def test_prepare(self):
"""Prepares a single base"""
mf = ModernaFragmentStrand(anchor=self.rna['4'], identifier='20')
mf.superimpose()
mf.prepare_anchor_residues()
mf.renumber(self.rna)
resis = list(mf.struc)
self.assertEqual(resis[1].identifier, '20')
self.assertEqual(str(resis[1].get_bp(self.rna['4'])), '20 +/+ 4')
def test_insert(self):
mf = ModernaFragmentStrand(anchor=self.rna['4'],
identifier='20',
new_sequence=Sequence('C'))
self.rna.insert_fragment(mf)
self.assertEqual(self.rna.get_sequence(),
Sequence('GCGGAUUUALCUCAG_C'))
self.assertEqual(self.rna.get_secstruc(), '...(...........)')
def test_insert_many(self):
SERIES = [
('2', '24', 'G'),
('3', '23', 'C'),
('4', '22', 'C'),
('5', '21', 'U'),
('6', '20', 'A'),
]
for num, ident, seq in SERIES:
mf = ModernaFragmentStrand(anchor=self.rna[num],
identifier=ident,
new_sequence=Sequence(seq))
self.rna.insert_fragment(mf)
self.rna.fix_backbone()
self.assertEqual(self.rna.get_secstruc(), '.(((((.........)))))')
self.assertEqual(self.rna.get_sequence(),
Sequence('GCGGAUUUALCUCAG_AU_CCG'))
def add_pair_to_base(model, anchor_id, new_id=None, new_sequence=None):
"""*add_pair_to_base(model, anchor_id, new_id=None, new_sequence=None)*
Adds Watson-Crick paired second strand to single nucleotide.
:Arguments:
* RNAModel object
* Identifier of residue to which a new base pair will be added
* New identifier for second strand
* New sequence for second strand
"""
model = validate_model(model)
anchor_id = validate_resnum(anchor_id)
if new_id: new_id = validate_resnum(new_id)
if new_sequence: new_sequence = validate_seq(new_sequence)
fr = ModernaFragmentStrand(anchor=model[anchor_id], identifier=new_id, new_sequence=new_sequence)
model.insert_fragment(fr)
def test_init(self):
mf = ModernaFragmentStrand(anchor=self.rna['4'], identifier='20')
#data_type='file', data=SINGLE_PAIR, chain_name='A', anchor=None, new_sequence=None, identifier=None, seq=None, strict=False, superposition_atoms=PAIR_SUPERPOSITION):
self.assertEqual(mf.anchor.fixed_resi.identifier, '4')