def create_model(template=None, alignment=None, model_chain_name=None):
"""*create_model(template=None, alignment=None, model_chain_name=None)*
Creates a RNA structure model.
Produces a RnaModel object that can be saved
in a variable (see example).
If no arguments are given, an empty RNAModel is created.
If both a Template and an Alignment are given as arguments,
the complete model is built automatically.
The chain id that the model should have can be specified optionally.
:Arguments:
* Template object (optional)
* Alignment object (optional)
* chain id of the model to be built
"""
if template: template = validate_template(template)
if alignment: alignment = validate_alignment(alignment)
model = RnaModel(template=template, alignment=alignment, model_chain_name=model_chain_name, data_type=None, data=None)
if template and alignment:
if not match_template_with_alignment(template,alignment):
raise ModernaError("""Template and alignment sequences do not match!
The model cannot be built automatically.
Template : %s
Alignment: %s
"""%(template.get_sequence(),alignment.template_seq))
model.create_model()
match_alignment_with_model(alignment,model)
return model
def test_model_with_5p3p_ends(self):
a = read_alignment('''> target
CAUGCGGAYYYALCUCAGGUA
> mini_template
---GCGGAUUUALCUCAG---
''')
m = RnaModel(self.t, a)
m.create_model()
self.assertEqual(m.get_sequence(), Sequence('CAUGCGGAYYYALCUCAGGUA'))
def test_model_with_hydro_template(self):
"""If the template contains hydrogens, modifications should be added."""
t = Template(RNA_HYDRO, 'file', 'B')
a = read_alignment("""> 3tra_A.pdb Z73314.1/2358-2429
UPA
> 1qru_B.pdb X55374.1/1-72
CAA
""")
m = RnaModel(t, a)
m.create_model()
self.assertEqual(m.get_sequence(), Sequence('UPA'))
def test_number_gap(self):
"""Builds model with numbering gap in the template."""
a = read_alignment("""> target
CCGACCUUCGGCCACCUGACAGUCCUGUGCGGGAAACCGCACAGGACUGUCAACCAGGUAAUAUAACCACCGGGAAACGGUGGUUAUAUUACCUGGUACGCCUUGACGUGGGGGAAACCCCACGUCAAGGCGUGGUGGCCGAAGGUCGG
> template
CCGACCUUCGGCCACCUGACAGUCCUGUGCGG----CCGCACAGGACUGUCAACCAGGUAAUAUAACCACCGG----CGGUGGUUAUAUUACCUGGUACGCCUUGACGUGGGG----CCCCACGUCAAGGCGUGGUGGCCGAAGGUCGG
""")
t = Template(JMB_TEMPLATE, 'file')
clean_structure(t)
m = RnaModel(t, a)
m.create_model()
self.assertEqual(m.get_sequence().seq_without_breaks, a.target_seq)
def test_model_with_alignment_adjustment(self):
"""Introduces small corrections on alignment."""
a = read_alignment("""> target
ACUGUGAYUA[UACCU#P-G
> template with small errors.
GCG7A----U.UAGCUCA_G
""")
t = Template(MINI_TEMPLATE, 'file')
match_template_with_alignment(t, a)
m = RnaModel(t, a)
m.create_model()
self.assertEqual(m.get_sequence(), Sequence("ACUGUGAYUA[UACCU#PG"))
def test_model_with_close_gaps(self):
t = Template('test_data/rna_structures/2du3_excerpt.ent', 'file', 'D')
a = read_alignment('''> 1qru_B.pdb X55374.1/1-72
GCA-UUCCG
> 2du3_D.pdb
CUUUA-CCC
''')
m = RnaModel()
copy_some_residues([t['944'], t['946'], t['947']], m)
lc = find_fragment(m, '946', '947', Sequence('U'))
insert_fragment(m, lc[0])
lc = find_fragment(m, '944', '946', Sequence(''))
insert_fragment(m, lc[0])
return #TODO: remove
# generate model
m = RnaModel(t, a)
m.create_model()
def test_gap_optimization_example_2(self):
t = Template('test_data/gaps/mini_1h4s_T_gap2.pdb', 'file', 'T')
a = read_alignment('test_data/gaps/ali_gap2.fasta')
m = RnaModel(t, a)
m.create_model()
def test_create_model_with_unknown(self):
"""Alignment that contains unknown bases in the target."""
a = read_alignment(MINI_ALIGNMENT_WITH_UNK)
m = RnaModel(self.t, a)
m.create_model()
self.assertEqual(m.get_sequence(), Sequence('..CUGUQQUACCU#P'))