def handle(self, *args, **options):
tmp = os.path.abspath(options['tmp'])
if not os.path.exists(tmp):
os.makedirs(tmp)
qs = PDB.objects.filter(code=options["pdb"]) if options["pdb"] else PDB.objects.all()
total = qs.count()
utils = PDBs(options["pdbs_dir"])
with tqdm(qs, total=total) as pbar:
for pdb in pbar:
pbar.set_description(pdb.code)
try:
fpocket2sql = FPocket2SQL()
fpocket2sql.create_or_get_pocket_properties()
fpocket2sql.load_pdb(pdb.code)
fpocket2sql.run_fpocket(options['tmp'],pdb_path=utils.pdb_path(pdb.code),
pockets_path=utils.pdb_pockets_path(pdb.code),
force=options["force"])
fpocket2sql.load_pockets()
# res.delete_dir()
except IOError as ex:
traceback.print_exc()
self.stderr.write("error processing pockets from %s: %s" % (pdb.code, str(ex)))
except Exception as ex:
traceback.print_exc()
raise CommandError(ex)
def handle(self, *args, **options):
if options["verbose"] == 1:
import logging
logging.basicConfig(level=logging.DEBUG)
pdbs = PDBs(options["pdbs_dir"])
pdbs.url_pdb_entries = options["entries_url"]
if not os.path.exists(options["entries_path"]):
pdbs.download_pdb_entries()
pdbio = PDBIO(options['pdbs_dir'] + "/", options['entries_path'],
options['tmp'])
pdbio.init()
try:
pdbs.update_pdb(options['code'])
pdbio.process_pdb(options['code'],
force=options['force'],
pocket_path=pdbs.pdb_pockets_path(
options['code']),
pdb_path=pdbs.pdb_path(options['code']))
except IOError as ex:
traceback.print_exc()
self.stderr.write("error processing pockets from %s: %s" %
(options['code'], str(ex)))
except Exception as ex:
traceback.print_exc()
raise CommandError(ex)
def handle(self, *args, **options):
pdbs_utils = PDBs(pdb_dir=options['pdbs_dir'])
pdbs_utils.url_pdb_entries = options["entries_url"]
if not options['entries_path']:
options['entries_path'] = options['pdbs_dir'] + "/entries.idx"
if (datetime.now() - datetime.fromtimestamp(
os.path.getctime(options["entries_path"]))).days > 7:
pdbs_utils.download_pdb_entries()
pdb2sql = PDB2SQL(options['pdbs_dir'], options['entries_path'])
pdb2sql.load_entries()
if options["only_annotated"]:
self.stderr.write("only_annotated option activated by default")
from bioseq.models.Dbxref import Dbxref
pdbs = [(x.accession.lower(),
pdbs_utils.pdb_path(x.accession.lower()))
for x in Dbxref.objects.filter(dbname="PDB")]
else:
pdbs = list(tqdm(iterpdbs(options['pdbs_dir'])))
# 4zux 42 mer 2lo7("5my5","/data/databases/pdb/divided/my/pdb5my5.ent")
# ("4zu4", "/data/databases/pdb/divided/zu/pdb4zu4.ent")
with tqdm(pdbs) as pbar:
for code, pdb_path in pbar:
code = code.lower()
if PDBsWS.is_obsolete(code):
self.stderr.write(f"{code} entry is obsolete")
continue
try:
pdb_path = pdbs_utils.update_pdb(code)
except KeyboardInterrupt:
raise
except:
self.stderr.write("PDB %s could not be downloaded" % code)
continue
if PDB.objects.filter(code=code).exists():
self.stderr.write("PDB %s already exists" % code)
continue
pbar.set_description(code)
try:
pdb2sql.create_pdb_entry(code, pdb_path)
pdb2sql.update_entry_data(code, pdb_path)
except KeyboardInterrupt:
raise
except Exception as ex:
import traceback
traceback.print_exc()
raise CommandError(ex)
def load_pdb_pocket(self, pdb, pdb_dir="/data/databases/pdb/"):
utils = PDBs(pdb_dir)
if not os.path.exists(utils.pdb_pockets_path(pdb)):
utils.update_pdb(pdb)
fpocket = FPocket(utils.pdb_path(pdb))
result = fpocket.hunt_pockets()
mkdir(os.path.dirname(utils.pdb_pockets_path(pdb)))
result.save(utils.pdb_pockets_path(pdb))
with open(utils.pdb_pockets_path(pdb)) as h:
result = json.load(h)
self.pdb_data[pdb]["pockets"] = result
return self.pdb_data[pdb]["pockets"]
def handle(self, *args, **options):
pdbs = PDBs(pdb_dir=options['pdbs_dir'])
pdbs.url_pdb_entries = options["entries_url"]
if not os.path.exists(options["entries_path"]):
pdbs.download_pdb_entries()
pdb2sql = PDB2SQL(options['pdbs_dir'], options['entries_path'])
pdb2sql.load_entries()
if options["only_annotated"]:
self.stderr.write("only_annotated option activated by default")
from bioseq.models.Dbxref import Dbxref
pdbs = [(x.accession.lower(),pdbs.pdb_path( x.accession.lower()))
for x in Dbxref.objects.filter(dbname="PDB")]
else:
pdbs = list(tqdm(iterpdbs(options['pdbs_dir'])))
# 4zux 42 mer 2lo7("5my5","/data/databases/pdb/divided/my/pdb5my5.ent")
# ("4zu4", "/data/databases/pdb/divided/zu/pdb4zu4.ent")
with tqdm(pdbs) as pbar:
for code,pdb_path in pbar:
code = code.lower()
try:
pdb_path = pdb2sql.download(code)
except:
self.stderr.write("PDB %s could not be downloaded" % code)
continue
if PDB.objects.filter(code=code).exists():
self.stderr.write("PDB %s already exists" % code)
continue
pbar.set_description(code)
try:
pdb2sql.create_pdb_entry(code, pdb_path)
pdb2sql.update_entry_data(code, pdb_path)
except Exception as ex:
raise CommandError(ex)
class StructureVariant:
def __init__(self, pdb_dir="/data/databases/pdb/"):
self.utils = PDBs(pdb_dir)
self.seqs_path = "/tmp/seq.faa"
self.aln_path = "/tmp/msa.faa"
self.ref_seq = None
self.pdbfile = None
self.pdb_data = defaultdict(dict)
def load_msa(self, input_sequence, pdb_code, pdb_chain=None):
pdb_code = pdb_code.lower()
self.utils.update_pdb(pdb_code)
self.ref_seq = bpio.read(input_sequence, "fasta")
self.pdbfile = PDBFile(pdb_code, self.utils.pdb_path(pdb_code))
with open(self.seqs_path, "w") as h:
bpio.write(self.ref_seq, h, "fasta")
bpio.write(self.pdbfile.seq(selected_chain=pdb_chain), h, "fasta")
cmd = docker_wrap_command(
f'mafft --quiet --localpair --maxiterate 1000 {self.seqs_path} > {self.aln_path} '
)
execute(cmd)
self.msa = MSAMap.from_msa(self.aln_path)
self.res_map = self.pdbfile.residues_map(pdb_chain)
def residues_from_pos(self, pos):
pos_data = []
for sample in self.msa.samples():
if sample != self.ref_seq.id:
pdb, chain = sample.split("_")[:2]
if self.msa.exists_pos(self.ref_seq.id, pos, sample):
msa_pos = self.msa.pos_seq_msa_map[self.ref_seq.id][pos]
sample_pos = self.msa.pos_from_seq(self.ref_seq.id, pos,
sample)
line = {
"pos": pos + 1,
"ref": self.msa.seqs[self.ref_seq.id][msa_pos],
"alt": self.msa.seqs[sample][msa_pos],
"pdb": pdb,
"chain": chain,
"resid": str(self.res_map[chain][sample_pos][1]),
"icode": str(self.res_map[chain][sample_pos][2]),
"pdb_pos": sample_pos
}
pos_data.append(line)
return pos_data
def residues_from_aln_seq(self, input_sequence, pdb_code, pdb_chain=None):
self.load_msa(input_sequence, pdb_code, pdb_chain)
variants = [
(k, v)
for k, v in sorted(self.msa.variants(self.ref_seq.id).items(),
key=lambda x: int(x[0].split("_")[1]))
]
output = []
for ref_pos, alt_samples in variants:
ref, pos = ref_pos.split("_")
pos = int(pos)
for alt, samples in alt_samples.items():
if alt != self.msa.gap_code:
pos_data = self.residues_from_pos(pos)
output += pos_data
return pd.DataFrame(output)
def annotate_resid(self, pdb: str, resid: str,
structure_annotator: StructureAnnotator):
pdb = pdb.lower()
data = {}
if pdb not in self.pdb_data:
self.load_pdb_ann(pdb, structure_annotator)
if str(resid) in self.pdb_data[pdb]["binding"]:
data["binding"] = self.pdb_data[pdb]["binding"][str(resid)]
if str(resid) in self.pdb_data[pdb]["pockets"]:
data["pockets"] = self.pdb_data[pdb]["pockets"][str(resid)]
return data
def load_pdb_ann(self, pdb, structure_annotator: StructureAnnotator):
binding_data = structure_annotator.load_pdb_binding_data(pdb)
binding_dict = defaultdict(list)
for site in binding_data:
for site_res in site["site_residues"]:
res = str(site_res["residue_number"]) + (site_res.get(
"author_insertion_code", "") or "")
binding_dict[res].append({
"site_id":
site["site_id"],
"details":
site["details"],
"ligands": [{
c: x[c]
for c in
["chain_id", "author_residue_number", "chem_comp_id"]
} for x in site["site_residues"]
if x["chem_comp_id"] in binding_dict and (
x["chem_comp_id"] != "HOH")]
})
self.pdb_data[pdb]["binding"] = binding_dict
pockets_data = structure_annotator.load_pdb_pocket(
pdb, self.utils.pdb_dir)
pockets_dict = defaultdict(list)
for pocket in pockets_data:
for residue in set(pocket["residues"]):
pockets_dict[residue].append({
"pocket_num":
pocket["number"],
"druggabilitty":
pocket["properties"]['Druggability Score']
})
self.pdb_data[pdb]["pockets"] = dict(pockets_dict)
def annotate_residue_list(self, df,
structure_annotator: StructureAnnotator):
"""
:param df: columns=["pdb", "chain", "resid", "alt", "ref", "pos"] or generated by residues_from_aln_seq
:return:
"""
output = {}
for i, r in df.iterrows():
output[
f'{r.pdb}_{r.chain}_{r.resid}_{r.alt}'] = self.annotate_resid(
r.pdb, str(r.resid), structure_annotator)
return output
x["name"]: 1
for x in db.structures.find({"seq_collection_name": "pdb"},
{"name": 1})
}
pdbs = list(pdbUtils)
for (pdb, pdb_file) in tqdm(pdbs):
if pdb in procesados:
if pdb in procesados_sin_pocket:
q = ExperimentalStructure.objects(seq_collection_name="pdb",
name=pdb).no_cache()
if q:
strdoc = q.get()
try:
structure = parser.get_structure(
pdb, pdbUtils.pdb_path(pdb))
try:
complete_pockets(pdb, strdoc, structure, pdbUtils)
strdoc.save()
except:
pass
complete_pdb_attrs(pdb, strdoc, pdbUtils)
strdoc.save()
except Exception as ex:
traceback.print_exc()
_log.warn("ERROR " + pdb + " : " + str(ex))
continue
else:
for y in [x ["templates"][0]["aln_hit"]["name"].split("_")[0] for x in db.structures.find({"templates.0":{"$exists":1}},{"templates.aln_hit.name":1})]:
pdbs[y] = 1
pbar = tqdm(pdbs.keys())
for pdb in pbar:
pbar.set_description(pdb)
if pdb in procesados:
if not args.review_pockets:
continue
if pdb in procesados_sin_pocket:
q = ExperimentalStructure.objects(seq_collection_name="pdb", name=pdb).no_cache()
if q:
strdoc = q.get()
try:
structure = parser.get_structure(pdb, pdbUtils.pdb_path(pdb))
try:
complete_pockets(pdb, strdoc, structure,pdbUtils)
strdoc.save()
except:
pass
complete_pdb_attrs(pdb, strdoc,pdbUtils)
strdoc.save()
except Exception as ex:
traceback.print_exc()
_log.warn("ERROR " + pdb + " : " + str(ex))
continue
else: