def run(self):
curated_pdb = self.input().path
proasis_hit = ProasisHits.objects.get(crystal_name_id=self.crystal_id, refinement_id=self.refinement_id)
ligand_list = eval(proasis_hit.ligand_list)
ligand_list = proasis_api_funcs.get_lig_strings(ligand_list)
crystal_name = proasis_hit.crystal_name.crystal_name
target_name = proasis_hit.crystal_name.target.target_name.upper()
pdb_file = open(curated_pdb, 'r')
ligid = 0
for l in ligand_list:
ligid += 1
for line in pdb_file:
if any(lig in line for lig in ligand_list):
continue
else:
with open(os.path.join(self.hit_directory, target_name,
crystal_name, str(crystal_name + '_' + str(ligid)),
str(crystal_name + '_apo_' + str(ligid) + '.pdb')), 'a') as f:
f.write(line)
out_entry = ProasisOut.objects.filter(proasis=proasis_hit, ligid=ligid)
out_entry.apo = str(crystal_name + '_apo_' + str(ligid) + '.pdb')
out_entry.save()
def run(self):
proasis_hit = ProasisHits.objects.get(crystal_name_id=self.crystal_id, refinement_id=self.refinement_id)
strucid = proasis_hit.strucid
ligands = eval(proasis_hit.ligand_list)
ligand_list = proasis_api_funcs.get_lig_strings(ligands)
crystal_name = proasis_hit.crystal_name.crystal_name
target_name = proasis_hit.crystal_name.target.target_name
ligid = 0
for lig in ligand_list:
ligid += 1
curated_pdb = proasis_api_funcs.get_struc_file(strucid,
os.path.join(
self.hit_directory, target_name.upper(), str(crystal_name +
'_' +
str(ligid)),
str(crystal_name + str('_' + str(ligid) + '.pdb'))),
'curatedpdb')
proasis_out = ProasisOut.objects.get_or_create(proasis=proasis_hit,
crystal=proasis_hit.crystal_name,
ligand=lig,
ligid=ligid,
root=os.path.join(self.hit_directory,
proasis_hit.crystal_name.target.target_name.upper()),
start=str(proasis_hit.crystal_name.crystal_name + '/' +
proasis_hit.crystal_name.crystal_name + '_' +
ligid),
curated=curated_pdb.split('/')[-1]
)
proasis_out[0].save()
def output(self):
proasis_hit = ProasisHits.objects.get(crystal_name_id=self.crystal_id, refinement_id=self.refinement_id)
crystal_name = proasis_hit.crystal_name.crystal_name
target_name = proasis_hit.crystal_name.target.target_name.upper()
ligands = eval(proasis_hit.ligand_list)
ligand_list = proasis_api_funcs.get_lig_strings(ligands)
return [luigi.LocalTarget(os.path.join(
self.hit_directory, target_name, crystal_name, str(crystal_name + str(i)), str(crystal_name + '_apo_' + str(i) + '.pdb')))
for i in range(1, len(ligand_list)+1)]
def run(self):
self.ligands = eval(self.ligands)
print((len(self.ligands)))
# if len(list(self.ligands))>1:
# raise Exception('Structures containing more than 1 ligand are currently unsupported')
conn, c = dbf.connectDB()
c.execute('SELECT curated_name from proasis_out WHERE strucid=%s',
(self.strucid, ))
rows = c.fetchall()
print((len(rows)))
if len(rows) > 1:
raise Exception('Multiple files where found for this structure: ' +
str(rows))
if len(rows) > 0 and len(rows[0]) == 0:
# raise Exception('No entries found for this strucid... check the datasource!')
c.execute('DELETE from proasis_out WHERE curated_name=%s',
(str(self.crystal + '_' + 'curated.pdb'), ))
conn.commit()
shutil.rmtree(os.path.join(self.root_dir, self.docking_dir))
raise Exception(
'DB problem... resetting the datasource and files for this crystal'
)
for row in rows:
curated_pdb = str(row[0])
try:
print(curated_pdb)
except:
c.execute('DELETE from proasis_out WHERE curated_name=%s',
(str(self.crystal + '_' + 'curated.pdb'), ))
conn.commit()
shutil.rmtree(os.path.join(self.root_dir, self.docking_dir))
raise Exception(
'DB problem... resetting the datasource and files for this crystal'
)
ligand_string = paf.get_lig_strings(self.ligands)
working_dir = os.getcwd()
os.chdir(os.path.join(self.root_dir, self.docking_dir))
try:
pdb_file = open(curated_pdb, 'r')
except:
raise Exception(str(rows))
for line in pdb_file:
if any(lig in line for lig in ligand_string):
continue
else:
with open(self.output().path, 'a') as f:
f.write(line)
os.chdir(working_dir)