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jr-marchand / caviar

// PROJECT PAUSED FOR NOW (lack of capacity) // Protein cavity identification and automatic subpocket decomposition
https://jr-marchand.github.io/caviar
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Crash if PDB is not conform with the PDB format (missing element column) #5

Open jr-marchand opened 4 years ago

jr-marchand commented 4 years ago

If a PDB is truncated and does not have the element column (column 77-78 of the PDB format), the function "find_protein_points_variablevolumn" in cavitydetect.py glitches.

It doesn't find any atom of the protein and prints out "CAVIAR does not find a cavity".

The selection tool in this function is based on element, there may be a work around with a selection based on atom "name".