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)
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_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_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_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_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 _create_frag(self, helix, seq, anchor5, anchor3, upper5, upper3,
model):
"""Returns a ModernaFragment class"""
seq = seq.seq_without_breaks
if upper5 and upper3:
return ModernaFragment2D(helix, \
anchor5=anchor5, anchor3=anchor3, \
anchor5_upper=upper5, \
anchor3_upper=upper3, \
frag5_upper=helix.strand5[-1], \
frag3_upper=helix.strand3[0], \
new_sequence=seq, \
superposition_atoms=HELIX_SUPERPOSITION,
model=model
)
elif upper5:
return ModernaFragment553
elif upper3:
return ModernaFragment533
else:
return ModernaFragment53(helix, \
anchor5=anchor5, anchor3=anchor3, \
new_sequence=seq, \
sup_r5=HELIX_SUPERPOSITION, \
sup_r3=HELIX_SUPERPOSITION, \
strict=False
)
def create_fragment(pdb_path, anchor5=None, anchor3=None, chain_name='A', sequence=None):
"""*create_fragment(pdb_path, anchor5=None, anchor3=None, chain_name='A', sequence=None)*
To insert small pieces of custom PDB structures into models, fragments can be used.
This command loads a fragment, and defines one or two connection points, to which
the fragment will be inserted by superposition. It returns a ModernaFragment object.
To add a ModernaFragment object to a model, the insert_fragment command should be used.
The scenarios for adding either involve superposition of a single residue with the model
on the 5' end of the fragment, or on the 3' end, or both.
:Arguments:
* path to pdb file with the fragment
* residue to which the 5' end of the fragment will be superimposed
* residue to which the 3' end of the fragment will be superimposed
* chain name of the fragment in the file (optional; A by default)
* sequence that should be modeled onto the fragment upon insertion (optional; the sequence should not include the 1-2 anchor residues, it therefore has to be shorter than the fragment)
"""
pdb_path = validate_path(pdb_path)
if anchor5: anchor5 = validate_resi(anchor5)
if anchor3: anchor3 = validate_resi(anchor3)
if sequence: sequence = validate_seq(sequence)
struc = ModernaStructure(data_type='file', data=pdb_path, chain_name=chain_name)
if anchor5 and anchor3:
fr = ModernaFragment53(struc, anchor5=anchor5, anchor3=anchor3, new_sequence=sequence, strict=False)
elif anchor5:
fr = ModernaFragment5(struc, anchor5=anchor5, new_sequence=sequence, strict=False)
elif anchor3:
fr = ModernaFragment3(struc, anchor3=anchor3, new_sequence=sequence, strict=False)
else:
raise ModernaError("Anchor residues need to be specified.")
return fr
def setUp(self):
self.s = ModernaStructure('file', MINI_TEMPLATE)
self.t = Template(MINI_TEMPLATE, 'file')
self.m = RnaModel(None, None, 'A', 'file', MINI_TEMPLATE)
self.f = ModernaFragment53(self.s,
anchor5=self.m['1'],
anchor3=self.m['14'])
self.struc = PDBParser().get_structure('test_struc', MINI_TEMPLATE)
def make_helix_longer(self, helix): #, dest_length):
"""Adds base pairs to a helix."""
helix2 = self._get_helix()
helix2 = ModernaFragment53(helix2, anchor5=helix.strand5[-1], \
anchor3=helix.strand3[0], strict=False)
finsert = FragmentInserter()
finsert.insert_fragment(helix2, helix)
self.renumber_helix(helix)
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)
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_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_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_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)
def test_all_records(self):
"""All records in the entire LIR db should be readable."""
library = StructureLibrary(PATH_TO_LIR_STRUCTURES)
f = open(LIR_DATABASE_PATH)
for i, line in enumerate(f):
print i, line
if line.startswith('loop length'): continue
line = line.strip().split('\t')
if len(line) == 17:
st = library.get_structure_part(line[1], line[2], line[3],
line[4])
seq = Sequence(line[6])
fr = ModernaFragment53('residues', st[line[3]:line[4]],
line[2], st[line[3]], st[line[4]], None,
None, None)
assert len(fr) - 2 == int(line[0])
fr_seq = fr.get_sequence()
print '1', seq, '2', fr_seq
assert seq == fr_seq
if i % 100 == 0: print i
def test_insert(self):
"""Inserts fragment into a model"""
f1 = ModernaFragment53(self.s1, anchor5=self.m['10'],anchor3=self.m['13'])
finsert = FragmentInserter()
finsert.insert_fragment(f1, self.m)
self.assertEqual(self.m.get_sequence(),Sequence("GCGGAUUUALCGCAG"))
def get_fragment_part(self, name, chain, resi_from, resi_to, \
anchor5, anchor3, sequence, keep, seq):
"""Returns a ModernaFragment53 from the library."""
struc = self.get_structure_part(name, chain, resi_from, resi_to, seq)
return ModernaFragment53(struc, anchor5, anchor3, sequence, keep=keep)