prevent un-necessary recalculation of RMSD matrix #20
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shruthivis
approved these changes
Nov 19, 2021
benmwebb
requested changes
Dec 2, 2021
| inner_data = rmsd_calculation.get_rmsds_matrix( | ||
| conforms, args.mode, args.align, args.cores, symm_groups) | ||
| conforms, args.mode, args.align, args.cores, symm_groups) |
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This diff seems unnecessary since you don't change any logic, only whitespace. In fact, it may even cause flake8 to complain.
| # afterwards (so that we retain the original IMP orientation) | ||
| numpy.save("conforms", conforms) | ||
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| if not os.path.isfile("Distances_Matrix.data.npy"): |
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What happens if the user
- runs a simulation
- does analysis, creating
Distances_Matrix.data.npy - goes back and runs a new simulation
- does a 2nd round of analysis?
Won't this file then be out of date and result in a hard-to-diagnose issue (matrix is for the first run but is used in the second run)? If so, one fix might be to stat the matrix/RMF/PDB files and only skip the matrix creation if the .npy file is newer than all RMF/PDB. Another would be to never reuse your cached matrix unless the user explicitly requests it with a --use-cache option or similar. Always better to err on the side of caution with caching.
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all-by-all RMSD distance matrix is calculated only when sampling_precision calculated is requested. However, I have a use-case where I don't want to calculate sampling precision, but rather have prior information about the cluster threshold. I want to just cluster the models based on this threshold, and obtain the cluster precision. But model precision calculation without doing sampling precision calculation is possibly only when the
Distances_Matrix.data.npyfile is already created and contains the RMSD distance matrix.So, I changed this to the RMSD distance matrix being calculated and stored in
Distances_Matrix.data.npyalways (irrespective of whether sampling precision calculation is skipped or not), except when the script is being re-run and that file already exists.