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

[Lenna Peterson]

On Tue, Apr 24, 2012 at 11:38 AM, Eric Talevich <eric.talevich at gmail.com> wrote:
>
> 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


Eric,

Okay, I've changed the bad model num generic warning to a
PDBConstructionException.

New pull request to get MMCIF to the same state as PDB:
https://github.com/biopython/biopython/pull/36

So are chains accessed by 0, 1, 2 or by A, B, C?

Lenna