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

[Eric Talevich]

On Tue, Apr 24, 2012 at 12:25 AM, Lenna Peterson <arklenna at gmail.com> wrote:
> 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

I left another nitpick on b453a, but besides that it looks exactly right to me.

The string/int distinction would indeed be weird, especially for newer
Python users coming from Perl or Javascript. I don't see a direct
analogue for get_model(serial_num) in the other Entities (Residue,
Chain, Model, Structure), so I'm inclined to put off the decision for
now (i.e. leave it out of this patch set).

-Eric