Activity for WISP
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jdurrant posted a comment on discussion General Discussion
Hi Wesley. Wanted to let you know that the latest version is posted here: https://git.durrantlab.pitt.edu/jdurrant/wisp All the best.
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Hi Douglas. Wanted to let you know that the latest version is posted here: https://git.durrantlab.pitt.edu/jdurrant/wisp All the best.
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Douglas Houston posted a comment on discussion General Discussion
That's great! I'd be very interested in trying out this new version ...
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Wesley posted a comment on discussion General Discussion
Yes, feel free to include me in the CONTRIBUTORS file if the patch checks out. That would be great! Hopefully it will help others. It's always frustrating when api changes in dependencies break previously functional packages and libraries. All the best, -Dr. Wesley Botello-Smith On Tue, Jul 30, 2019 at 5:06 PM jdurrant jdurrant@users.sourceforge.net wrote: Hi Wesley. Just wanted to let you know that I got your code. Much thanks for this contribution! I've gotten this version running on Python 3 as...
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Hi Wesley. Just wanted to let you know that I got your code. Much thanks for this contribution! I've gotten this version running on Python 3 as well. We're going to test it intnerally for a bit and then publish it for others to use. Can I include you in the CONTRIBUTORS.md file? All the best.
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Hi, I tried sending the code you, but I got a reply that the message was not delivered: Delivery has failed to these recipients or groups: Your message wasn't delivered due to a permission or security issue. It may have been rejected by a moderator, the address may only accept email from certain senders, or another restriction may be preventing delivery. i am going to attache the code here. I have just tested it on a new iMac workstation working with a fresh install of conda (4.6.14, via anaconda),...
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Wesley, please forgive me for my delay in getting back to you! My sourceforge emails were going to my old UCSD email address, but I'm now at the University of Pittsburgh. Wonderful that you were able to patch the code to work with the latest version of networkx. Would you mind emailing your updated code to me at durrantj at pitt dot edu? All the best.
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SUCCESS! After the above bug fixes, wisp.py is now sufficiently compatible with networkx >= 2.0 such that it can successfully run the 'simple-example' that comes with the installation. Can anyone point me to who to contact to construct a patch / update / bug fix/ etc?
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After the above fix, another quirk of newer networkx versions was found. Line 766: temp[0]=temp[0]+G.edge[temp[-2]][temp[-1]]['weight'] needs to be changed to temp[0]=temp[0]+G.edges[temp[-2],temp[-1]]['weight'] in order to accomadate the new syntax for edge (or edges in v>2.0) access
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The above fix seems to just open up a related problem... it seems that previous versions of networkx use 'list' objects as return values for the 'neighbors' function, but newer versions use 'dictionary-keyiterator' objects. So the solution is to wrap the result being fed into 'node_neighbors' in 'list()' e.g. line 761 node_neighbors=G.neighbors(paths_growing_out_from_source[i][-1]) becomes node_neighbors=list(G.neighbors(paths_growing_out_from_source[i][-1]))
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It seems that the error is again do to a different signature. Some searching reveals that this was written for networkx versions below 2.0. New versions of networkx (2.0 and up) have had several major changes, such as the signature of the 'Graph' constructor. There are 2 uses of this constructor in 'wisp.py' line 1216 and line 1001 in both cases, 'Graph(data=' needs to be replaced with 'Graph(incoming_graph_data=' when using networkx >= 2.0 Fixing these issues leads to a new bug, however: On line...
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The bug fix seems to work and the shortest path is computed, however, a new error is coming up after 'Starting serial portion of path-finding algorithm': # Calculating paths... # Calculating the shortest path between any of the specified sources and any of the specified sinks... # The shortest path has length 1.136358953726239 # Identifying the cutoff required to produce 15 paths... # Testing the cutoff 1.136358953726239... # Starting serial portion of path-finding algorithm (will run for 5.0 seconds)......
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I think I may have tracked part of the error. It looks like wisp.py is using G=networkx.Graph(data=correlation_matrix However, under networkx 2.2, the signature for networkx.Graph is: 'networkx.Graph(self, incoming_graph_data=None, **attr)' rather than 'networkx.Graph(self,data=None, **attr)' as it is in some versions... I am checking to see if updating this line will fix the bug
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I am attempting to run the simple_example for the lastest version of wisp, but I am getting the following error: # Calculating paths... # Calculating the shortest path between any of the specified sources and any of the specified sinks... Traceback (most recent call last): File "../wisp.py", line 1464, in <module> paths = GetPaths(correlation_matrix, sources, sinks, parameters, correlation_matrix_object.average_pdb.residue_identifiers_in_order) File "../wisp.py", line 1006, in __init__ shortest_length,...
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I am attempting to run the simple_example for the lastest version of wisp, but I am getting the following error: # Calculating paths... # Calculating the shortest path between any of the specified sources and any of the specified sinks... Traceback (most recent call last): File "../wisp.py", line 1464, in <module> paths = GetPaths(correlation_matrix, sources, sinks, parameters, correlation_matrix_object.average_pdb.residue_identifiers_in_order) File "../wisp.py", line 1006, in __init__ shortest_length,...
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Amin Sagar posted a comment on discussion General Discussion
Hello. I am trying to use WISP to analyze my MD simulations. But I keep getting the following error. File "C:\Python27\lib\site-packages\networkx\algorithms\shortest_paths\weighted.py", line 794, in _dijkstra_multisource for u, e in G_succ[v].items(): KeyError: 9 I have tried on both Linux and Windows system. I am using Python 27 with latest versions of numpy, scipy and networkx. I would be really grateful for any help. Regards, Amin.
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WISP released /1.0/wisp-1.0.zip
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