[Biopython] RFC on WIP - internal coordinates, structure / prediction folk please read

[João Rodrigues]

Hi Rob,

This is an extremely interesting contribution. Thanks for the time you took
to write this. It would be very useful to have a conversion from cartesian
to internal coordinates, as far as I know, there isn't a tool that does
that (they usually do one way or the other). What is the convention you use
for the conversion? How do you handle say, chain breaks or gaps? Is there a
publication or small write-up you can provide about this (maybe it's in the
documentation and I missed it)?

Cheers,

João

rob miller <rob.miller.gh at gmail.com> escreveu no dia terça, 9/04/2019 à(s)
06:09:

> Hi,
>
> This is a request for feedback on code I would like to contribute to
> Biopython.  I want to do more cleaning, testing, polishing and documenting
> before making a pull request, so don't worry yet :-).  This post is to
> query whether there's sufficient interest to accept the facility into
> Biopython when I'm ready, hopefully gather some positive feedback and
> ideas, and to make it publicly available now as it's working for me for
> most structures.
>
> This branch ( https://github.com/rob-miller/biopython/tree/rtm-pic ) adds
> infrastructure for internal coordinates under a .pic attribute on Bio.PDB
> Chain and Residue objects.  'Internal coordinates' means phi, psi, omega,
> chi<X> dihedral angles, all bond angles and bond lengths.  Internal
> coordinates can be read from a PDB structure and used to regenerate
> identical coordinate PDB chains (HETATMs not withstanding, although there
> is some support).
>
> While my primary application is to support structure prediction work,
> there are some useful side effects.  Probably most interesting is the
> ability to generate OpenSCAD files to 3D print protein structure models, as
> it uses the same algorithm for assembly of bond length, angle and dihedral
> angle data.  (Please be aware that the initial OpenSCAD rendering is
> reasonably quick, but the detailed rendering to generate an .stl file for
> printing can take hours depending on your hardware.)  Of lesser note,
> filtering options add support for removing Hydrogens from PDB structures,
> and obviously one can make Ramachandran plots and database projects looking
> at different subsets of chi rotamers and other aspects of protein
> structure.
>
> I've made a gist at
> https://gist.github.com/rob-miller/0be208b73fe2ab36fadeeef60831fc92
> to access the basic functionality.  Hopefully this is easy to get working
> in your hands, if you have a local pdb mirror there is a place to configure
> access to it near the beginning of the script.
>
> If you are playing with OpenSCAD and your protein has chain breaks (or you
> excised lysozyme from a GPCR), increase the -maxp cutoff in the gist
> options to treat the gap as an extra long peptide bond.
>
> All development so far has been exclusively on python3, so yes more
> versions to support.  I am aware of the related projects FragBuilder and
> PeptideBuilder.
>
> I hope you like it; please be gentle with me.
>
> Rob.
>
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