def load_all(self):
tree = ET.parse('./test_data/Cross-ring-data.xml')
sugars = {}
by_name = {}
for cls in tree.iterfind(".//class"):
sugar_class = {}
for case in cls.iterfind(".//sugar"):
isomers = [tag.attrib['abbr'] for tag in case.findall(".//isomer")]
frags = defaultdict(dict)
for frag in case.iterfind(".//fragment"):
data = [frag.attrib[n] for n in ["name", "mass_mono", "mass_pm_mono", "cleav1", "cleav2", "type"]]
rec = self.FragmentRecord(*data)
rec.composition = dict(map(
lambda x: (x.attrib['element'], x.attrib['count']), frag.findall(".//composition")))
frags[rec.cleave_1, rec.cleave_2][rec.kind] = rec
sugar_class[case.attrib['subclass']] = frags
for name in isomers:
by_name[name] = frags
sugars[cls.attrib['name']] = sugar_class
return by_name
def parse(self):
for evt, entity in ET.iterparse(self.handle, ("start", "end")):
if evt != "end":
if entity.tag == "sugar":
self.state = START
elif entity.tag == 'residues':
if self.state == START:
self.state = RES
else:
raise GlycoCTXMLError("<residues> not the first section encountered")
elif entity.tag == 'linkages':
if self.state != RES:
raise GlycoCTXMLError("<linkages> not following <residues>")
elif entity.tag in {'repeat'}:
raise GlycoCTXMLSectionUnsupported("<{}> section is not supported".format(entity.tag))
continue
if entity.tag == "stemtype":
self.buffer['stem'].append(entity.attrib['type'][1:])
self.buffer['configuration'].append(entity.attrib['type'][0])
elif entity.tag == "modification":
self.buffer['modification'].append(
(entity.attrib['type'], try_int(entity.attrib['pos_one'])))
elif entity.tag == "basetype":
id, anomer, superclass, ring_start, ring_end = basetype_unpacker(entity.attrib)
superclass = superclass_map[superclass.upper()]
anomer = anomer_map[anomer]
id = int(id)
modifications = OrderedMultiMap()
mods = self.buffer.pop("modification", None)
if mods is not None:
for mod, pos in mods:
modifications[pos] = modification_map[mod]
is_reduced = "aldi" in modifications[1]
if is_reduced:
modifications.pop(1, "aldi")
residue = monosaccharide.Monosaccharide(
anomer=anomer, superclass=superclass, stem=self.buffer.pop('stem'),
configuration=self.buffer.pop("configuration"), ring_start=ring_start,
ring_end=ring_end, modifications=modifications, reduced=is_reduced, id=id)
self.graph[id] = residue
if self.root is None:
self.root = residue
elif entity.tag == "substituent":
substituent_obj = substituent.Substituent(entity.attrib['name'])
self.graph[int(entity.attrib['id'])] = substituent_obj
elif entity.tag == "connection":
parent_id = try_int(entity.attrib['parent'])
child_id = try_int(entity.attrib['child'])
parent_node = self.graph[parent_id]
child_node = self.graph[child_id]
link.Link(
parent_node, child_node, parent_position=self.buffer.pop("parent_position"),
child_position=self.buffer.pop("child_position"),
parent_loss=self.buffer.pop('parent_loss'), child_loss=self.buffer.pop('child_loss'),
id=self.buffer.pop('id'))
elif entity.tag == "parent":
self.buffer['parent_position'] = int(entity.attrib['pos'])
elif entity.tag == "child":
self.buffer['child_position'] = int(entity.attrib['pos'])
elif entity.tag == "linkage":
self.buffer["id"] = int(entity.attrib['id'])
self.buffer["parent_loss"] = link_replacement_composition_map[entity.attrib['parentType']]
self.buffer["child_loss"] = link_replacement_composition_map[entity.attrib['childType']]
elif entity.tag == 'sugar':
if self.root is not None:
yield glycan.Glycan(self.root)
self._reset()
