def test_build_model_gaps(self):
"""Test build_model() with gaps"""
import modeller.automodel
def mocked_loopmodel_make(self):
self.loop.outputs.append({
'failure': None,
'name': 'input.pdb',
'Normalized DOPE score': -1.
})
with utils.temporary_working_directory() as tmpdir:
with open('alignment.pir', 'w') as fh:
fh.write(">P1;XXX\n")
fh.write("structureX:input.pdb:1:A:2:A::::\n")
fh.write("A--A*\n")
fh.write(">P1;xxx_X\n")
fh.write("sequence:input::::::::\n")
fh.write("AAAA*\n")
with open('input.pdb', 'w') as fh:
fh.write(pdb_line + '\n')
fh.write(pdb_line[:25] + '2' + pdb_line[26:] + '\n')
with utils.mocked_object(modeller.automodel.loopmodel, 'make',
mocked_loopmodel_make):
cleaning.build_model('XXX', ['A'])
os.unlink('XXX_mdl.pdb')
def test_build_model_no_gaps(self):
"""Test build_model() with no gaps"""
with utils.temporary_working_directory() as tmpdir:
with open('alignment.pir', 'w') as fh:
fh.write(">P1;XXX\n")
fh.write("structureX:input.pdb:1:A:1:A::::\n")
fh.write("A*\n")
fh.write(">P1;xxx_X\n")
fh.write("sequence:input::::::::\n")
fh.write("A*\n")
with open('input.pdb', 'w') as fh:
fh.write(pdb_line + '\n')
cleaning.build_model('XXX', ['A'])
os.unlink('XXX_mdl.pdb')
def test_build_model_no_gaps(self):
"""Test build_model() with no gaps"""
with utils.temporary_working_directory() as tmpdir:
with open('alignment.pir', 'w') as fh:
fh.write(">P1;XXX\n")
fh.write("structureX:input.pdb:1:A:1:A::::\n")
fh.write("A*\n")
fh.write(">P1;xxx_X\n")
fh.write("sequence:input::::::::\n")
fh.write("A*\n")
with open('input.pdb', 'w') as fh:
fh.write(pdb_line + '\n')
cleaning.build_model('XXX', ['A'])
os.unlink('XXX_mdl.pdb')
def test_build_model_gaps(self):
"""Test build_model() with gaps"""
import modeller.automodel
def mocked_loopmodel_make(self):
self.loop.outputs.append({'failure':None, 'name':'input.pdb',
'Normalized DOPE score':-1.})
with utils.temporary_working_directory() as tmpdir:
with open('alignment.pir', 'w') as fh:
fh.write(">P1;XXX\n")
fh.write("structureX:input.pdb:1:A:2:A::::\n")
fh.write("A--A*\n")
fh.write(">P1;xxx_X\n")
fh.write("sequence:input::::::::\n")
fh.write("AAAA*\n")
with open('input.pdb', 'w') as fh:
fh.write(pdb_line + '\n')
fh.write(pdb_line[:25] + '2' + pdb_line[26:] + '\n')
with utils.mocked_object(modeller.automodel.loopmodel, 'make',
mocked_loopmodel_make):
cleaning.build_model('XXX', ['A'])
os.unlink('XXX_mdl.pdb')
