Hi RDKitters,
I've been looking at using RDKit to view molecules in PyMol as Greg showed at
the UGM. I found the test file in the source and started firstly to replicate
this, which threw and error so I then tried to run the test "python
Code/RDKit/RDKit_2012_06_1/rdkit/Chem/Subshape/testCombined.py" and this also
threw the same error which is below
Traceback (most recent call last):
File "testCombined.py", line 30, in <module>
v = MolViewer()
File "/usr/local/lib/python2.7/site-packages/rdkit/Chem/PyMol.py", line 29,
in __init__
serv.ping()
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xmlrpclib.py",
line 1224, in __call__
return self.__send(self.__name, args)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xmlrpclib.py",
line 1575, in __request
verbose=self.__verbose
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xmlrpclib.py",
line 1264, in request
return self.single_request(host, handler, request_body, verbose)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xmlrpclib.py",
line 1292, in single_request
self.send_content(h, request_body)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xmlrpclib.py",
line 1439, in send_content
connection.endheaders(request_body)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 951, in endheaders
self._send_output(message_body)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 811, in _send_output
self.send(msg)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 773, in send
self.connect()
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py",
line 754, in connect
self.timeout, self.source_address)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py",
line 571, in create_connection
raise err
So first question is, can anyone help me to get this working? Second question,
is there a way to push RDKit molecules from C++ programs into PyMol?
Also while I'm bothering you Greg (as I assume you will read this), currently
the smiles reader will read dummy atoms if they are [*] however neither [R] or
[A]. Is there anyway the smiles reader can read [R] molecules? It's pretty
simple to work round, but I thought it might be nice to go in RDKit
Thanks in advance.
Best,
Nick
Nicholas Firth, Ph.D. Student
Ph.D. Student
Institute of Cancer Research
15 Cotswold Road
Belmont
Surrey
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