def pp_from_pdb_id(self, pdb_id):
"""Gathers data from a single PDB pdb_id."""
pdb_struct = parsePDB(pdb_id)
reference = parsePDBHeader(pdb_id, 'reference')
pmid = int(reference['pmid']) if 'pmid' in reference else 0
pdb_mapping.map_atom_group(pdb_struct)
up_interactions = self.map_interactions(
pdb_id, self.get_interactions_list(pdb_struct))
uids = set(pdb_struct.getData('uids'))
if None in uids:
uids.remove(None)
uid2data = self.get_up_data(uids)
uid2struct = pdb_mapping.extract_secondary_structures(pdb_id, uid2data)
# Protein interactions.
for u1c1, u2c2 in up_interactions:
u1, c1 = u1c1
u2, c2 = u2c2
p1 = uid2data[u1]
p2 = uid2data[u2]
p1_struct = uid2struct[u1]
p2_struct = uid2struct[u2]
if p1['length'] < MIN_PROTEIN_LEN or p2['length'] < MIN_PROTEIN_LEN:
continue
pairs = list(up_interactions[(u1c1, u2c2)])
yield {
'pdb_id': pdb_id,
'p1_uni_id': p1['accession'],
'p2_uni_id': p2['accession'],
'p1_len': p1['length'],
'p2_len': p2['length'],
'p1_seq': p1['sequence'],
'p2_seq': p2['sequence'],
'p1_struct': p1_struct,
'p2_struct': p2_struct,
'organism': p2['organism'],
'pmid': pmid,
'interaction_type': 'protein-protein',
'p1_pfam': p1['pfam'],
'p2_pfam': p2['pfam'],
'p1_pdb_chain': c1,
'p2_pdb_chain': c2,
'interacting_residues': pairs
}
def pl_from_pdb_id(self, pdb_id):
pdb_struct = parsePDB(pdb_id)
reference = parsePDBHeader(pdb_id, 'reference')
pmid = int(reference['pmid']) if 'pmid' in reference else 0
pdb_mapping.map_atom_group(pdb_struct)
up_interactions = self.map_interactions(
pdb_id, self.get_interactions_list(pdb_struct))
uids = set(pdb_struct.getData('uids'))
if None in uids:
uids.remove(None)
uid2data = self.get_up_data(uids)
uid2struct = pdb_mapping.extract_secondary_structures(pdb_id, uid2data)
# Ligands interactions.
chemicals = {}
for c in parsePDBHeader(pdb_id, 'chemicals'):
if not c.resname in chemicals:
chemicals[c.resname] = c
for chemical in chemicals.itervalues():
ligand_interactions = self.get_ligand_interactions(
pdb_id, chemical.resname, pdb_struct)
for uid in ligand_interactions:
if not uid in uid2data:
uid2data[uid] = self.up_parser.get_uniprot_entry(uid)
p = uid2data[uid]
p_struct = uid2struct[uid]
yield {
'ligand_name': chemical.name,
'ligand_formula': chemical.formula,
'pdb_id': pdb_id,
'p_uni_id': p['accession'],
'p_len': p['length'],
'p_seq': p['sequence'],
'p_struct': p_struct,
'p_pfam': p['pfam'],
'organism': p['organism'],
'pmid': pmid,
'interaction_type': 'protein-ligand',
'interacting_residues': list(ligand_interactions[uid])
}
def ptm_from_pdb_id(self, pdb_id):
pdb_struct = parsePDB(pdb_id)
reference = parsePDBHeader(pdb_id, 'reference')
pmid = int(reference['pmid']) if 'pmid' in reference else 0
pdb_mapping.map_atom_group(pdb_struct)
up_interactions = self.map_interactions(
pdb_id, self.get_interactions_list(pdb_struct))
uids = set(pdb_struct.getData('uids'))
if None in uids:
uids.remove(None)
uid2data = self.get_up_data(uids)
uid2struct = pdb_mapping.extract_secondary_structures(pdb_id, uid2data)
# PTMs.
for u, p in uid2data.iteritems():
ptm_residues = {}
for ptm in p['ptm_features']:
if not ptm[0] in ptm_residues:
ptm_residues[ptm[0]] = []
ptm_residues[ptm[0]].extend(
range(int(ptm[2][0]),
int(ptm[2][1]) + 1))
p_struct = uid2struct[u]
for ptm in ptm_residues:
yield {
'ptm_type': ptm,
'pdb_id': pdb_id,
'p_uni_id': p['accession'],
'p_len': p['length'],
'p_seq': p['sequence'],
'p_struct': p_struct,
'p_pfam': p['pfam'],
'organism': p['organism'],
'pmid': pmid,
'interaction_type': 'ptm',
'affected_residues': ptm_residues[ptm]
}