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npolizzi / Combs

Convergent motifs for binding sites
MIT License
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Hi, can this project be deployed on Windows? #21

Open ptf010 opened 4 months ago

ptf010 commented 4 months ago

Hello Nicholas, can this project be deployed on Windows? thanks, ptf010

npolizzi commented 4 months ago

Hi, I would recommend using the published version of Combs2, which can be found in Version V2 of this Zenodo deposit: https://doi.org/https://doi.org/10.5281/zenodo.10653015. The code is written for linux and mac. You would need to install a linux partition on your Windows machine to use it, I would think.

ptf010 commented 4 months ago

Got it. Thanks a lot.
Hey there! Could you possibly tell me the difference between param_gly and param_ala files? Or how I should get them？ Thanks so much! ptf010

npolizzi commented 4 months ago

param_gly are parametric bundles with glycine residues, param_ala are parametric bundles with alanine residues

ptf010 commented 3 months ago

Hello I'm getting this error. Can you help me see what's wrong? Thank you very much.

(env_combs) [tengfei416@mu01 biotin]$ python run_design.py /home/tengfei416/miniconda3/envs/env_combs/lib/python3.8/site-packages/numba/np/ufunc/parallel.py:355: NumbaWarning: The TBB threading layer requires TBB version 2019.5 or later i.e., TBB_INTERFACE_VERSION >= 11005. Found TBB_INTERFACE_VERSION = 6103. The TBB threading layer is disabled. warnings.warn(problem) Input directory: /home/tengfei416/combs/combs/tutorials/files/HPC_scripts/biotin/ Output directory: /home/tengfei416/combs/combs/tutorials/files/HPC_scripts/biotin/output/ @> 850 atoms and 1 coordinate set(s) were parsed in 0.01s. @> 1213 atoms and 1 coordinate set(s) were parsed in 0.01s. Traceback (most recent call last): File "run_design.py", line 287, in main() File "run_design.py", line 44, in main template.set_alpha_hull(pdb_ala, alpha=9) File "/home/tengfei416/combs/combs/combs2/design/template.py", line 228, in set_alpha_hull self.alpha_hull.set_coords(pdb_w_CB) File "/home/tengfei416/combs/combs/combs2/design/convex_hull.py", line 116, in set_coords self._set_coords(pdb) File "/home/tengfei416/combs/combs/combs2/design/convex_hull.py", line 124, in _set_coords self.coords = pdb.select('name CB or (resname GLY and name CA)').getCoords() File "/home/tengfei416/miniconda3/envs/env_combs/lib/python3.8/site-packages/prody/atomic/atomic.py", line 234, in select return SELECT.select(self, selstr, kwargs) File "/home/tengfei416/miniconda3/envs/env_combs/lib/python3.8/site-packages/prody/atomic/select.py", line 891, in select indices = self.getIndices(atoms, selstr, kwargs) File "/home/tengfei416/miniconda3/envs/env_combs/lib/python3.8/site-packages/prody/atomic/select.py", line 949, in getIndices torf = self.getBoolArray(atoms, selstr, **kwargs) File "/home/tengfei416/miniconda3/envs/env_combs/lib/python3.8/site-packages/prody/atomic/select.py", line 1000, in getBoolArray parser = self._getParser(selstr) File "/home/tengfei416/miniconda3/envs/env_combs/lib/python3.8/site-packages/prody/atomic/select.py", line 1096, in _getParser parser = pp.operatorPrecedence(expr, oplist) AttributeError: module 'pyparsing' has no attribute 'operatorPrecedence'