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Discngine / fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).
MIT License
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Non ASCII character in atom_site.type_symbol written in pocket files #141

Closed PeyratG closed 3 months ago

PeyratG commented 3 months ago

Describe the bug fpocket writes non ASCII characters in pocket files when there is a Se in the structure. In the field _atom_site.type_symbol

To Reproduce Steps to reproduce the behavior:

  1. run fpocket command fpocket -f 6a5k.cif -d -w cif -l 1

Expected behavior Getting pocket files only ASCII characters, and Se as type symbol for Se instead of Se<non-ascii>MSE

Screenshots image

Desktop (please complete the following information):

Additional context I run fpocket from its image with the command export UID && docker run -v $(pwd)/data/:/data/ -u $UID:$UID fpocket/fpocket fpocket -f /data/my_structures/6a5k.cif -d -w cif -l 1

File to reproduce : 6a5k.cif.zip

PeyratG commented 3 months ago

I also run fpocket with the same options on the PDB structure 6whl which writes the ASCII control character stx in one of the pocket files generated: image

pschmidtke commented 3 months ago

seems to happen only in the linux container:

image

this is what I get on osx compiled with clang:

image