[Biopython] Deprecating Bio.Crystal

[Peter Cock]

Hello all,

We've merged https://github.com/biopython/biopython/pull/2272
declaring Bio.Crystal as obsolete, but would there be any objection
to moving directly to declaring it deprecated with a warning on
import?

https://biopython.org/wiki/Deprecation_policy

Assuming no objections, we'll likely do that in early October.

Peter

On Wed, Sep 18, 2019 at 1:07 AM Sergio Valqui <svalqui at unimelb.edu.au> wrote:
>
>
> Hi All,
>
>
> There is no implementation of the classes defined on Bio.Crystal on Biopython, so the module will be removed.
>
>
> NDB Only files should be open with the Bio.PDB Module which will handle the HETATM records; Today Biopython uses Bio.PDB to work with PDB files, any work related should be place under Bio.PBD.
>
>
> Bio.Crystal.Hetero sustitute is Bio.PDB.Atom
>
> Bio.Crystal.Chain sustitute is Bio.PDB.Chain
>
> Bio.Crystal.Crystal sustiture is Bio.PDB.Structure
>
>
> Using Bio.PDB you can navigate the file data as below.
>
>
> from Bio.PDB.PDBParser import PDBParser
>
> parser = PDBParser(PERMISSIVE=1)
>
> # PDB NDB Only file
>
> structure = parser.get_structure(“001”, "001_msd.pbd")
>
> for model in structure:
>
>     print(‘Model ‘,model)
>
>     for chain in model:
>
>         print('Chain ', chain)
>
>         for residue in chain:
>
>             print('Res ', residue)
>
>             for atom in residue:
>
>                 print('Atom ', atom)
>
>
> Since there is no implementation of the classes and their function are already covered by Bio.PDB, Bio.Crystal will be deprecated.
>
>
> If you use BioCrystal please let us now, by replying to the list of commenting on the below Pull Request.
>
>
> https://github.com/biopython/biopython/pull/2272
>
>
> Regards,
>
> Sergio.
>
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