def get_sifts_xml_contents(self, pdb_id):
self.log_lookup('SIFTS xml {0}'.format(pdb_id))
pdb_id = pdb_id.upper()
if not self.sifts_xml_contents.get(pdb_id):
if self.sifts_objects.get(pdb_id):
self.add_sifts_xml_contents(pdb_id, self.sifts_objects[pdb_id].xml_contents)
elif self.cache_dir:
self.add_sifts_xml_contents(pdb_id, download_sifts_xml(pdb_id, self.cache_dir, silent = True))
else:
self.add_sifts_xml_contents(pdb_id, retrieve_sifts_xml(pdb_id, silent = True))
return self.sifts_xml_contents[pdb_id]
def get_sifts_object(self, pdb_id, acceptable_sequence_percentage_match = 90.0, restrict_match_percentage_errors_to_these_uniparc_ids = None):
# todo: we need to store all/important parameters for object creation and key on those as well e.g. "give me the SIFTS object with , restrict_match_percentage_errors_to_these_uniparc_ids = <some_set>"
# otherwise, unexpected behavior may occur
self.log_lookup('SIFTS object {0}'.format(pdb_id))
pdb_id = pdb_id.upper()
if not self.sifts_objects.get(pdb_id):
if not self.sifts_xml_contents.get(pdb_id):
if self.cache_dir:
self.add_sifts_xml_contents(pdb_id, download_sifts_xml(pdb_id, self.cache_dir, silent = True))
else:
self.add_sifts_xml_contents(pdb_id, retrieve_sifts_xml(pdb_id, silent = True))
self.add_sifts_object(pdb_id, SIFTS.retrieve(pdb_id, cache_dir = self.cache_dir, acceptable_sequence_percentage_match = acceptable_sequence_percentage_match, bio_cache = self, restrict_match_percentage_errors_to_these_uniparc_ids = restrict_match_percentage_errors_to_these_uniparc_ids))
return self.sifts_objects[pdb_id]