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) ------------------ [0;31m[0m [0;31mgaierror[0mTraceback (most recent call last) [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/urllib/request.py[0m in [0;36mdo_open[0;34m(self, http_class, req, **http_conn_args)[0m [1;32m 1353[0m [0;32mtry[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0;32m-> 1354[0;31m h.request(req.get_method(), req.selector, req.data, headers, [0m[1;32m 1355[0m encode_chunked=req.has_header('Transfer-encoding')) [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/http/client.py[0m in [0;36mrequest[0;34m(self, method, url, body, headers, encode_chunked)[0m [1;32m 1255[0m [0;34m"""Send a complete request to the server."""[0m[0;34m[0m[0;34m[0m[0m [0;32m-> 1256[0;31m [0mself[0m[0;34m.[0m[0m_send_request[0m[0;34m([0m[0mmethod[0m[0;34m,[0m [0murl[0m[0;34m,[0m [0mbody[0m[0;34m,[0m [0mheaders[0m[0;34m,[0m [0mencode_chunked[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 1257[0m [0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/http/client.py[0m in [0;36m_send_request[0;34m(self, method, url, body, headers, encode_chunked)[0m [1;32m 1301[0m [0mbody[0m [0;34m=[0m [0m_encode[0m[0;34m([0m[0mbody[0m[0;34m,[0m [0;34m'body'[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0;32m-> 1302[0;31m [0mself[0m[0;34m.[0m[0mendheaders[0m[0;34m([0m[0mbody[0m[0;34m,[0m [0mencode_chunked[0m[0;34m=[0m[0mencode_chunked[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 1303[0m [0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/http/client.py[0m in [0;36mendheaders[0;34m(self, message_body, encode_chunked)[0m [1;32m 1250[0m [0;32mraise[0m [0mCannotSendHeader[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0;32m-> 1251[0;31m [0mself[0m[0;34m.[0m[0m_send_output[0m[0;34m([0m[0mmessage_body[0m[0;34m,[0m [0mencode_chunked[0m[0;34m=[0m[0mencode_chunked[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 1252[0m [0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/http/client.py[0m in [0;36m_send_output[0;34m(self, message_body, encode_chunked)[0m [1;32m 1010[0m [0;32mdel[0m [0mself[0m[0;34m.[0m[0m_buffer[0m[0;34m[[0m[0;34m:[0m[0;34m][0m[0;34m[0m[0;34m[0m[0m [0;32m-> 1011[0;31m [0mself[0m[0;34m.[0m[0msend[0m[0;34m([0m[0mmsg[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 1012[0m [0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/http/client.py[0m in [0;36msend[0;34m(self, data)[0m [1;32m 950[0m [0;32mif[0m [0mself[0m[0;34m.[0m[0mauto_open[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0;32m--> 951[0;31m [0mself[0m[0;34m.[0m[0mconnect[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 952[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/http/client.py[0m in [0;36mconnect[0;34m(self)[0m [1;32m 921[0m [0;34m"""Connect to the host and port specified in __init__."""[0m[0;34m[0m[0;34m[0m[0m [0;32m--> 922[0;31m self.sock = self._create_connection( [0m[1;32m 923[0m (self.host,self.port), self.timeout, self.source_address) [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/socket.py[0m in [0;36mcreate_connection[0;34m(address, timeout, source_address)[0m [1;32m 786[0m [0merr[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0;34m[0m[0m [0;32m--> 787[0;31m [0;32mfor[0m [0mres[0m [0;32min[0m [0mgetaddrinfo[0m[0;34m([0m[0mhost[0m[0;34m,[0m [0mport[0m[0;34m,[0m [0;36m0[0m[0;34m,[0m [0mSOCK_STREAM[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 788[0m [0maf[0m[0;34m,[0m [0msocktype[0m[0;34m,[0m [0mproto[0m[0;34m,[0m [0mcanonname[0m[0;34m,[0m [0msa[0m [0;34m=[0m [0mres[0m[0;34m[0m[0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/socket.py[0m in [0;36mgetaddrinfo[0;34m(host, port, family, type, proto, flags)[0m [1;32m 917[0m [0maddrlist[0m [0;34m=[0m [0;34m[[0m[0;34m][0m[0;34m[0m[0;34m[0m[0m [0;32m--> 918[0;31m [0;32mfor[0m [0mres[0m [0;32min[0m [0m_socket[0m[0;34m.[0m[0mgetaddrinfo[0m[0;34m([0m[0mhost[0m[0;34m,[0m [0mport[0m[0;34m,[0m [0mfamily[0m[0;34m,[0m [0mtype[0m[0;34m,[0m [0mproto[0m[0;34m,[0m [0mflags[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 919[0m [0maf[0m[0;34m,[0m [0msocktype[0m[0;34m,[0m [0mproto[0m[0;34m,[0m [0mcanonname[0m[0;34m,[0m [0msa[0m [0;34m=[0m [0mres[0m[0;34m[0m[0;34m[0m[0m [0;31mgaierror[0m: [Errno -2] Name or service not known During handling of the above exception, another exception occurred: [0;31mURLError[0mTraceback (most recent call last) [0;32m[0m in [0;36m[0;34m[0m [0;32m----> 1[0;31m [0mt[0m [0;34m=[0m [0mmd[0m[0;34m.[0m[0mload_pdb[0m[0;34m([0m[0;34m'http://www.rcsb.org/pdb/files/2EQQ.pdb'[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 2[0m [0mprint[0m[0;34m([0m[0mt[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0;32m/nix/store/rg3m2aq0i0897r4cmx3a3cy1gjx0ragp-python3.8-mdtraj-0.0/lib/python3.8/site-packages/mdtraj/formats/pdb/pdbfile.py[0m in [0;36mload_pdb[0;34m(filename, stride, atom_indices, frame, no_boxchk, standard_names)[0m [1;32m 151[0m [0;34m[0m[0m [1;32m 152[0m [0mfilename[0m [0;34m=[0m [0mstr[0m[0;34m([0m[0mfilename[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0;32m--> 153[0;31m [0;32mwith[0m [0mPDBTrajectoryFile[0m[0;34m([0m[0mfilename[0m[0;34m,[0m [0mstandard_names[0m[0;34m=[0m[0mstandard_names[0m[0;34m)[0m [0;32mas[0m [0mf[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 154[0m [0matom_slice[0m [0;34m=[0m [0mslice[0m[0;34m([0m[0;32mNone[0m[0;34m)[0m [0;32mif[0m [0matom_indices[0m [0;32mis[0m [0;32mNone[0m [0;32melse[0m [0matom_indices[0m[0;34m[0m[0;34m[0m[0m [1;32m 155[0m [0;32mif[0m [0mframe[0m [0;32mis[0m [0;32mnot[0m [0;32mNone[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0;32m/nix/store/rg3m2aq0i0897r4cmx3a3cy1gjx0ragp-python3.8-mdtraj-0.0/lib/python3.8/site-packages/mdtraj/formats/pdb/pdbfile.py[0m in [0;36m__init__[0;34m(self, filename, mode, force_overwrite, standard_names)[0m [1;32m 255[0m [0;34m[0m[0m [1;32m 256[0m [0;32mif[0m [0m_is_url[0m[0;34m([0m[0mfilename[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0;32m--> 257[0;31m [0mself[0m[0;34m.[0m[0m_file[0m [0;34m=[0m [0murlopen[0m[0;34m([0m[0mfilename[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 258[0m [0;32mif[0m [0mfilename[0m[0;34m.[0m[0mlower[0m[0;34m([0m[0;34m)[0m[0;34m.[0m[0mendswith[0m[0;34m([0m[0;34m'.gz'[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [1;32m 259[0m [0;32mif[0m [0msix[0m[0;34m.[0m[0mPY3[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/urllib/request.py[0m in [0;36murlopen[0;34m(url, data, timeout, cafile, capath, cadefault, context)[0m [1;32m 220[0m [0;32melse[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [1;32m 221[0m [0mopener[0m [0;34m=[0m [0m_opener[0m[0;34m[0m[0;34m[0m[0m [0;32m--> 222[0;31m [0;32mreturn[0m [0mopener[0m[0;34m.[0m[0mopen[0m[0;34m([0m[0murl[0m[0;34m,[0m [0mdata[0m[0;34m,[0m [0mtimeout[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 223[0m [0;34m[0m[0m [1;32m 224[0m [0;32mdef[0m [0minstall_opener[0m[0;34m([0m[0mopener[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/urllib/request.py[0m in [0;36mopen[0;34m(self, fullurl, data, timeout)[0m [1;32m 523[0m [0;34m[0m[0m [1;32m 524[0m [0msys[0m[0;34m.[0m[0maudit[0m[0;34m([0m[0;34m'urllib.Request'[0m[0;34m,[0m [0mreq[0m[0;34m.[0m[0mfull_url[0m[0;34m,[0m [0mreq[0m[0;34m.[0m[0mdata[0m[0;34m,[0m [0mreq[0m[0;34m.[0m[0mheaders[0m[0;34m,[0m [0mreq[0m[0;34m.[0m[0mget_method[0m[0;34m([0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0;32m--> 525[0;31m [0mresponse[0m [0;34m=[0m [0mself[0m[0;34m.[0m[0m_open[0m[0;34m([0m[0mreq[0m[0;34m,[0m [0mdata[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 526[0m [0;34m[0m[0m [1;32m 527[0m [0;31m# post-process response[0m[0;34m[0m[0;34m[0m[0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/urllib/request.py[0m in [0;36m_open[0;34m(self, req, data)[0m [1;32m 540[0m [0;34m[0m[0m [1;32m 541[0m [0mprotocol[0m [0;34m=[0m [0mreq[0m[0;34m.[0m[0mtype[0m[0;34m[0m[0;34m[0m[0m [0;32m--> 542[0;31m result = self._call_chain(self.handle_open, protocol, protocol + [0m[1;32m 543[0m '_open', req) [1;32m 544[0m [0;32mif[0m [0mresult[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/urllib/request.py[0m in [0;36m_call_chain[0;34m(self, chain, kind, meth_name, *args)[0m [1;32m 500[0m [0;32mfor[0m [0mhandler[0m [0;32min[0m [0mhandlers[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [1;32m 501[0m [0mfunc[0m [0;34m=[0m [0mgetattr[0m[0;34m([0m[0mhandler[0m[0;34m,[0m [0mmeth_name[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0;32m--> 502[0;31m [0mresult[0m [0;34m=[0m [0mfunc[0m[0;34m([0m[0;34m*[0m[0margs[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 503[0m [0;32mif[0m [0mresult[0m [0;32mis[0m [0;32mnot[0m [0;32mNone[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [1;32m 504[0m [0;32mreturn[0m [0mresult[0m[0;34m[0m[0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/urllib/request.py[0m in [0;36mhttp_open[0;34m(self, req)[0m [1;32m 1381[0m [0;34m[0m[0m [1;32m 1382[0m [0;32mdef[0m [0mhttp_open[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mreq[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0;32m-> 1383[0;31m [0;32mreturn[0m [0mself[0m[0;34m.[0m[0mdo_open[0m[0;34m([0m[0mhttp[0m[0;34m.[0m[0mclient[0m[0;34m.[0m[0mHTTPConnection[0m[0;34m,[0m [0mreq[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 1384[0m [0;34m[0m[0m [1;32m 1385[0m [0mhttp_request[0m [0;34m=[0m [0mAbstractHTTPHandler[0m[0;34m.[0m[0mdo_request_[0m[0;34m[0m[0;34m[0m[0m [0;32m/nix/store/5f36vg11fdfl6x6sva70cb0jqf722qqn-python3-3.8.11/lib/python3.8/urllib/request.py[0m in [0;36mdo_open[0;34m(self, http_class, req, **http_conn_args)[0m [1;32m 1355[0m encode_chunked=req.has_header('Transfer-encoding')) [1;32m 1356[0m [0;32mexcept[0m [0mOSError[0m [0;32mas[0m [0merr[0m[0;34m:[0m [0;31m# timeout error[0m[0;34m[0m[0;34m[0m[0m [0;32m-> 1357[0;31m [0;32mraise[0m [0mURLError[0m[0;34m([0m[0merr[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [0m[1;32m 1358[0m [0mr[0m [0;34m=[0m [0mh[0m[0;34m.[0m[0mgetresponse[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m [1;32m 1359[0m [0;32mexcept[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m [0;31mURLError[0m: URLError:

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