def parse_atoms(self):
'''All ATOM lines are parsed even though only one per residue needs to be parsed. The reason for parsing all the
lines is just to sanity-checks that the ATOMs within one residue are consistent with each other.'''
atom_site_header_tag = self.main_tag.getElementsByTagName("PDBx:atom_siteCategory")
assert(len(atom_site_header_tag) == 1)
atom_site_header_tag = atom_site_header_tag[0]
atom_site_tags = atom_site_header_tag.getElementsByTagName("PDBx:atom_site")
residue_map = {}
residues_read = {}
int_type = types.IntType
for t in atom_site_tags:
r, seqres, ResidueAA, Residue3AA = PDBML_slow.parse_atom_site(t, self.modified_residues)
if r:
# skip certain ACE residues
if not(self.pdb_id in cases_with_ACE_residues_we_can_ignore and Residue3AA == 'ACE'):
full_residue_id = str(r)
if residues_read.get(full_residue_id):
assert(residues_read[full_residue_id] == (r.ResidueAA, seqres))
else:
residues_read[full_residue_id] = (r.ResidueAA, seqres)
residue_map[r.Chain] = residue_map.get(r.Chain, {})
assert(type(seqres) == int_type)
residue_map[r.Chain][str(r)] = seqres
## Create SequenceMap objects to map the ATOM Sequences to the SEQRES Sequences
atom_to_seqres_sequence_maps = {}
for chain_id, atom_seqres_mapping in residue_map.iteritems():
atom_to_seqres_sequence_maps[chain_id] = SequenceMap.from_dict(atom_seqres_mapping)
self.atom_to_seqres_sequence_maps = atom_to_seqres_sequence_maps
def end_element(self, name):
tag_content = ("".join(self.tag_data)).strip()
if self._BLOCK != None:
handler = self._end_handlers.get(self._BLOCK)
if handler:
handler(name, tag_content)
if name == 'PDBx:atom_site' or name == "PDBx:pdbx_database_PDB_obs_sprCategory":
self._BLOCK = None
elif name == 'PDBx:atom_siteCategory':
self.in_atom_sites_block = False
## Create SequenceMap objects to map the ATOM Sequences to the SEQRES Sequences
atom_to_seqres_sequence_maps = {}
for chain_id, atom_seqres_mapping in self._residue_map.iteritems():
atom_to_seqres_sequence_maps[chain_id] = SequenceMap.from_dict(atom_seqres_mapping)
self.atom_to_seqres_sequence_maps = atom_to_seqres_sequence_maps
