def remove_one_modification_copy(self, residue, number_in_model):
"""
"""
temp_resi = RNAResidue(residue)
num = number_in_model or temp_resi.number
remove_modification(temp_resi)
self.add_residue(temp_resi, str(num))
log.write_message('Residue %s: modification removed (%s ---> %s).' %
(num, residue.long_abbrev, temp_resi.long_abbrev))
def test_mods_sanity(self):
"""Adding and removing many times should work as well."""
#for mod in ['m1A','m66A','Am','t6A']:
for mod in ['m1A', 'm6Am', 'Am', 't6A']:
# there is no modification named m66A. There is m6Am
self.assertEqual(BaseRecognizer().identify_resi(self.adenosine),
'A')
add_modification(self.adenosine, mod)
self.assertEqual(BaseRecognizer().identify_resi(self.adenosine),
mod)
remove_modification(self.adenosine)
def test_dna_exchange(self):
"""All combinations of DNA->DNA exchanges should work."""
bases = ['dT', 'dA', 'dG', 'dC']
br = BaseRecognizer()
r = self.adenosine
for b1 in bases:
add_modification(r, b1)
self.assertEqual(br.identify_resi(r), b1)
for b2 in bases:
remove_modification(r)
add_modification(r, b2)
self.assertEqual(br.identify_resi(r), b2)
def remove_all_modifications_copy(self):
"""
Removes all unnecessary modifications from model acordong given alignment.
Copies all this residues without modification into model.
"""
if self.alignment and self.template:
for ap in self.recipe.remove_modifications:
res = self.template.template_residues[str(
ap.template_position)]
temp_resi = RNAResidue(res)
remove_modification(temp_resi)
if temp_resi != ap.target_letter:
exchange_base(temp_resi, ap.target_letter.original_base)
self.add_residue(temp_resi)
log.write_message(
'Residue %s: modification removed (%s ---> %s).' %
(temp_resi.identifier, res.long_abbrev,
temp_resi.long_abbrev))
else:
raise RnaModelError('There is no template or/and alignmnt')
def remove_modification(residue, model=None, new_number=None):
"""*remove_modification(residue, model=None, new_number=None)*
Removes base modifications from a single residue. The nucleotide is
transformed into the standard base from which the modification originated.
A RnaModel can be given optionally. If this is given, the
modified residue is subsequently copied to it.
Note that desoxynucleotides count as modified bases as well.
:Arguments:
* residue from a Template or RnaModel object
* RnaModel object (optional)
* new residue number after copying (optional)
"""
residue = validate_resi(residue)
if model: model = validate_model(model)
if new_number: new_number = validate_resnum(new_number)
if model:
model.remove_one_modification_copy(residue, new_number)
else:
modifications.remove_modification(residue)
def test_res_names_remove_modif(self):
"""Names should be consistent after adding modifications."""
remove_modification(self.s['10'])
self.s.write_pdb_file(TEST_OUTPUT)
rn = self.get_resnames(TEST_OUTPUT)
self.assertEqual(rn[4], ' A')
def remove_all_modifications(self):
"""Removes all modifications from the model."""
for resi in self:
if resi.modified:
remove_modification(resi)
def test_remove_deoxy(self):
struc = ModernaStructure('file', DNA_WITH_MISMATCH, 'E')
r10 = struc['10']
self.assertEqual(BaseRecognizer().identify_resi(r10), 'dG')
remove_modification(r10)
self.assertEqual(BaseRecognizer().identify_resi(r10), 'G')
def test_remove(self):
struc = ModernaStructure('file', MINI_TEMPLATE)
r10 = struc['10']
self.assertEqual(BaseRecognizer().identify_resi(r10), 'm2G')
remove_modification(r10)
self.assertEqual(BaseRecognizer().identify_resi(r10), 'G')