Tool to convert between atom names conventions

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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Tool to convert between atom names conventions #114

Closed joaomcteixeira closed 1 year ago

joaomcteixeira commented 2 years ago

Follows discussion on #113

For now, adds two conversion tables between:

BMRB/PDBv3/Amber
Old PDB

The input pdb atom name format is guessed on the fly, hence there is a bit of computation penalty.

TODO:

~~implement XPLOR~~
tests
improve docs
~~N-terminal Hs, also PRO~~
~~histidines~~
make trick to implement OT1 like atoms.

What are your thoughts?

Still, I think #113 is a valuable tool.

joaomcteixeira commented 2 years ago

I am checking and they are the same as xplor. One difference is that xplor (according to here) has HB2/HB1 swapped with 1HB/2HB with the other nomenclatures. Did you know anything about this for CNS?

Another important change is:

! CNS v1.3 (27-Feb-10): changed OT1, OT2 to O, OXT, respectively. xplor keeps OT1 and OT2.

joaomcteixeira commented 2 years ago

I think this is it. tests okay in py27 and py38. @JoaoRodrigues have your say.

joaomcteixeira commented 2 years ago

A user from the forum is requesting this tool -> https://ask.bioexcel.eu/t/prodigy-fails-to-calculate-binding-energy-of-protein-protein-complex/3420/3

I think is it's a useful tool and we should merge it soon.

JoaoRodrigues commented 1 year ago

I'm gonna go ahead and close this since we discussed online that this falls a little out of the scope of the tools and requires a lot of maintenance (all the conversion schemes, etc need to be maintained).