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 __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 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 pdbs_seq_for_modelling(self,
out_fasta=None,
pdbsIter=None,
reuse_previours=None):
if pdbsIter == None:
pdbsIter = PDBs(self.pdb_dir)
if not out_fasta:
out_fasta = self.pdb_dir + "processed/seqs_from_pdb.fasta"
pdb_codes = {x.lower(): 1 for x in self.entries_df().IDCODE}
reuse = defaultdict(lambda: [])
if reuse_previours:
for x in bpio.parse(reuse_previours, "fasta"):
pdb = x.id.split("_")[0]
reuse[pdb].append(x)
reuse = dict(reuse)
pdblist = list(pdbsIter)
with open(out_fasta, "w") as out_fasta_handle:
for (pdb, pdb_file_path) in tqdm(pdblist):
if pdb in pdb_codes:
if pdb in reuse:
bpio.write(reuse[pdb], out_fasta_handle, "fasta")
else:
self.seq_from_pdb(out_fasta_handle, pdb, pdb_file_path)
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 add_arguments(self, parser):
pdbs = PDBs()
parser.add_argument('--code', required=True, help="4 letter PDB code")
parser.add_argument('--tmp', default="data/tmp/load_pdb")
parser.add_argument('--pdbs_dir',
default="/data/databases/pdb/divided/")
parser.add_argument('--entries_path',
default="/data/databases/pdb/entries.idx")
parser.add_argument('--entries_url', default=pdbs.url_pdb_entries)
def add_arguments(self, parser):
pdbs = PDBs()
parser.add_argument('--pdbs_dir', default="data/pdb/")
parser.add_argument('--entries_path', default=None)
parser.add_argument(
'--only_annotated',
action='store_false',
help="by default only cross referenced pdbs are downloaded")
parser.add_argument('--entries_url', default=pdbs.url_pdb_entries)
def add_arguments(self, parser):
pdbs = PDBs()
parser.add_argument('--code', required=True, help="4 letter PDB code")
parser.add_argument('--tmp', default="data/tmp/load_pdb")
parser.add_argument('--pdbs_dir', default="/data/databases/pdb/")
parser.add_argument('--entries_path',
default="/data/databases/pdb/entries.idx")
parser.add_argument('--entries_url', default=pdbs.url_pdb_entries)
parser.add_argument('--force', action="store_true")
parser.add_argument('--verbose', default=0, choices=[0, 1], type=int)
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_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(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)
parser = ArgumentParser(formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("-i", "--data_path", default='/data/databases/pdb/')
parser.add_argument(
"-o",
"--output_path",
default='/data/databases/pdb/processed/domain_analisis')
args = parser.parse_args()
domains = defaultdict(lambda: [])
for seq in bpio.parse(args.data_path + "/processed/domains.fasta",
"fasta"):
domains["_".join(seq.id.split("_")[0:2])].append(seq.id.split("_"))
for (code, pdb_path) in tqdm(PDBs(pdb_dir=args.data_path)):
pdb_model = PDB(code=code)
pdb_model.save()
p = PDBParser(PERMISSIVE=True, QUIET=True)
try:
for chain in p.get_structure(code, pdb_path).get_chains():
chains_dir = args.output_path + "/chains/" + code[1:3] + "/"
mkdir(chains_dir)
cs = ChainSplitter(chains_dir)
process_chain(pdb_path, code, chain.id, pdb_model)
for (_, _, res_start, res_end, dn, dn_start,
dn_end) in domains[code + "_" + chain.id]:
# 1r9d_A_2_787_PF02901.14_8_648
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
def old_or_inexistent(filepath, period=30):
return not os.path.exists(filepath) or ((
(time.time() - os.path.getatime(filepath)) / 60 / 60 / 24) > period)
#os.environ["http_proxy"] = "http://proxy.fcen.uba.ar:8080"
#os.environ["ftp_proxy"] = "http://proxy.fcen.uba.ar:8080"
mkdir("/data/pdb/")
download_file("ftp://ftp.wwpdb.org/pub/pdb/derived_data/index/entries.idx",
"/data/pdb/entries.idx",
ovewrite=True)
pdbs = PDBs("/data/pdb/")
pdbs.download_pdb_seq_ses()
pdbs.update_pdb_dir()
mkdir("/data/pdb/processed/")
pdbs.pdbs_seq_for_modelling()
execute("makeblastdb -dbtype prot -in /data/pdb/processed/seqs_from_pdb.fasta")
if old_or_inexistent("/data/uniprot/uniref/uniref90/uniref90.fasta"):
mkdir("/data/uniprot/uniref/uniref90")
download_file(
"ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz",
"/data/uniprot/uniref/uniref90/uniref90.fasta.gz",
ovewrite=True)
execute("gunzip /data/uniprot/uniref/uniref90/uniref90.fasta.gz")
if old_or_inexistent("/data/uniprot/uniref/uniref90/uniref90.fasta.pal"):
def main(argv=None): # IGNORE:C0111
'''Command line options.'''
if argv is None:
argv = sys.argv
else:
sys.argv.extend(argv)
parser = ArgumentParser( formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("-v", "--verbose", dest="verbose", action="count",
help="set verbosity level [default: %(default)s]")
# parser.add_argument("-dir", "--structs_dir", required = True )
parser.add_argument("-db", "--database_name", default='pdb')
parser.add_argument("-host", "--db_host", default='127.0.0.1')
parser.add_argument( "--csa", default='/data/databases/csa/csa.txt')
parser.add_argument( "--hmm", default='/data/databases/pdb/pdb_seq_res.hmm')
parser.add_argument( "--pdbs", default='/data/databases/pdb/')
parser.add_argument( "--distances", default='/data/databases/pdb/processed/distances.tbl')
args = parser.parse_args()
# pdbs = PDBs()
# pdbs.update('/data/pdb/divided/')
BioMongoDB(args.database_name) #args.db_host
# update_quaternary()
# # clusters cd hit
# update_clusters()
#
# residues near ligands --> metal drug/cofactor
if not os.path.exists(args.csa):
sys.stderr.write("%s not found. Download it from %s" % (
args.csa,
"http://www.ebi.ac.uk/thornton-srv/databases/CSA/downloads/CSA_2_0_121113.txt"
))
sys.exit(1)
if not os.path.exists(args.pdbs):
sys.stderr.write("%s not found. Specify where is pdbs/divided directory" % (
args.pdbs
))
sys.exit(1)
if not os.path.exists(args.distances):
sys.stderr.write("%s not found. Run extended_domain.py script to create it." % (
args.distances
))
sys.exit(1)
pdbUtils = PDBs(pdb_dir=args.pdbs)
print("Update Quaternary")
update_quaternary(pdbUtils)
print("Update CSA")
update_csa(args.csa)
print("Update CYS/TYR")
free_cys_tyr(pdbUtils)
print("Update Importan Pfam")
important_pfam(args.hmm)
print("Update Binding residues")
update_binding_residues(args.distances)
_log.info("update pdb properties finished!!")
parser.add_argument("-p", "--dbpass", required=True)
parser.add_argument("-i", "--pdb_dir", default="/data/databases/pdb/")
parser.add_argument("-db", "--dbname", default="pdbdb")
parser.add_argument("-u", "--dbuser", default="root")
args = parser.parse_args()
from peewee import MySQLDatabase
mysql_db = MySQLDatabase(args.dbname,
user=args.dbuser,
password=args.dbpass)
mysql_db.close()
sqldb.initialize(mysql_db)
pdb_utils = PDBs(pdb_dir=args.pdb_dir)
df = pdb_utils.entries_df()
pdbs = list(pdb_utils)
with tqdm(pdbs) as pbar:
for (code, pdb_path) in pbar:
mysql_db.connect(reuse_if_open=True)
pbar.set_description(code)
try:
entry = df[df.IDCODE == code.upper()].iloc[0]
except IndexError:
continue
pdb_model = PDB(code=code, experiment=str(entry.EXPERIMENT))
try:
resolution = float(entry.RESOLUTION)
parser = ArgumentParser(formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("-p", "--dbpass", required=True)
parser.add_argument("-i", "--pdb_dir", default="/data/databases/pdb/")
parser.add_argument("-db", "--dbname", default="pdbdb")
parser.add_argument("-u", "--dbuser", default="root")
args = parser.parse_args()
from peewee import MySQLDatabase
mysql_db = MySQLDatabase(args.dbname,
user=args.dbuser,
password=args.dbpass)
sqldb.initialize(mysql_db)
pdb_utils = PDBs(pdb_dir=args.pdb_dir)
props = {x.name: x for x in Property.select()}
pdbs = list(pdb_utils)
with tqdm(pdbs) as pbar:
for (code, pdb_path) in pbar:
pdb_model = PDB.select().where(PDB.code == code).first()
p = PDBParser(PERMISSIVE=True, QUIET=True)
try:
for chain in p.get_structure(code, pdb_path).get_chains():
chains_dir = args.pdb_dir + "/chains/" + code[1:3] + "/"
mkdir(chains_dir)
cs = ChainSplitter(chains_dir)
process_chain(pdb_path, code, chain.id, pdb_model, props)
def add_arguments(self, parser):
pdbs = PDBs()
parser.add_argument('--pdbs_dir', default="data/pdb/")
parser.add_argument('--entries_path', default="data/pdb/entries.idx")
parser.add_argument('--only_annotated', action='store_false')
parser.add_argument('--entries_url', default=pdbs.url_pdb_entries)
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
"--verbose",
dest="verbose",
action="count",
help="set verbosity level [default: %(default)s]")
parser.add_argument("-host", "--db_host", default='127.0.0.1')
parser.add_argument("-db", "--db_name", default='tdr')
parser.add_argument("--pdb_entries",
default='/data/databases/pdb/entries.idx')
parser.add_argument("--pdbs", default='/data/databases/pdb/')
args = parser.parse_args()
BioMongoDB(args.db_name)
pdbUtils = PDBs(pdb_dir=args.pdbs)
db = MongoClient(args.db_host)["pdb"]
col_name = "pdb"
if not os.path.exists(args.pdb_entries):
sys.stderr.write("%s does not exists" % args.pdb_entries)
sys.exit(1)
"""
collection = SeqCollection.objects(name=col_name)
if len(collection):
collection = collection.get()
else:
collection = SeqCollection(name=col_name, description="Protein Data Bank", organism="?")
collection.save()
"""
parser = argparse.ArgumentParser(description='PDB utils')
subparsers = parser.add_subparsers(help='commands', description='valid subcommands', dest='command')
update_pdb = subparsers.add_parser('update', help='List contents')
update_pdb.add_argument('-i', '--pdbs_dir', help="pdbs_directory", default="/data/databases/pdb/")
# update_pdb = subparsers.add_parser('getpdb', help='List contents')
# update_pdb.add_argument('-i', '--pdb_code', help="4 letter code", required=True)
# update_pdb.add_argument('-o', '--ouput_file', help="output file")
args = parser.parse_args()
if args.command == "update":
# remzemeber to configure ftp
pdbs = PDBs(pdb_dir=args.pdbs_dir)
pdbs.download_pdb_entries()
pdbs.update_pdb_dir()
pdbs.download_pdb_seq_ses()
sys.exit(0)
# os.environ["ftp_proxy"] = "http://proxy.fcen.uba.ar:8080"
# pdbs.download_pdb_seq_ses()
# 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
help='pdb files directory')
parser.add_argument('--tmp_dir',
default=mkdtemp(),
help='temporal directory')
parser.add_argument('--cpus', default=1, type=int, help='cpu cores to use')
# parser.add_argument('--max_alns', default=3, type=int, help='max different templates to use')
parser.add_argument('-t',
"--templates_to_use",
default=3,
type=int,
help='max amount of templates to use.')
args = parser.parse_args()
pdbs_dir = args.pdbs_dir + ("/" if args.pdbs_dir[-1] != "/" else "")
mkdir(f'{pdbs_dir}/divided')
pdb_utils = PDBs(pdbs_dir)
# pbar = tqdm(args.alns)
sys.stderr.write(str(args))
sys.stderr.write(f'reading alignment file\n')
alns = [{
"aln_file": x,
"templates2use": args.templates_to_use,
"output_dir": args.output_dir,
"tmp_dir": args.tmp_dir
} for x in args.alns]
mkdir(args.output_dir)
assert os.path.exists(
args.output_dir), f'"{args.output_dir}" could not be created'
sys.stderr.write(f'processing alignment files\n')
help="set verbosity level [default: %(default)s]")
parser.add_argument("-host", "--db_host", default='127.0.0.1')
parser.add_argument("-db", "--db_name", default='tdr')
parser.add_argument( "--pdb_entries", default='/data/databases/pdb/entries.idx')
parser.add_argument( "--pdbs", default='/data/databases/pdb/')
parser.add_argument( "--pdb_timeout", default=60,type=int)
parser.add_argument( "--review_pockets", action="store_true")
parser.add_argument("--organism_name", default=None)
args = parser.parse_args()
mdb = BioMongoDB(args.db_name,host=args.db_host)
pdbUtils = PDBs(pdb_dir=args.pdbs)
db = MongoClient(args.db_host)["pdb"]
col_name = "pdb"
if not os.path.exists(args.pdb_entries):
sys.stderr.write("%s does not exists" % args.pdb_entries)
sys.exit(1)
"""
collection = SeqCollection.objects(name=col_name)
if len(collection):
collection = collection.get()
else:
collection = SeqCollection(name=col_name, description="Protein Data Bank", organism="?")
collection.save()