Hello, Doctors, I have encountered a network problem, I have not fixed it.
Describe the bug
The problem is described as follows :
TO15 _ protein _ ligand _ docking
1354 h.request ( req.get _ method ( ), req.selector, req.data, headers.
1355 encode _ chunked = req.has _ header ( ' Transfer-encoding ' ) )
To Reproduce
SSLEOFError Traceback (most recent call last)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:1354, in AbstractHTTPHandler.do_open(self, http_class, req, **http_conn_args)
1353 try:
-> 1354 h.request(req.get_method(), req.selector, req.data, headers,
1355 encode_chunked=req.has_header('Transfer-encoding'))
1356 except OSError as err: # timeout error
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:1256, in HTTPConnection.request(self, method, url, body, headers, encode_chunked)
1255 """Send a complete request to the server."""
-> 1256 self._send_request(method, url, body, headers, encode_chunked)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:1302, in HTTPConnection._send_request(self, method, url, body, headers, encode_chunked)
1301 body = _encode(body, 'body')
-> 1302 self.endheaders(body, encode_chunked=encode_chunked)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:1251, in HTTPConnection.endheaders(self, message_body, encode_chunked)
1250 raise CannotSendHeader()
-> 1251 self._send_output(message_body, encode_chunked=encode_chunked)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:1011, in HTTPConnection._send_output(self, message_body, encode_chunked)
1010 del self._buffer[:]
-> 1011 self.send(msg)
1013 if message_body is not None:
1014
1015 # create a consistent interface to message_body
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:951, in HTTPConnection.send(self, data)
950 if self.auto_open:
--> 951 self.connect()
952 else:
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:1425, in HTTPSConnection.connect(self)
1423 server_hostname = self.host
-> 1425 self.sock = self._context.wrap_socket(self.sock,
1426 server_hostname=server_hostname)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/ssl.py:500, in SSLContext.wrap_socket(self, sock, server_side, do_handshake_on_connect, suppress_ragged_eofs, server_hostname, session)
494 def wrap_socket(self, sock, server_side=False,
495 do_handshake_on_connect=True,
496 suppress_ragged_eofs=True,
497 server_hostname=None, session=None):
498 # SSLSocket class handles server_hostname encoding before it calls
499 # ctx._wrap_socket()
--> 500 return self.sslsocket_class._create(
501 sock=sock,
502 server_side=server_side,
503 do_handshake_on_connect=do_handshake_on_connect,
504 suppress_ragged_eofs=suppress_ragged_eofs,
505 server_hostname=server_hostname,
506 context=self,
507 session=session
508 )
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/ssl.py:1040, in SSLSocket._create(cls, sock, server_side, do_handshake_on_connect, suppress_ragged_eofs, server_hostname, context, session)
1039 raise ValueError("do_handshake_on_connect should not be specified for non-blocking sockets")
-> 1040 self.do_handshake()
1041 except (OSError, ValueError):
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/ssl.py:1309, in SSLSocket.do_handshake(self, block)
1308 self.settimeout(None)
-> 1309 self._sslobj.do_handshake()
1310 finally:
SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1131)
During handling of the above exception, another exception occurred:
URLError Traceback (most recent call last)
Cell In[4], line 3
1 # retrieve structure from the Protein Data Bank
2 pdb_id = "2ito"
----> 3 structure = Structure.from_pdbid(pdb_id)
4 # element information maybe missing, but important for subsequent PDBQT conversion
5 if not hasattr(structure.atoms, "elements"):
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/site-packages/opencadd/structure/core.py:20, in Structure.from_pdbid(cls, pdbid)
16 @classmethod
17 def from_pdbid(cls, pdbid):
18 import mmtf
---> 20 return cls(mmtf.fetch(pdbid))
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/site-packages/mmtf/api/default_api.py:84, in fetch(pdb_id)
79 """Return a decoded API to the data from a PDB id.
80
81 :param pdb_id: the input PDB id
82 :return an API to decoded data """
83 decoder = MMTFDecoder()
---> 84 decoder.decode_data(get_raw_data_from_url(pdb_id))
85 return decoder
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/site-packages/mmtf/api/default_api.py:56, in get_raw_data_from_url(pdb_id, reduced)
54 request = urllib2.Request(url)
55 request.add_header('Accept-encoding', 'gzip')
---> 56 response = urllib2.urlopen(request)
57 if response.info().get('Content-Encoding') == 'gzip':
58 data = ungzip_data(response.read())
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:222, in urlopen(url, data, timeout, cafile, capath, cadefault, context)
220 else:
221 opener = _opener
--> 222 return opener.open(url, data, timeout)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:525, in OpenerDirector.open(self, fullurl, data, timeout)
522 req = meth(req)
524 sys.audit('urllib.Request', req.full_url, req.data, req.headers, req.get_method())
--> 525 response = self._open(req, data)
527 # post-process response
528 meth_name = protocol+"_response"
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:542, in OpenerDirector._open(self, req, data)
539 return result
541 protocol = req.type
--> 542 result = self._call_chain(self.handle_open, protocol, protocol +
543 '_open', req)
544 if result:
545 return result
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:502, in OpenerDirector._call_chain(self, chain, kind, meth_name, *args)
500 for handler in handlers:
501 func = getattr(handler, meth_name)
--> 502 result = func(*args)
503 if result is not None:
504 return result
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:1397, in HTTPSHandler.https_open(self, req)
1396 def https_open(self, req):
-> 1397 return self.do_open(http.client.HTTPSConnection, req,
1398 context=self._context, check_hostname=self._check_hostname)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:1357, in AbstractHTTPHandler.do_open(self, http_class, req, **http_conn_args)
1354 h.request(req.get_method(), req.selector, req.data, headers,
1355 encode_chunked=req.has_header('Transfer-encoding'))
1356 except OSError as err: # timeout error
-> 1357 raise URLError(err)
1358 r = h.getresponse()
1359 except:
URLError: <urlopen error EOF occurred in violation of protocol (_ssl.c:1131)>
Expected behavior
Excuse me, when will this problem be fixed?
Screenshots
Hello, Doctors, I have encountered a network problem, I have not fixed it.
Describe the bug
The problem is described as follows :
TO15 _ protein _ ligand _ docking
1354 h.request ( req.get _ method ( ), req.selector, req.data, headers.
1355 encode _ chunked = req.has _ header ( ' Transfer-encoding ' ) )
To Reproduce
SSLEOFError Traceback (most recent call last)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:1354, in AbstractHTTPHandler.do_open(self, http_class, req, **http_conn_args)
1353 try:
-> 1354 h.request(req.get_method(), req.selector, req.data, headers,
1355 encode_chunked=req.has_header('Transfer-encoding'))
1356 except OSError as err: # timeout error
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:1256, in HTTPConnection.request(self, method, url, body, headers, encode_chunked)
1255 """Send a complete request to the server."""
-> 1256 self._send_request(method, url, body, headers, encode_chunked)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:1302, in HTTPConnection._send_request(self, method, url, body, headers, encode_chunked)
1301 body = _encode(body, 'body')
-> 1302 self.endheaders(body, encode_chunked=encode_chunked)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:1251, in HTTPConnection.endheaders(self, message_body, encode_chunked)
1250 raise CannotSendHeader()
-> 1251 self._send_output(message_body, encode_chunked=encode_chunked)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:1011, in HTTPConnection._send_output(self, message_body, encode_chunked)
1010 del self._buffer[:]
-> 1011 self.send(msg)
1013 if message_body is not None:
1014
1015 # create a consistent interface to message_body
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:951, in HTTPConnection.send(self, data)
950 if self.auto_open:
--> 951 self.connect()
952 else:
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/http/client.py:1425, in HTTPSConnection.connect(self)
1423 server_hostname = self.host
-> 1425 self.sock = self._context.wrap_socket(self.sock,
1426 server_hostname=server_hostname)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/ssl.py:500, in SSLContext.wrap_socket(self, sock, server_side, do_handshake_on_connect, suppress_ragged_eofs, server_hostname, session)
494 def wrap_socket(self, sock, server_side=False,
495 do_handshake_on_connect=True,
496 suppress_ragged_eofs=True,
497 server_hostname=None, session=None):
498 # SSLSocket class handles server_hostname encoding before it calls
499 # ctx._wrap_socket()
--> 500 return self.sslsocket_class._create(
501 sock=sock,
502 server_side=server_side,
503 do_handshake_on_connect=do_handshake_on_connect,
504 suppress_ragged_eofs=suppress_ragged_eofs,
505 server_hostname=server_hostname,
506 context=self,
507 session=session
508 )
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/ssl.py:1040, in SSLSocket._create(cls, sock, server_side, do_handshake_on_connect, suppress_ragged_eofs, server_hostname, context, session)
1039 raise ValueError("do_handshake_on_connect should not be specified for non-blocking sockets")
-> 1040 self.do_handshake()
1041 except (OSError, ValueError):
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/ssl.py:1309, in SSLSocket.do_handshake(self, block)
1308 self.settimeout(None)
-> 1309 self._sslobj.do_handshake()
1310 finally:
SSLEOFError: EOF occurred in violation of protocol (_ssl.c:1131)
During handling of the above exception, another exception occurred:
URLError Traceback (most recent call last)
Cell In[4], line 3
1 # retrieve structure from the Protein Data Bank
2 pdb_id = "2ito"
----> 3 structure = Structure.from_pdbid(pdb_id)
4 # element information maybe missing, but important for subsequent PDBQT conversion
5 if not hasattr(structure.atoms, "elements"):
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/site-packages/opencadd/structure/core.py:20, in Structure.from_pdbid(cls, pdbid)
16 @classmethod
17 def from_pdbid(cls, pdbid):
18 import mmtf
---> 20 return cls(mmtf.fetch(pdbid))
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/site-packages/mmtf/api/default_api.py:84, in fetch(pdb_id)
79 """Return a decoded API to the data from a PDB id.
80
81 :param pdb_id: the input PDB id
82 :return an API to decoded data """
83 decoder = MMTFDecoder()
---> 84 decoder.decode_data(get_raw_data_from_url(pdb_id))
85 return decoder
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/site-packages/mmtf/api/default_api.py:56, in get_raw_data_from_url(pdb_id, reduced)
54 request = urllib2.Request(url)
55 request.add_header('Accept-encoding', 'gzip')
---> 56 response = urllib2.urlopen(request)
57 if response.info().get('Content-Encoding') == 'gzip':
58 data = ungzip_data(response.read())
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:222, in urlopen(url, data, timeout, cafile, capath, cadefault, context)
220 else:
221 opener = _opener
--> 222 return opener.open(url, data, timeout)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:525, in OpenerDirector.open(self, fullurl, data, timeout)
522 req = meth(req)
524 sys.audit('urllib.Request', req.full_url, req.data, req.headers, req.get_method())
--> 525 response = self._open(req, data)
527 # post-process response
528 meth_name = protocol+"_response"
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:542, in OpenerDirector._open(self, req, data)
539 return result
541 protocol = req.type
--> 542 result = self._call_chain(self.handle_open, protocol, protocol +
543 '_open', req)
544 if result:
545 return result
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:502, in OpenerDirector._call_chain(self, chain, kind, meth_name, *args)
500 for handler in handlers:
501 func = getattr(handler, meth_name)
--> 502 result = func(*args)
503 if result is not None:
504 return result
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:1397, in HTTPSHandler.https_open(self, req)
1396 def https_open(self, req):
-> 1397 return self.do_open(http.client.HTTPSConnection, req,
1398 context=self._context, check_hostname=self._check_hostname)
File /opt/anaconda3/envs/teachopencadd/lib/python3.8/urllib/request.py:1357, in AbstractHTTPHandler.do_open(self, http_class, req, **http_conn_args)
1354 h.request(req.get_method(), req.selector, req.data, headers,
1355 encode_chunked=req.has_header('Transfer-encoding'))
1356 except OSError as err: # timeout error
-> 1357 raise URLError(err)
1358 r = h.getresponse()
1359 except:
URLError: <urlopen error EOF occurred in violation of protocol (_ssl.c:1131)>
Expected behavior
Excuse me, when will this problem be fixed?
Screenshots