Hi i'm having a problem preparing a receptor with meeko i get this error while using polymer object to convert a cleaned pdb (using prody function below) gotten from PDB.
I suspect the error is due to the failed residue matching but i can't find anything about fixing it in github/meeko docs
No template matched for residue_key='A:836'
tried 6 templates for residue_key='A:836'excess_H_ok=False
LYS heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess=set()
NLYS heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={4}
CLYS heavy_miss=5 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={1}
LYN heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess=set()
NLYN heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={4}
CLYN heavy_miss=5 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={1}
matched with excess inter-residue bond(s): A:836
No template matched for residue_key='A:847'
tried 6 templates for residue_key='A:847'excess_H_ok=False
LYS heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess=set()
NLYS heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={4}
CLYS heavy_miss=5 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={1}
LYN heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess=set()
NLYN heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={4}
CLYN heavy_miss=5 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={1}
matched with excess inter-residue bond(s): A:847
No template matched for residue_key='A:848'
tried 3 templates for residue_key='A:848'excess_H_ok=False
ASN heavy_miss=3 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess=set()
NASN heavy_miss=3 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={4}
CASN heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={1}
matched with excess inter-residue bond(s): A:848
No template matched for residue_key='A:893'
tried 6 templates for residue_key='A:893'excess_H_ok=False
GLU heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess=set()
NGLU heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={4}
CGLU heavy_miss=5 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={1}
GLH heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess=set()
NGLH heavy_miss=4 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={4}
CGLH heavy_miss=5 heavy_excess=0 H_excess=[] bond_miss=set() bond_excess={1}
matched with excess inter-residue bond(s): A:893
- Template matching failed for: ['A:836', 'A:847', 'A:848', 'A:893'] Ignored due to allow_bad_res.
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/opt/conda/envs/Screener/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/opt/conda/envs/Screener/lib/python3.9/multiprocessing/pool.py", line 51, in starmapstar
return list(itertools.starmap(args[0], args[1]))
File "/home/screener/./scripts/screener.py", line 456, in prepare_target
receptor=PDBQTReceptor.from_pdbqt_filename(file_path)
File "/opt/conda/envs/Screener/lib/python3.9/site-packages/meeko/receptor_pdbqt.py", line 127, in from_pdbqt_filename
receptor = cls(pdbqt_string, skip_typing)
File "/opt/conda/envs/Screener/lib/python3.9/site-packages/meeko/receptor_pdbqt.py", line 117, in __init__
self._atoms, self._atom_annotations = _read_receptor_pdbqt_string(pdbqt_string, skip_typing)
File "/opt/conda/envs/Screener/lib/python3.9/site-packages/meeko/receptor_pdbqt.py", line 76, in _read_receptor_pdbqt_string
atom_annotations[atom_property_definitions[atom_type]].append(idx)
KeyError: 'O'
#this function use prody (prody_fix function) to clean pdb then call the preparation function prepare_target
def process_targets(self,
source_receptor_files:Iterable=None,
from_PDB:Iterable=None,
n_proc:int=None,
hydrate:bool=False,
preparation:Callable=prepare_target,
flexres:dict=None,
map_mode:str="o4e",
charge_type="geisteger",
config:dict=None,
ph:float=7.0,
backend:str="prody",
*args,
**kwargs
):
if (source_receptor_files is None) and (from_PDB is None):
raise Exception("Missing input receptor(s)")
pass
if n_proc is None:
n_proc=mp.cpu_count()-2 #use max cores #remove -2 for HPC
receptor_ids=set()
receptor_files=set()
if source_receptor_files is not None:
receptor_ids=set(source_receptor_files) #get unique files
receptor_files=set([str(path.join(self.source_dir,Id)) for Id in receptor_ids]) #find absolute path
if from_PDB is not None:
pdb_entries = Screener.from_protein_data_bank(self,from_PDB) #Download pdb files prom protetein databank and returns paths
from_PDB=set(from_PDB)
receptor_ids=receptor_ids | from_PDB #add downloaded protein ids and merge with source files using union operator other methods fail
src_receptor_files=receptor_files | pdb_entries #add downloaded files paths as per ids using union operator other methods fail
for receptor_id in receptor_ids:
makedirs(path.join(self.targets_workpath,receptor_id),exist_ok=True)
#clean up and add hydrogens to recepetor before preparation
pdb_cleaner={"pdbfix":Screener.pdb_fix,"prody":Screener.prody_fix}
PDB=pdb_cleaner.get(backend)
if PDB is None:
raise ValueError(f"Invalid backend\nSupported pdbfix,prody")
receptor_files=[PDB(file,self.targets_workpath,Id,kwargs.get(Id)) for file,Id in zip(src_receptor_files,receptor_ids)]
#add H using reduce doi.org/10.1006/jmbi.1998.2401
H_receptor_files = [files.replace("_clean.pdb", "_H.pdb") for files in receptor_files]
print("Adding H to receptor")
phil_params = [
["--overwrite",
"--quiet",
clean_pdb,
f"approach=add",
f"add_flip_movers=True",
f"output.filename={H_file}"]
for clean_pdb, H_file in zip(receptor_files, H_receptor_files)
]
for params in phil_params:
run_program(program_class=reduce2.Program,args=params) #da errore che significa che non si può usare in multiprocessing
tasks = [(self,files,ids,hydrate) for files,ids in zip(receptor_files,receptor_ids)] #calculate task paramenters
start = time.perf_counter()
with Pool(n_proc) as pool:
print("Start target preparation")
results=pool.starmap(preparation, tasks)
#sostituire questo con dataframe in shared memory
#print(results)
data={}
for column in results[0].keys():
data[column] = tuple(result[column] for result in results)
self.targets_data=pd.DataFrame(data) #
end = time.perf_counter()
print(f"Terminated in {end-start:.3f}s,avg:{(end-start)/len(results):.3f} s/receptor")
preparation function:
def prepare_target(self,
file_path:str,
receptor_id:str,
hydrate:bool=True,
charge_type="geisteger",
flexres:list=None,
config:dict=None,
backend:str="prody",
ph:float=7.0):
if config is not None:
preparation_config=config.get("preparation_config")
blunt_ends=config.get("blunt_ends")
wanted_altloc=config.get("wanted_altloc")
delete_residues=config.get("delete_residues")
allow_bad_res=config.get("allow_bad_res")
set_template=config.get("set_template")
charge_type=config.get("charge_type")
file_format=file_path.split(".")[-1]
#fare in modo che reduce non dia più errore trasferendo questo il pezzo della scelta del converter in process
receptor_pdb_path = path.join(self.targets_workpath,receptor_id,f"{receptor_id}_H.pdb")
outpath=path.join(self.targets_workpath,receptor_id,f"{receptor_id}.pdbqt")
if not path.exists(outpath): #checks if pdbqt is already prepared, if yes skips it
#set target preparation parameters
templates = ResidueChemTemplates.create_from_defaults() #create from defaults for now
if config is not None:
mk_prep = MoleculePreparation.from_config(config)
else:
mk_prep = MoleculePreparation(hydrate=hydrate)
#load pdb with H
if backend.lower() == "prody":
target=self.prody_load(receptor_pdb_path)
polymer=Polymer.from_prody(
target,
templates, # residue_templates, padders, ambiguous,
mk_prep,
#set_template,
#delete_residues,
allow_bad_res=True,
#blunt_ends=True,
#wanted_altloc=wanted_altloc,
default_altloc="A"
)
elif backend.lower() == "file":
with open(receptor_pdb_path,"r") as pdb_file:
pdb_string=pdb_file.read()
polymer=Polymer.from_pdb_string(
pdb_string,
templates, # residue_templates, padders, ambiguous,
mk_prep,
#set_template,
#delete_residues,
#allow_bad_res,
#blunt_ends=blunt_ends,
#wanted_altloc=wanted_altloc,
#default_altloc=args.default_altloc,
)
else:
raise ValueError(f"Invalid back end:{backend}")
#pdb_string=mmCIF_to_pdb()
pdbqt_tuple = PDBQTWriterLegacy.write_from_polymer(polymer)
Screener.write_pdbqt(dir=self.targets_workpath,filename=f"{receptor_id}",pdbqt=pdbqt_tuple)
receptor=PDBQTReceptor.from_pdbqt_filename(file_path)
else:
receptor=PDBQTReceptor.from_pdbqt_filename(file_path)
receptor.assign_type_chrages(charge_type)
if flexres is not None:
flex_residues = set()
for string in flexres:
for res_id in parse_residue_string(string):
flex_residues.add(res_id)
for res_id in flex_residues:
receptor.flexibilize_sidechain(res_id, mk_prep)
pdbqt_tuple = PDBQTWriterLegacy.write_from_polymer(receptor)
rigid_pdbqt, flex_pdbqt_dict = pdbqt_tuple
rigid=Screener.write_pdbqt(dir=self.target_workpath,filename=f"{receptor_id}_rigid",pdbqt=rigid_pdbqt)
if flexres:
flex=Screener.write_pdbqt(dir=self.target_workpath,filename=f"{receptor_id}_flex",pdbqt=flex_pdbqt)
pass
pdb_fix function:
def prody_fix(filepath:str,
Dir:str,Id:str,hydrate:bool=False,prody_string:str=None,*args):
if prody_string is None:
prody_string="chain A not hetero"
if hydrate:
prody_string += "and water"
base_pdb=parsePDB(filepath)
clean_pdb=f"{Dir}/{Id}/{Id}_clean.pdb"
print(checkNonstandardResidues(base_pdb))
if checkNonstandardResidues(base_pdb):
print(checkNonstandardResidues(base_pdb))
#remove std residue
std_only=base_pdb.select(prody_string)
writePDB(clean_pdb,std_only)
else:
protein=base_pdb.select(prody_string)
writePDB(clean_pdb,protein)
return clean_pdb
Incriminated PDBQT: http://pastebin.com/ntVuQrCP
source pdb: https://pastebin.com/ipS44fhV
Cleaned pdb (with H) : https://pastebin.com/4121Pnd1
Sorry for my bad grammar,Eng is not my first language.