])
self.assertEqual(f1.struc.get_sequence(), Sequence("GCGG"))
self.assertTrue(str(f1))
# anchor residues
self.assertEqual(len(f1.anchor_residues), 2)
self.assertEqual(f1.anchor_residues[0].mobile_resi.identifier, '1')
self.assertEqual(f1.anchor_residues[1].mobile_resi.identifier, '4')
f1.prepare_anchor_residues()
self.assertEqual(f1.anchor_residues[0].mobile_resi.identifier, '1')
self.assertEqual(f1.anchor_residues[1].mobile_resi.identifier, '4')
# non-anchors
self.assertEqual(len(f1.nonanchor_residues), 2)
# second example
f2 = ModernaFragment53(self.s2,
anchor5=self.m['1'],
anchor3=self.m['4'],
new_sequence=Sequence('GL'))
self.assertEqual(len(f2.struc), 4)
self.assertEqual(f2.struc.get_sequence(), Sequence("GCGG"))
self.assertEqual(f2.new_sequence, Sequence("GL"))
def test_get_resi_to_remove(self):
"""Should return resi identifiers between anchors and of anchors itself."""
f1 = ModernaFragment53(self.s1,
anchor5=self.m['10'],
anchor3=self.m['13'])
result = f1.get_resi_to_remove(self.m)
self.assertEqual(result, ['10', '11', '12', '13'])
def test_renumber(self):
"""New numbering should start at anchor5, and then go through alphabet."""
f1 = ModernaFragment53(self.s1,
anchor5=self.m['10'],
anchor3=self.m['13'])
f1.prepare_anchor_residues()
f1.renumber()
self.assertEqual([r.identifier for r in self.s1],
['10', '10A', '10B', '13'])
# second example
f2 = ModernaFragment53(self.s2,
anchor5=self.m['1'],
anchor3=self.m['4'],
new_sequence=Sequence('GL'))
f2.prepare_anchor_residues()
f2.renumber()
self.assertEqual([r.identifier for r in self.s2],
['1', '1A', '1B', '4'])
def test_superimpose_fragment(self):
"""Should apply superimposition and return RMSD"""
f1 = ModernaFragment53(self.s1,
anchor5=self.m['10'],
anchor3=self.m['13'])
rmsd = f1.superimpose()
self.assertAlmostEqual(rmsd, 1.0, 0) # MM: ? 1.1253267913922658
# second fragment should fit perfectly
f2 = ModernaFragment53(self.s2,
anchor5=self.m['1'],
anchor3=self.m['4'],
new_sequence=Sequence('GL'))
rmsd = f2.superimpose()
self.assertAlmostEqual(rmsd, 0.00)
def test_refine(self):
"""Should change both numbers and sequence, and superimpose."""
f2 = ModernaFragment53(self.s2,
anchor5=self.m['1'],
anchor3=self.m['4'],
new_sequence=Sequence('GL'))
f2.superimpose()
f2.prepare_anchor_residues()
f2.renumber()
f2.apply_seq()
numbers = [r.identifier for r in self.s2]
self.assertEqual(numbers, ['1', '1A', '1B', '4'])
self.assertEqual(self.s2.get_sequence(), Sequence('GGLG'))
def test_clash(self):
"""Should not clash with a given piece of structure."""
f1 = ModernaFragment53(self.s1,
anchor5=self.m['10'],
anchor3=self.m['13'])
self.assertFalse(f1.has_clashes(self.m['8':'10']))
f2 = ModernaFragment53(self.s2,
anchor5=self.m['1'],
anchor3=self.m['4'],
new_sequence=Sequence('GL'))
self.assertTrue(f2.has_clashes(self.m['1':'4']))
def test_create_long_fragment(self):
"""Fragments with 26+ residues should be OK."""
t = load_template(RNA_1C0A, 'B')
resis = t['5':'45']
long_seq = Sequence("AUAUAUAUAUGCGCGCGCGCAUAUAUAUAUGCGCGCGCG")
struc = ModernaStructure('residues', resis)
frag = ModernaFragment53(struc,
anchor5=t['5'],
anchor3=t['45'],
new_sequence=long_seq)
frag.superimpose()
frag.prepare_anchor_residues()
frag.renumber()
frag.apply_seq()
self.assertEqual(struc.get_sequence(),
Sequence("CAUAUAUAUAUGCGCGCGCGCAUAUAUAUAUGCGCGCGCGG"))
def test_add_numbering_letters(self):
"""Model numbers should change accordingly."""
middle1 = ModernaFragment53(self.s1,
anchor5=self.m['9'],
anchor3=self.m['14'],
keep=keep_nothing)
middle1.prepare_anchor_residues()
middle1.renumber(self.m)
self.m.insert_fragment(middle1)
numbers = [r.identifier for r in self.m]
expected = [
'1', '2', '3', '4', '5', '6', '7', '8', '9', '9A', '9B', '14', '15'
]
self.assertEqual(numbers, expected)
def test_add_keep_numbers(self):
"""Model numbers should change accordingly."""
middle1 = ModernaFragment53(self.s1,
anchor5=self.m['9'],
anchor3=self.m['14'],
keep=keep_first_last)
middle1.prepare_anchor_residues()
middle1.renumber(self.m)
self.m.insert_fragment(middle1)
numbers = [r.identifier for r in self.m]
expected = [
'1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '13', '14', '15'
]
self.assertEqual(numbers, expected)
def test_add_continuous_exact(self):
"""Model sequence should change accordingly."""
f2 = ModernaFragment53(self.s2,
anchor5=self.m['1'],
anchor3=self.m['4'],
new_sequence=Sequence('GL'))
self.m.insert_fragment(f2)
self.assertEqual(self.m.get_sequence(), Sequence("GGLGAUUUALCUCAG"))
self.assertAlmostEqual(f2.rmsd, 0.000, 2)