Fetching data with BCIF instead of MMTF?

[dominiquesydow]

Hello :)

With MMTF replaced now with BCIF (see announcement here), do you know the equivalent to the following code for the BCIF API?

import mmtf
mmtf.fetch(pdbid)

Thanks!

[piehld]

Hi @dominiquesydow,

There are a few options that I can share:

• The way I actually recommend working with BCIF (both reading and writing) is using our rcsb.utils.io package, which is a wrapper for py-mmcif, since it lets you easily switch between format types without having to import different modules. The README.md there offers some general examples on its usage: https://github.com/rcsb/py-rcsb_utils_io (in which, for the case of reading BCIF, you would use fmt="bcif").
• If you specifically want to use py-mmcif, though, you can take a look at the testBinaryCifReader.py file, e.g.: https://github.com/rcsb/py-mmcif/blob/f7c5f1498d687115a72618d79f176b7af26f5ea7/mmcif/tests/testBinaryCifReader.py#L91-L92. (Also note that there is a testBinaryCifWriter.py file next to that one.)

Please let me know if you'd like more details or need any help with either of the above options. I can certainly elaborate as needed. Hope this helps as a start at least!

[dominiquesydow]

Hi @piehld,

Many thanks for your quick help!
I will try this out later this week and come back here if I get stuck.

Leaving it up to you if you'd like to close this issue as solved already.
Leaving it open could be nice for visibility in case others also still use the mmtf package and are in search of alternatives.

Many thanks again!