async def matchStrandToClass(pdbid: str, strand_id: str) -> str or None:
CYPHER = f"""
match (r:RibosomeStructure{{rcsb_id: "{pdbid.upper()}"}})-[]-(rp:RibosomalProtein)-[]-(n:NomenclatureClass) where rp.strand_id contains "{strand_id}"
return n.class_id"""
banClass = _neoget(CYPHER)
if len(banClass) != 1: return None
else: return banClass
def parseLigandNeighborhoods(pdbid:str):
"""
@pdibd is the 4-letter rcsb id.
"""
pdbid=pdbid.upper()
entry:List = _neoget("""match (l:Ligand)-[]-(r:RibosomeStructure{{rcsb_id:"{pdbid}"}})
return {{struct: r.rcsb_id, ligs: collect({{ id:l.chemicalId, name: l.chemicalName }})}}""".format_map({ "pdbid":pdbid }))[0]
if len(entry) == 0:
print(f"No ligands found for {pdbid} the DB. Exiting..")
return
else:
print("Received ligands for {}: ".format(pdbid), entry)
ligandsResponse:List[str] = entry[0]['ligs']
ligandIds = [* map(lambda x : filterIons(x), ligandsResponse) ]
ligandIds = [i for i in ligandIds if i]
pathtostruct = os.path.join(STATIC_ROOT,pdbid,'{}.cif'.format(pdbid))
"""Iterate over"""
for x in ligandIds:
savepath = os.path.join(STATIC_ROOT, pdbid, 'LIGAND_{}.json'.format(x))
#! These structures and ligand either take forever to render or fail silently. Why?
if x in ["A"]:
continue
# if pdbid in ['4U3N'] or x in ['A', 'OHX', ]:
# print("Skipping problematic {}".format(pdbid))
# continue
# if pdbid in ['5TGM'] or x in ['A', 'OHX', 'LEU']:
# continue
# if os.path.exists(savepath):
# print(savepath, " already exists. Skipping rendering.")
# continue
# else:
struct = fetchStructure(pdbid, pathtostruct)
print("Parsing residues of {}".format(x))
asresiudes = getLigandResIds(x, struct, 'res')
internals = [addBanClass( ResidueId(residue) ) for residue in asresiudes ]
nbrs = getLigandNbrs(asresiudes, struct)
for nbr in nbrs:
run(matchStrandToClass(nbr[ 'struct' ],nbr[ 'strand_id' ]))
ligprofile = {'constituents': internals,'nbrs': nbrs}
with open(savepath, 'w') as json_file:
json.dump(ligprofile,json_file)
print(f'Wrote to {savepath}')
async def matchClassToStrand(pdbid: str, banClass: str) -> str:
CYPHER = f"""
match (r:RibosomeStructure{{rcsb_id: "{pdbid.upper()}"}})-[]-(rp:RibosomalProtein)-[]-(n:NomenclatureClass{{class_id:'{banClass}'}})
return rp.strand_id"""
strand_id = _neoget(CYPHER)
if len(strand_id) != 1:
print(
'ERROR: Matched none or multiple subchains for a single nomenclature class {} in {}'
.format(banClass, pdbid))
raise NameError
print(
f"Matched strand {strand_id[0][0]} of {pdbid} to nomenclature class {banClass}"
)
return strand_id[0][0]
async def matchStrandToClass(pdbid:str, strand_id:str)->str:
CYPHER="""match (r:RibosomeStructure{{rcsb_id: "{}"}})-[]-(rp:RibosomalProtein{{entity_poly_strand_id:"{}"}})-[]-(n:NomenclatureClass)
return n.class_id""".format(pdbid.upper(), strand_id)
# CYPHER="""match (r:RibosomeStructure{rcsb_id:"4U3N"})-[]-(rp:RibosomalProtein)-[]-(n:NomenclatureClass) where rp.entity_poly_strand_id contains "s8"
# return n""".format()
resp = _neoget(CYPHER)
print(CYPHER)
print("RESP", resp)
if len(resp) > 0:
return resp[0]
else:
return None
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 getConstrictedProteins(pdbid: str) -> List[str]:
cypher = """
match (n:RibosomeStructure{{rcsb_id:"{pdbid}"}})-[]-(rp:RibosomalProtein)
where "uL4" in rp.nomenclature or "uL22" in rp.nomenclature
return rp.entity_poly_strand_id,rp.nomenclature, n.rcsb_id
""".format_map({"pdbid": pdbid.upper()})
response = _neoget(cypher)
resplist = [
*map(
lambda x:
(x['rp.nomenclature'][0], x['rp.entity_poly_strand_id']), response)
]
uL22 = None
uL4 = None
for nom in resplist:
if nom[0] == "uL22":
uL22 = nom[1]
if nom[0] == "uL4":
uL4 = nom[1]
return {"uL4": uL4, "uL22": uL22}
def add_nomenclature_map_to_report(pdbid: str, path_to_report: str):
with open(path_to_report, mode='rb') as reportfile:
report = json.load(reportfile)
chains = []
for chain in report['adjacent_strands'].keys():
chains.append(chain)
chains = ",".join(map(lambda x: "\"{}\"".format(x), chains))
nresponse = _neoget("""
match (r:RibosomeStructure{{rcsb_id:"{}"}})-[]-(n) where n.entity_poly_strand_id in [{}]
return {{strand:n.entity_poly_strand_id,type: n.entity_poly_polymer_type, nomenclature:n.nomenclature}};
""".format(pdbid, chains))
report['nomenclatureMap'] = {}
for strand in nresponse:
strand_profile = [*strand.values()][0]
nomenclature = strand_profile['nomenclature']
strand = strand_profile['strand']
polytype = strand_profile['type']
report['nomenclatureMap'][strand] = {
"type": polytype,
"nomenclature": nomenclature
}
with open(path_to_report, 'w') as reportfile:
json.dump(report, reportfile)
print("Added nomenclature map to {}".format(path_to_report))
# x = InitWalls(PDBID)
from ciftools.Neoget import _neoget
prs = FastMMCIFParser(QUIET=True)
io = MMCIFIO()
for pdbid in [
'1vy4',
]:
pdbid = pdbid.upper()
struct: Structure = prs.get_structure(f'{pdbid}', f'{pdbid}.cif')
for chain in struct[0].child_list:
strand_id = chain.id
nomclass_result = _neoget(
f"""match (r:RibosomeStructure{{rcsb_id: "{pdbid.upper()}"}})-[]-(rp:RibosomalProtein)-[]-(n:NomenclatureClass)
where rp.entity_poly_strand_id = "{strand_id}" return n.class_id""")
print(nomclass_result)
if len(nomclass_result) > 0:
struct[0][strand_id].id = f"{strand_id}[{nomclass_result[0][0]}]"
print("got nomcalss", nomclass_result[0][0])
else:
struct[0][strand_id].id = f"{strand_id}[-]"
print("got empty")
io.set_structure(struct)
io.save(f'{pdbid}+.cif')
# print(run(matchStrandToClass('3j9m','D')))
# k:Model =struct[0]
# chain:Chain;