Baker-Hubbard Hydrogen Bond Identification

An error occurred while executing the following cell: ------------------ t = md.load_pdb('http://www.rcsb.org/pdb/files/2EQQ.pdb') print(t) ------------------  gaierrorTraceback (most recent call last) /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/urllib/request.py in do_open(self, http_class, req, **http_conn_args)  1349 h.request(req.get_method(), req.selector, req.data, headers, -> 1350 encode_chunked=req.has_header('Transfer-encoding'))  1351 except OSError as err: # timeout error /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/http/client.py in request(self, method, url, body, headers, encode_chunked)  1276 """Send a complete request to the server.""" -> 1277 self._send_request(method, url, body, headers, encode_chunked)  1278  /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/http/client.py in _send_request(self, method, url, body, headers, encode_chunked)  1322 body = _encode(body, 'body') -> 1323 self.endheaders(body, encode_chunked=encode_chunked)  1324  /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/http/client.py in endheaders(self, message_body, encode_chunked)  1271 raise CannotSendHeader() -> 1272 self._send_output(message_body, encode_chunked=encode_chunked)  1273  /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/http/client.py in _send_output(self, message_body, encode_chunked)  1031 del self._buffer[:] -> 1032 self.send(msg)  1033  /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/http/client.py in send(self, data)  971 if self.auto_open: --> 972 self.connect()  973 else: /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/http/client.py in connect(self)  943 self.sock = self._create_connection( --> 944 (self.host,self.port), self.timeout, self.source_address)  945 self.sock.setsockopt(socket.IPPROTO_TCP, socket.TCP_NODELAY, 1) /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/socket.py in create_connection(address, timeout, source_address)  706 err = None --> 707 for res in getaddrinfo(host, port, 0, SOCK_STREAM):  708 af, socktype, proto, canonname, sa = res /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/socket.py in getaddrinfo(host, port, family, type, proto, flags)  751 addrlist = [] --> 752 for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  753 af, socktype, proto, canonname, sa = res gaierror: [Errno -2] Name or service not known During handling of the above exception, another exception occurred: URLErrorTraceback (most recent call last)  in  ----> 1 t = md.load_pdb('http://www.rcsb.org/pdb/files/2EQQ.pdb')  2 print(t) /nix/store/b5m1cbwnd72r6lfr9bysxv5nwmi2yx51-python3.7-mdtraj-0.0/lib/python3.7/site-packages/mdtraj/formats/pdb/pdbfile.py in load_pdb(filename, stride, atom_indices, frame, no_boxchk, standard_names)  151   152 filename = str(filename) --> 153 with PDBTrajectoryFile(filename, standard_names=standard_names) as f:  154 atom_slice = slice(None) if atom_indices is None else atom_indices  155 if frame is not None: /nix/store/b5m1cbwnd72r6lfr9bysxv5nwmi2yx51-python3.7-mdtraj-0.0/lib/python3.7/site-packages/mdtraj/formats/pdb/pdbfile.py in __init__(self, filename, mode, force_overwrite, standard_names)  255   256 if _is_url(filename): --> 257 self._file = urlopen(filename)  258 if filename.lower().endswith('.gz'):  259 if six.PY3: /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/urllib/request.py in urlopen(url, data, timeout, cafile, capath, cadefault, context)  220 else:  221 opener = _opener --> 222 return opener.open(url, data, timeout)  223   224 def install_opener(opener): /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/urllib/request.py in open(self, fullurl, data, timeout)  523 req = meth(req)  524  --> 525 response = self._open(req, data)  526   527 # post-process response /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/urllib/request.py in _open(self, req, data)  541 protocol = req.type  542 result = self._call_chain(self.handle_open, protocol, protocol + --> 543 '_open', req)  544 if result:  545 return result /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/urllib/request.py in _call_chain(self, chain, kind, meth_name, *args)  501 for handler in handlers:  502 func = getattr(handler, meth_name) --> 503 result = func(*args)  504 if result is not None:  505 return result /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/urllib/request.py in http_open(self, req)  1376   1377 def http_open(self, req): -> 1378 return self.do_open(http.client.HTTPConnection, req)  1379   1380 http_request = AbstractHTTPHandler.do_request_ /nix/store/dgjm8090l365id2m7zhi6l7864kkb3n7-python3-3.7.10/lib/python3.7/urllib/request.py in do_open(self, http_class, req, **http_conn_args)  1350 encode_chunked=req.has_header('Transfer-encoding'))  1351 except OSError as err: # timeout error -> 1352 raise URLError(err)  1353 r = h.getresponse()  1354 except: URLError: URLError:

(hbonds.ipynb; hbonds_eval.ipynb; hbonds.py)