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)