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Support writing multiple `AtomArray` to structure file

Open dnlbauer opened this issue 4 years ago • 5 comments

The pdb specification allows pdb files with multiple different models. biotite can read these files, but there is no way to write them.

dnlbauer avatar Sep 10 '19 12:09 dnlbauer

You are right, this is definitely something Biotite should support. This involves not only the PDB format but all formats supported by Biotite. However, solving this issue requires quite a bunch of work, so it may take some time until I get to fix this.

padix-key avatar Sep 10 '19 12:09 padix-key

Is this issue still a problem? When I try to write an AtomArrayStack to a pdb file I correctly get all models written to the file.

ncoish avatar Feb 06 '23 15:02 ncoish

This issue is about writing different models in terms of different atoms per model (e.g. an additional atom), not just different coordinates. In other words the problem is that a list of AtomArray cannot be given to set_structure(), although the format specification would allow it.

padix-key avatar Feb 06 '23 16:02 padix-key

The issue title is a bit misleading, so I will clarify it.

padix-key avatar Feb 06 '23 16:02 padix-key

This issue is about writing different models in terms of different atoms per model (e.g. an additional atom), not just different coordinates. In other words the problem is that a list of AtomArray cannot be given to set_structure(), although the format specification would allow it.

Understood. Thanks for the clarification!

ncoish avatar Feb 06 '23 16:02 ncoish