Fraction of Native Contacts

An error occurred while executing the following cell: ------------------ # pull a random protein from the PDB # (The unitcell info happens to be wrong) traj = md.load_pdb('http://www.rcsb.org/pdb/files/2MI7.pdb') # just for example, use the first frame as the 'native' conformation q = best_hummer_q(traj, traj[0]) ------------------ --------------------------------------------------------------------------- gaierror Traceback (most recent call last) /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/urllib/request.py in do_open(self, http_class, req, **http_conn_args)  1345 try: -> 1346 h.request(req.get_method(), req.selector, req.data, headers,  1347 encode_chunked=req.has_header('Transfer-encoding')) /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/http/client.py in request(self, method, url, body, headers, encode_chunked)  1284 """Send a complete request to the server.""" -> 1285 self._send_request(method, url, body, headers, encode_chunked)  1286  /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/http/client.py in _send_request(self, method, url, body, headers, encode_chunked)  1330 body = _encode(body, 'body') -> 1331 self.endheaders(body, encode_chunked=encode_chunked)  1332  /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/http/client.py in endheaders(self, message_body, encode_chunked)  1279 raise CannotSendHeader() -> 1280 self._send_output(message_body, encode_chunked=encode_chunked)  1281  /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/http/client.py in _send_output(self, message_body, encode_chunked)  1039 del self._buffer[:] -> 1040 self.send(msg)  1041  /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/http/client.py in send(self, data)  979 if self.auto_open: --> 980 self.connect()  981 else: /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/http/client.py in connect(self)  945 """Connect to the host and port specified in __init__.""" --> 946 self.sock = self._create_connection(  947 (self.host,self.port), self.timeout, self.source_address) /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/socket.py in create_connection(address, timeout, source_address)  822 err = None --> 823 for res in getaddrinfo(host, port, 0, SOCK_STREAM):  824 af, socktype, proto, canonname, sa = res /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/socket.py in getaddrinfo(host, port, family, type, proto, flags)  953 addrlist = [] --> 954 for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  955 af, socktype, proto, canonname, sa = res gaierror: [Errno -2] Name or service not known During handling of the above exception, another exception occurred: URLError Traceback (most recent call last) /build/ipykernel_1266/2720045451.py in   1 # pull a random protein from the PDB  2 # (The unitcell info happens to be wrong) ----> 3 traj = md.load_pdb('http://www.rcsb.org/pdb/files/2MI7.pdb')  4   5 # just for example, use the first frame as the 'native' conformation /nix/store/18mxfwq28nqq0vk1lwvysdqrfkdz337w-python3.9-mdtraj-1.9.8.dev0/lib/python3.9/site-packages/mdtraj/formats/pdb/pdbfile.py in load_pdb(filename, stride, atom_indices, frame, no_boxchk, standard_names, top)  153 atom_indices = cast_indices(atom_indices)  154  --> 155 with PDBTrajectoryFile(filename, standard_names=standard_names, top=top) as f:  156 atom_slice = slice(None) if atom_indices is None else atom_indices  157 if frame is not None: /nix/store/18mxfwq28nqq0vk1lwvysdqrfkdz337w-python3.9-mdtraj-1.9.8.dev0/lib/python3.9/site-packages/mdtraj/formats/pdb/pdbfile.py in __init__(self, filename, mode, force_overwrite, standard_names, top)  262   263 if _is_url(filename): --> 264 self._file = urlopen(filename)  265 if filename.lower().endswith('.gz'):  266 if six.PY3: /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/urllib/request.py in urlopen(url, data, timeout, cafile, capath, cadefault, context)  212 else:  213 opener = _opener --> 214 return opener.open(url, data, timeout)  215   216 def install_opener(opener): /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/urllib/request.py in open(self, fullurl, data, timeout)  515   516 sys.audit('urllib.Request', req.full_url, req.data, req.headers, req.get_method()) --> 517 response = self._open(req, data)  518   519 # post-process response /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/urllib/request.py in _open(self, req, data)  532   533 protocol = req.type --> 534 result = self._call_chain(self.handle_open, protocol, protocol +  535 '_open', req)  536 if result: /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/urllib/request.py in _call_chain(self, chain, kind, meth_name, *args)  492 for handler in handlers:  493 func = getattr(handler, meth_name) --> 494 result = func(*args)  495 if result is not None:  496 return result /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/urllib/request.py in http_open(self, req)  1373   1374 def http_open(self, req): -> 1375 return self.do_open(http.client.HTTPConnection, req)  1376   1377 http_request = AbstractHTTPHandler.do_request_ /nix/store/rppr9s436950i1dlzknbmz40m2xqqnxc-python3-3.9.9/lib/python3.9/urllib/request.py in do_open(self, http_class, req, **http_conn_args)  1347 encode_chunked=req.has_header('Transfer-encoding'))  1348 except OSError as err: # timeout error -> 1349 raise URLError(err)  1350 r = h.getresponse()  1351 except: URLError: URLError:

(native-contact.ipynb; native-contact_eval.ipynb; native-contact.py)