[Biopython-dev] pull request: Handle MMCIF with multiple models (closes 2943)

[Lenna Peterson]

On Mon, Apr 23, 2012 at 4:10 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
>
> Ack, I didn't look at that closely enough. Check out this patch to see
> the current situation:
> https://github.com/biopython/biopython/commit/abdab1a1132ec811f9636f8ba805bbb6cda6dbe9
>
> The models associated with a structure are numbered with a sequential
> integer id, starting from 0. It's always been like that in our PDB
> parser and we haven't changed it. To ensure that model numbers
> specified in the PDB file are preserved when writing the PDB back to
> file, the above patch introduced a new attribute on the Model object
> called serial_num (also an integer, equal to model.id unless specified
> otherwise). That attribute is only used when writing a new PDB file;
> Model.__getitem__ still uses Model.id as before.
>
> Perhaps that's surprising now that we read the serial numbers, but it
> kept backward compatibility. Plus, it preserves list-like behavior
> (item access via integers), even though the models are actually stored
> in a dict.
>
> So!
>
> In the mmCIF parser, the calls to structure_builder.init_model should
> be given two arguments instead of one: an integer id counting from 0,
> and then another integer (probably) containing the model "serial
> number" specified in the mmCIF file. In the event that an mmCIF file
> doesn't specify the model number, the serial number should be the same
> as the sequential id.
>
> Cool? This will also help us convert between PDB and mmCIF formats in
> the future.
>
> As for accessing the models by their serial number, using string keys
> seems like an effective workaround, but still obviously a workaround
> rather than an ideal situation. Let's discuss that a little more,
> perhaps file another bug when we've reached some consensus.
>
> Best,
> Eric


Hi Eric,

I believe I've implemented the model_id/serial_id system found in PDB:

https://github.com/lennax/biopython/commit/b453a2968d18e157aac1f99f9f3cfeb4c09bc77d

Please let me know if you think that looks right. I couldn't find an
mmCIF file without a model column to test, but I believe in that case
it will assign model_id and serial_id to 0. Would that be the correct
behavior?

I also modified the unit test to check the model serial_num.
https://github.com/lennax/biopython/commit/b0443e788438b8ff72979c7a3bc0e531d4cd5cf6

Currently serial_num is int() of the CIF model column. Regarding
access by string serial_num, I am concerned that the int/string access
would be too subtle (structure[0] == structure['1']; structure[1] ==
structure['2']?). Perhaps an accessor function? i.e.
structure.get_model('1')

Let me know if you think I should write get_model() or something along
those lines.

Lenna