[Biopython] Overhauling of Bio.PDB module
Patrick Kunzmann
padix.kleber at gmail.com
Mon Oct 21 10:20:31 UTC 2019
Hello Joao,
sounds like a good idea. How do I join the 3DSIG Slack workspace?
Best regards,
Patrick Kunzmann
On 16.10.19 19:54, João Rodrigues wrote:
> Hi Patrick,
>
> Thank you again for bringing this up. I do agree with you that this is
> a necessity.
>
> When Bio.PDB first showed up, there were not so many Python libraries
> out there for molecular structures. Now there are a few, so we should
> think carefully about what features we want to offer - not to overlap
> with others and duplicate efforts. My opinion is that BioPython is
> very good at generally handling structures, allowing you do change
> fields, select bits, etc, and do very simple calculations like
> distances or superimpositions. At the CodeFest in Basel, we talked
> that it would be awesome to have a selection language built-in
> bioptyhon to allow us to do something like `mol.select("chain
> A").write("chain_A.pdb")`. This also requires an overhaul of the data
> structures we use to store atomic data.
>
> I have some time in the next few months I could spare to work on this.
> Interfacing with Biotite would be interesting as well (as well as with
> other packages). I'll start a #biopython channel at the 3DSIG slack so
> that we can coordinate efforts. How does this sound?
>
> Cheers and again, thanks for bringing this up!
>
> Joao
>
> Patrick Kunzmann <padix.kleber at gmail.com
> <mailto:padix.kleber at gmail.com>> escreveu no dia quarta, 16/10/2019
> à(s) 09:38:
>
> Hello Biopythoneers,
>
> at the BOSC this year we talked about overhauling the Bio.PDB module.
> The problem is that currently the atom coordinates are stored in a
> separate NumPy array for each atom. This design prevents efficient
> computation of all kinds of analyses (distances, angles,
> superimpositions, etc.). One proposed possible solution to this
> problem,
> we talked about, was to put the coordinates of the entire
> structure in
> one NumPy array, and let the Atom, Residue, Chain and Structure
> objects
> point to positions in this array. The benefit of this approach is
> that
> functions could be directly applied onto the entire array, harnessing
> the power of vectorization.
>
> For the analysis we could adapt the vectorized functions from the
> Python
> package Biotite, a project I am currently working on
> (https://www.biotite-python.org/apidoc/biotite.structure.html).
> Usually,
> these functions already accept the coordinates as NumPy array, so I
> think only a few tweaks would be necessary for every function.
>
> However, we would require one person or a small team who makes the
> effort to implement the new structure types and adapts the analysis
> functions. I could offer a pair of helping hands in the adaption
> of the
> analysis functions, but I don't have the time for anything more.
>
> So the question is: Is there anyone out there, who is willing to
> do this
> work? Alternatively, I would propose to write a 'bridge' package
> between
> Biopython and Biotite, that converts the Biopython structure
> representation into the representation in Biotite and vice versa. I
> think, this solution is less elegant but would also require less
> effort.
>
> Best regards
>
> Patrick Kunzmann
>
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