def create_construct_data(self, filenames=False):
self.logger.info('ADDING EXPERIMENTAL CONSTRUCT DATA')
# read source files
if not filenames:
filenames = os.listdir(self.construct_data_dir)
for filename in filenames:
if filename[-4:] != 'json':
continue
filepath = os.sep.join([self.construct_data_dir, filename])
with open(filepath) as json_file:
d = json.load(json_file)
add_construct(d)
structures = Structure.objects.all()
for s in structures:
pdbname = str(s)
try:
protein = Protein.objects.filter(
entry_name=pdbname.lower()).get()
d = fetch_pdb_info(pdbname, protein)
add_construct(d)
except:
print(pdbname, 'failed')
self.logger.info('COMPLETED CREATING EXPERIMENTAL CONSTRUCT DATA')
def create_construct_data(self, filenames=False):
self.logger.info('ADDING EXPERIMENTAL CONSTRUCT DATA')
# read source files
if not filenames:
filenames = os.listdir(self.construct_data_dir)
for filename in filenames:
if filename[-4:]!='json':
continue
filepath = os.sep.join([self.construct_data_dir, filename])
with open(filepath) as json_file:
d = json.load(json_file)
add_construct(d)
structures = Structure.objects.all()
for s in structures:
pdbname = str(s)
try:
protein = Protein.objects.filter(entry_name=pdbname.lower()).get()
d = fetch_pdb_info(pdbname,protein)
add_construct(d)
except:
print(pdbname,'failed')
self.logger.info('COMPLETED CREATING EXPERIMENTAL CONSTRUCT DATA')
def create_construct_data(self, filenames=False):
self.logger.info('ADDING EXPERIMENTAL CONSTRUCT DATA')
# read source files
do_all = False
if not filenames:
do_all = True
# self.purge_construct_data()
# filenames = os.listdir(self.construct_data_dir)
if filenames:
for filename in filenames:
if filename[-4:] != 'json':
continue
filepath = os.sep.join([self.construct_data_dir, filename])
print('Adding ' + filepath)
with open(filepath) as json_file:
d = json.load(json_file)
add_construct(d)
if do_all:
structures = Structure.objects.all().exclude(refined=True)
for s in structures:
pdbname = str(s)
try:
exists = Construct.objects.filter(
structure__pdb_code__index=pdbname).exists()
if not exists:
print(pdbname)
protein = Protein.objects.filter(
entry_name=pdbname.lower()).get()
d = fetch_pdb_info(pdbname, protein)
add_construct(d)
else:
# pass
print("Entry for", pdbname, "already there")
except:
print(pdbname, 'failed')
self.logger.info('COMPLETED CREATING EXPERIMENTAL CONSTRUCT DATA')
def create_construct_data(self, filenames=False):
self.logger.info('ADDING EXPERIMENTAL CONSTRUCT DATA')
# read source files
do_all = False
if not filenames:
do_all = True
# self.purge_construct_data()
# filenames = os.listdir(self.construct_data_dir)
if filenames:
for filename in filenames:
if filename[-4:]!='json':
continue
filepath = os.sep.join([self.construct_data_dir, filename])
print('Adding '+filepath)
with open(filepath) as json_file:
d = json.load(json_file)
add_construct(d)
if do_all:
structures = Structure.objects.all().exclude(refined=True)
for s in structures:
pdbname = str(s)
try:
exists = Construct.objects.filter(structure__pdb_code__index=pdbname).exists()
if not exists:
# print(pdbname)
protein = Protein.objects.filter(entry_name=pdbname.lower()).get()
d = fetch_pdb_info(pdbname,protein)
add_construct(d)
else:
# pass
print("Entry for",pdbname,"already there")
except:
print(pdbname,'failed')
self.logger.info('COMPLETED CREATING EXPERIMENTAL CONSTRUCT DATA')
def create_construct_local_data(self, filenames=False):
self.logger.info('ADDING EXPERIMENTAL CONSTRUCT DATA')
#delete existing
self.purge_construct_data()
# read source files
if not filenames:
filenames = os.listdir(self.construct_data_dir)
for filename in sorted(filenames):
print('dealing with', filename)
if filename[-4:] != 'json':
continue
filepath = os.sep.join([self.construct_data_dir, filename])
with open(filepath) as json_file:
d = json.load(json_file)
add_construct(d)
filenames = os.listdir(self.construct_data_local_dir)
for filename in sorted(filenames):
print('dealing with', filename)
if filename[-4:] != 'json':
continue
filepath = os.sep.join([self.construct_data_local_dir, filename])
with open(filepath) as json_file:
d = json.load(json_file)
add_construct(d)
structures = Structure.objects.all()
for s in structures:
pdbname = str(s)
try:
exists = Construct.objects.filter(
structure__pdb_code__index=pdbname).exists()
if not exists:
print(pdbname)
protein = Protein.objects.filter(
entry_name=pdbname.lower()).get()
d = fetch_pdb_info(pdbname, protein)
add_construct(d)
else:
print("Entry for", pdbname, "already there")
except:
print(pdbname, 'failed')
def create_construct_local_data(self, filenames=False):
self.logger.info('ADDING EXPERIMENTAL CONSTRUCT DATA')
#delete existing
self.purge_construct_data()
# read source files
if not filenames:
filenames = os.listdir(self.construct_data_dir)
for filename in sorted(filenames):
print('dealing with',filename)
if filename[-4:]!='json':
continue
filepath = os.sep.join([self.construct_data_dir, filename])
with open(filepath) as json_file:
d = json.load(json_file)
add_construct(d)
filenames = os.listdir(self.construct_data_local_dir)
for filename in sorted(filenames):
print('dealing with',filename)
if filename[-4:]!='json':
continue
filepath = os.sep.join([self.construct_data_local_dir, filename])
with open(filepath) as json_file:
d = json.load(json_file)
add_construct(d)
structures = Structure.objects.all()
for s in structures:
pdbname = str(s)
try:
exists = Construct.objects.filter(structure__pdb_code__index=pdbname).exists()
if not exists:
print(pdbname)
protein = Protein.objects.filter(entry_name=pdbname.lower()).get()
d = fetch_pdb_info(pdbname,protein)
add_construct(d)
else:
print("Entry for",pdbname,"already there")
except:
print(pdbname,'failed')
