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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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Remove REMARK and general info lines #11

Closed joaomcteixeira closed 5 years ago

joaomcteixeira commented 5 years ago

I found myself today removing the REMARK and info lines manually from a series of PDB files.

Should there be a pdb_delinfo.py tool that keeps only lines from coordinates and connectivity ? If you agree, assign me for the task.

JoaoRodrigues commented 5 years ago

pdb_keepcoord? :)

joaomcteixeira commented 5 years ago

Apologies for that. It is difficult to have all tools in memory, I actually read over the list of tools a two or three times before submitting this issue to be sure it was not present, yet I didn't identified it.

Does it make sense to rename it? If what I look for is to remove A, why the tool name is keep B?

May be it happens only to me. Now you can see me as a user :-P.

JoaoRodrigues commented 5 years ago

We have 'sel' and 'del', usually for tools that do opposite tasks. Since there's no 'delcoord' and it doesn't make sense, I opted to call this one differently. I thought keep coord (as in, coordinate section) would be clear enough, apparently not :)

joaomcteixeira commented 5 years ago

I vote for pdb_deltitle, or pdb_delinfo :)

amjjbonvin commented 5 years ago

Confusing names to my opinion. pdb_keepcoord is clean and clear

JoaoRodrigues commented 5 years ago

I agree with @amjjbonvin , sorry .. The section of the file format is called 'coordinates'. At best we could call it pdb_delremarks but it's not so clear for those unfamiliar with the PDB format.