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self.stderr.write(f"{code} entry is obsolete")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 handle(self, *args, **options):
pdbs = PDBs()
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:
pdbio.process_pdb(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 = 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)
return self.pdbs_dir + pdb[1:3] + "/pdb" + pdb + ".ent"
@staticmethod
def sequence_from_residues(residues):
return "".join([
protein_letters_3to1[res.get_resname()[0] +
res.get_resname()[1:3].lower()]
for res in residues
])
if __name__ == '__main__':
from SNDG import init_log
import argparse
from SNDG.Structure.PDBs import PDBs
parser = argparse.ArgumentParser(description='PDB Update utils')
init_log()
pdbs = PDBs(pdb_dir="/data/databases/pdb/")
#os.environ["ftp_proxy"] = "http://proxy.fcen.uba.ar:8080"
# pdbs.download_pdb_seq_ses()
pdbs.download_pdb_entries()
pdbs.update_pdb_dir()
# from SNDG.Structure.PDBs import PDBs
# pdbs = PDBs(pdb_dir="/data/databases/pdb/")
# pdbs.pdbs_seq_for_modelling("/data/databases/pdb/processed/seqs_from_pdb.fasta")
#pepe = pdbs.entries_df()
#print pepe