def __init__(self, res:Residue):
fullid = list( res.get_full_id() )
self.structure = fullid[0]
self.model = fullid[1]
self.strand_id = fullid[2]
self.chemicalName = res.get_resname()
self.residue_id = [*fullid[3]][1]
def invert_amide_atoms(self, res: Residue):
""" Fix sidechains with incorrect amide assignments"""
amide_res = self.data_library.get_amide_data()[0]
res_type = res.get_resname()
if res_type not in amide_res:
raise NotAValidResidueError(res_type)
mu.swap_atoms(res[amide_res[res_type][0]], res[amide_res[res_type][1]])
def __init__(self, res: Residue):
fid = list(res.get_full_id())
self.model: int = fid[1]
self.resname: str = fid[3][0]
self.struct: str = fid[0]
self.chemicalName: str = res.get_resname()
self.strand_id: str = fid[2]
self.residue_id: int = [*fid[3]][1]
self.banClass: str = ""
def fix_chiral_chains(self, res: Residue):
""" Fix sidechains with chiral errors"""
chiral_res = self.data_library.get_chiral_data()
res_type = res.get_resname()
mu.swap_atoms(res[chiral_res[res_type][0]],
res[chiral_res[res_type][1]])
if res_type == 'ILE':
mu.delete_atom(res, 'CD1')
mu.build_atom(res, 'CD1', self.res_library, 'ILE')
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 makeResidueTuple(res:Residue)->Tuple[ str, int, NDArray[3] ]:
ac : Atom = get_alpha_carbon(res)
coords : NDArray[3] = ac.get_coord()
resi : int = res.get_id()
resn : str = res.get_resname()
return tuple(( resn, resi, coords ))
def res_full_id(res: Residue):
"""Return full residue identifier for thoroughly comparing residues."""
return (res.get_resname(), *res.get_id())
