def test_run_reduced(self):
file_name = self.setup_tempfile()
builder = glycan_source.TextFileGlycanHypothesisSerializer(
file_name, file_name + '.db', reduction="H2")
builder.start()
inst = builder.query(glycan_source.DBGlycanComposition).filter(
glycan_source.DBGlycanComposition.hypothesis_id == builder.hypothesis_id,
glycan_source.DBGlycanComposition.composition == "{Hex:3; HexNAc:2}$H2").one()
self.assertAlmostEqual(inst.calculated_mass, 912.3434, 3)
builder.engine.dispose()
self.clear_file(file_name + '.db')
self.clear_file(file_name)
def test_run_permethylated(self):
file_name = self.setup_tempfile()
builder = glycan_source.TextFileGlycanHypothesisSerializer(
file_name, file_name + '.db', reduction="H2", derivatization='methyl')
builder.start()
inst = builder.query(glycan_source.DBGlycanComposition).filter(
glycan_source.DBGlycanComposition.hypothesis_id == builder.hypothesis_id,
glycan_source.DBGlycanComposition.composition == "{Hex^Me:3; HexNAc^Me:2}$C1H4").one()
self.assertAlmostEqual(inst.calculated_mass, 1164.6251311968801, 3)
builder.engine.dispose()
self.clear_file(file_name + '.db')
self.clear_file(file_name)
def test_run(self):
file_name = self.setup_tempfile()
builder = glycan_source.TextFileGlycanHypothesisSerializer(
file_name, file_name + '.db')
builder.start()
inst = builder.query(glycan_source.DBGlycanComposition).filter(
glycan_source.DBGlycanComposition.hypothesis_id == builder.hypothesis_id,
glycan_source.DBGlycanComposition.composition == "{Hex:3; HexNAc:2}").one()
self.assertAlmostEqual(inst.calculated_mass, 910.32777, 3)
self.assertTrue("N-Glycan" in inst.structure_classes)
builder.engine.dispose()
self.clear_file(file_name + '.db')
self.clear_file(file_name)
def setup_compositions(self, source_file, database_path):
builder = glycan_source.TextFileGlycanHypothesisSerializer(
source_file, database_path)
builder.run()
return builder