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haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.
https://haddocking.github.io/pdb-tools/
Apache License 2.0
378 stars 113 forks source link

enhancement of pdb_wc #53

Closed joaomcteixeira closed 4 years ago

joaomcteixeira commented 4 years ago

After #51, we can consider increasing the detail of the pdb_wc report to enhance the user experience of both the command-line user as well as the pdb-tools web interface @brianjimenez is developing.

If I recall properly, we discussed altogether in the emails that pdb_wc could also report, for example, on the chain IDs, residue number ranges and atom ranges. This would facilitate the interaction of the user with the other tools such as pdb_chain.

I take no full credit for this idea, I am just registering an idea discussed by all which I found really interesting.

@brianjimenez how could this be integrated in the web interface? Do you find it useful for pdb_wc to do this? Or should it be another tool to do it?

I can take this if you all agree with the implementation.

brianjimenez commented 4 years ago

At the moment, not using pdb_wc for parsing, but BioPython library as we already have it installed for other services. I think pdb_wc should be focused on what users at cli level would need, no need to couple it for the moment with the web front-end.

JoaoRodrigues commented 4 years ago

51 does this already: e.g. pdb_wc -c it prints the chain details. The default pdb_wc prints an overall summary, which I thought was cleaner than having a very long output. Did you mean something different?

joaomcteixeira commented 4 years ago

Ah! I completely missed that.

I suggest changing slightly the documentation, currently it reads:

"Several options are available to produce only partial summaries:"

This only word mislead me. My bad. It led me to think that those options would reduce the default report instead of enhancing or providing more detail for specific sections.

Could we changed it to?:

"Several options are available to produce detailed partial summaries:"

JoaoRodrigues commented 4 years ago

Fixed by #59.

We should also think of a github action to update the webpage automatically..