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')