def addResidue(self, res: Residue) -> None:
parentStrand = res.get_parent().get_id()
if res.get_resname() not in [AMINO_ACIDS.keys(), *Nucleotides
] and res not in self.ligands:
self.ligands.append(res)
return
if parentStrand not in self.strands.keys():
self.strands[parentStrand] = []
if res not in self.strands[parentStrand]:
self.strands[parentStrand].append(res)
# response = _neoget("""
# match (n {{entity_poly_strand_id:"{parentStrand}"}})-[]-(r:RibosomeStructure{{rcsb_id:"{pdbid}"}}) \
# return {{type: n.entity_poly_polymer_type, nomenclature:n.nomenclature}};""".format_map({
# "parentStrand": parentStrand,
# "pdbid" : self.pdbid
# }))
# try:
# profile = response[0]
# if profile['type'] == 'RNA':
# self.adjacentRnaStrands.append(parentStrand)
# self.rna[parentStrand] = []
# if profile['type'] == 'Protein':
# self.adjacentRPStrands.append(parentStrand)
# self.rps [parentStrand] = []
# self.nomenclatureMap[parentStrand] = profile['nomenclature']
# except:
# pass
# if parentStrand in self.adjacentRnaStrands:
# if res in self.rna[parentStrand] :
# None
# else:
# self.rna[parentStrand].append(res)
# elif parentStrand in self.adjacentRPStrands:
# if res in self.rps[parentStrand]:
# None
# else:
# self.rps[parentStrand].append(res)
# print("added residue")
self.rescount += 1
def __deprecated_addResidue(self, res: Residue) -> None:
parentStrand = res.get_parent().get_id()
if res.get_resname() not in [AMINO_ACIDS.keys(), *Nucleotides
] and res not in self.ligands:
self.ligands.append(res)
if parentStrand not in self.adjacentRnaStrands and parentStrand not in self.adjacentRPStrands:
response = _neoget("""
match (n {{entity_poly_strand_id:"{parentStrand}"}})-[]-(r:RibosomeStructure{{rcsb_id:"{pdbid}"}}) \
return {{type: n.entity_poly_polymer_type, nomenclature:n.nomenclature}};"""
.format_map({
"parentStrand": parentStrand,
"pdbid": self.pdbid
}))
try:
profile = response[0]
if profile['type'] == 'RNA':
self.adjacentRnaStrands.append(parentStrand)
self.rna[parentStrand] = []
if profile['type'] == 'Protein':
self.adjacentRPStrands.append(parentStrand)
self.rps[parentStrand] = []
self.nomenclatureMap[parentStrand] = profile[
'nomenclature']
except:
pass
if parentStrand in self.adjacentRnaStrands:
if res in self.rna[parentStrand]:
None
else:
self.rna[parentStrand].append(res)
elif parentStrand in self.adjacentRPStrands:
if res in self.rps[parentStrand]:
None
else:
self.rps[parentStrand].append(res)
print("added residue")
self.rescount += 1
def from_bio_residue(
cls, residue: Residue,
residue_id_mapping: 'BiopythonToMmcifResidueIds.Mapping'):
return ResidueId(
residue_id_mapping.to_label_seq_id(BioResidueId(*residue.id)),
residue.get_parent().id)
