[Biopython] Deprecating Bio.Crystal

[Sergio Valqui]

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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