InSty: NameError: name 'Interactions' is not defined #2086
Replies: 11 comments
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Did you install the developed version of ProDy (from GitHub: https://github.com/prody/ProDy)? On the GitHub version, everything is working: In [1]: from prody import * |
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Yes and in the released versions it is not. We have the same issue in #1924 |
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In case someone does not know what to do:
Done. Enjoy using InSty and WatFinder. |
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Thank you. Re-install the developed version works for me. @> PDB file is found in working directory (5kqm.pdb). File /tools/ProDy/prody/proteins/interactions.py:2731, in Interactions.calcProteinInteractions(self, atoms, **kwargs) File /tools/ProDy/prody/proteins/interactions.py:434, in calcHydrogenBonds(atoms, **kwargs) File /tools/ProDy/prody/measure/contacts.py:306, in findNeighbors(atoms, radius, atoms2, unitcell, seqsep) File /tools/ProDy/prody/measure/contacts.py:217, in iterNeighbors(atoms, radius, atoms2, unitcell, seqsep) File /tools/ProDy/prody/kdtree/kdtree.py:179, in KDTree.call(self, radius, center) File /tools/ProDy/prody/kdtree/kdtree.py:259, in KDTree.getIndices(self) File /tools/ProDy/prody/kdtree/kdtree.py:291, in KDTree.getCount(self) AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count' |
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That's interesting. In [1]: from prody import * @> Connecting wwPDB FTP server RCSB PDB (USA). |
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Try this python setup.py build_ext --inplace --force |
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Building the C extensions should fix kdtree and using inplace and -e should make sure python can find them |
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problem solved! |
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Great. Let’s keep it open so other people see it |
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I believe we now have better build instructions inside prody so that this works but we need to double check |
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This should now be solved and released |
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Which module is this Interactions class dependent on?
interactions = Interactions()http://www.bahargroup.org/prody/tutorials/insty_tutorial/insty_tutorial.pdf
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