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_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')