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prevent un-necessary recalculation of RMSD matrix #20

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prevent un-necessary recalculation of RMSD matrix #20

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14 changes: 9 additions & 5 deletions pyext/src/exhaust.py
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Original file line number Diff line number Diff line change
Expand Up @@ -218,16 +218,20 @@ def main():

print("Size of conformation matrix", conforms.shape)

if not args.skip_sampling_precision:
# get_rmsds_matrix modifies conforms, so save it to a file and restore
# afterwards (so that we retain the original IMP orientation)
numpy.save("conforms", conforms)
# get_rmsds_matrix modifies conforms, so save it to a file and restore
# afterwards (so that we retain the original IMP orientation)
numpy.save("conforms", conforms)

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Won't this file then be out of date and result in a hard-to-diagnose issue (matrix is for the first run but is used in the second run)?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.

print("Computing RMSD matrix...")
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.

print("Size of RMSD matrix (flattened):", inner_data.shape)
del conforms
conforms = numpy.load("conforms.npy")
os.unlink('conforms.npy')
else:
print("Loading saved RMSD matrix")

from pyRMSD.matrixHandler import MatrixHandler
mHandler = MatrixHandler()
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