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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
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RFE: enhance pdb_selres to allow selection of random residue list #34

Closed truatpasteurdotfr closed 5 years ago

truatpasteurdotfr commented 5 years ago

Is your tool request related to a problem? Please describe. I would like to select any list of residue from a pdb file.

Describe the solution you'd like

pdb_selres 1,10,43,8 my.pdb would ouput the 1,8,10 and 43rd residues from the pdb file.

Does any of the existing tools or a combination of them do what you want? I can iterate with pdb_selres and extract each number in loop and concatenate the resulting output files

Remember Each pdb-tools should do one and one job only. If you have to describe what you want using an and, probably it is the job for at least two tools. We want simple tools that can be combined, for flexibility.

mtrellet commented 5 years ago

Hello @truatpasteurdotfr, thanks for the suggestion!

Sounds like a common usage for the tool. In the meantime, the overhead to loop over the desired residue IDs is not much. What's your take on this @JoaoRodrigues, @joaomcteixeira ?

JoaoRodrigues commented 5 years ago

On it, thanks! For some reason I was not getting email notifications ...

JoaoRodrigues commented 5 years ago

This has been addressed by #37

You can now do what you request, except that it isn't the 1st, 2nd, 3rd residues, but residue numbers 1, 2, and 3 (this was the original desired behavior anyway).