Implementation of from_alphafold by jauy123 · Pull Request #5457 · MDAnalysis/mdanalysis

jauy123 · 2026-08-12T03:24:55Z

Fixes #5432

Changes made in this Pull Request:

Implements from_alphafold using StaticFetcher

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no

PR Checklist

Issue raised/referenced?
Tests updated/added?
Documentation updated/added?
package/CHANGELOG file updated?
Is your name in package/AUTHORS? (If it is not, add it!)
I have read and understand the current AI Policy
LLM/AI disclosure was updated.

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

…afold

jauy123 · 2026-08-12T03:25:58Z

This diverged from #5436 using StaticFetcher as a base.

jauy123 · 2026-08-12T03:26:06Z

Docs need to be updated

read-the-docs-community · 2026-08-12T03:35:27Z

Documentation build overview

📚 MDAnalysis | 🛠️ Build #34026934 | 📁 Comparing d7eefc8 against latest (c882e5c)

🔍 Preview build

14 files changed · + 2 added · ± 12 modified

+ Added

± Modified

codecov · 2026-08-12T03:35:42Z

Codecov Report

❌ Patch coverage is 97.27891% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.88%. Comparing base (83bc9a2) to head (d7eefc8).
⚠️ Report is 5 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/fetch/fetchers.py	96.74%	3 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5457      +/-   ##
===========================================
+ Coverage    93.87%   93.88%   +0.01%     
===========================================
  Files          182      183       +1     
  Lines        22510    22650     +140     
  Branches      3202     3227      +25     
===========================================
+ Hits         21131    21266     +135     
- Misses         917      921       +4     
- Partials       462      463       +1

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

jauy123 · 2026-08-12T06:49:11Z

Docs are also done here

orbeckst

Impressive work, nice!

My comments are mostly docs and coding style.

I'll leave the heavy commenting to @BradyAJohnston @yuxuanzhuang @talagayev .

orbeckst · 2026-09-01T20:25:01Z

+# for rn
+package/doc/sphinx/build_docs.sh
+testsuite/MDAnalysisTests/fetch/run_tests.sh
+package/MDAnalysis/TEST.py
+


Please remove your private gitignores. Instead add them to your .git/info/exclude file, which is not revision-controlled.

orbeckst · 2026-09-01T20:25:59Z

Is this PR introducing StaticFetcher ?

Now I am seeing that the main PR is really #5436 – I'll add a quick comment there to send you back here. Sorry.

orbeckst · 2026-09-01T20:27:08Z

+
+        Primarily designed to be working with `FAIR`_
+        databases, this method works by sending a request to a web server and
+        caching them to a registry.The registry is in the format of a


space after period

orbeckst · 2026-09-01T20:50:24Z

+        Notes
+        -----
+        The download directory can be overridden by setting the environment
+        variable ``MDANALYSIS_FETCHER_DATA`` to a valid path. This class uses


Check the reST/sphinx markup for an environment variable (maybe :envvar: ?) and use it.

orbeckst · 2026-09-01T20:50:52Z

+        :mod:`pooch` as a backend for downloading and caching files. The
+        cache database is created on demand when ``db_name`` does not
+        exist relative to :attr:`cache_path`.
+


might need 2 blank lines.

Always check the rendered docs.

I checked and it rendered fine, which is good. In the past, double-blank lines were needed.

orbeckst · 2026-09-01T21:34:19Z

-    ]

-    return paths if not isinstance(pdb_ids, str) else paths[0]
+def from_ALPHAFOLD(id, cache_path=None, progressbar=False, file_format="cif"):


Why capitalized from_ALPHAFOLD when you refer to it elsewhere as AlphaFold? I'd be consistent and call the function from_AlphaFold().

orbeckst · 2026-09-01T21:35:29Z

+
+    Download a single AlphaFold file and convert it to a universe:
+
+    >>> mda.Universe(from_ALPHAFOLD("Q9I1F6"), files_format="pdb")


file_format

orbeckst · 2026-09-01T21:36:38Z

+    .. versionadded:: 2.11.0
+    """
+
+    if file_format not in _SUPPORTED_FILE_FORMATS_ALPHAFOLD.keys():


I don't think you need .keys(). in just works with dict keys.

orbeckst · 2026-09-01T21:39:19Z

+This suite of functions download structure files from the Research
+Collaboratory for Structural Bioinformatics (RCSB)
+`Protein Data Batabank`_ (PDB).


The header only talks about Protein Databank but the AlphaFold fetcher is also in here. Personally, I'd create a separate module for AlphaFold, similar to this one here.

However, if you and your mentors prefer to have it in the same file then please at least update the text here to also talk about the AF database (with link).

orbeckst · 2026-09-01T21:42:33Z

-#: Name of the :mod:`pooch` cache directory ``pooch.os_cache(DEFAULT_CACHE_NAME_DOWNLOADER)``;
-#: see :func:`pooch.os_cache` for further details.
+#: Alias to fetchers/DEFAULT_CACHE_NAME_DOWNLOADER
 #:
-#: .. versionadded:: 2.11.0
-DEFAULT_CACHE_NAME_DOWNLOADER = "MDAnalysis_pdbs"
+#: Maintained for backwards compatiblity
+#:
+from .fetchers import DEFAULT_CACHE_NAME_DOWNLOADER


Just remove what you do not want. Given that fetch_PDB had not been released yet (it's not in 2.10.0) you do not need to maintain any compatibility. Just write it as cleanly as you can.

jauy123 added 30 commits June 5, 2026 10:45

Added TODO

e3bc2ae

Added Pseudocode for Fetchers based on blog post

87a7b94

updated private methods

ad044ef

Added Dev Things

8fbd203

more dev stuff

c4c6b56

More Dev stuff yay

b921f53

More Dev stuff yay

f76554e

Added workflow

48e8925

Added workflow for StaticFetcher.fetch()

900ce8b

Added more notes

fc05684

Reworked to used pooch functions instead of writing own

b609fd6

Works but clunky!

93e777c

Updated TEST.py

dbd62be

Working single file fetch

f3837aa

Tests to fix for tomorrow

cefb95f

working test case

e175d6e

Working! Need to refactor

41d52be

Working! Need to refactor

1fb4857

test for gh-ci.yaml

0b8b439

Added pooch Downloader Support

3ad1d00

applied black

15e4ff9

Created Test Suite

b8de1eb

Finalized code -- test still need to be written

9312486

Made progressbar work

c4490b8

Github action working

d745faf

Repo guard removed?

7b9281d

removed duplicate imports

56ecac2

added early docs

70628d8

added header to tests

bfe74b6

Docs can build now!

000f15c

jauy123 added 16 commits July 30, 2026 14:09

reenabled tests?

4715272

applied monkeypatch

0c427e7

Formalized Downloaders Test

519fe2e

fixed pooch import

99f5d53

added fetch(append_db=True)

4940428

Added to replicate

878e6a1

Merge remote-tracking branch 'upstream/develop' into Fetcher_Class

467cdf4

Updated docs

423f7b5

applied flake8

b550fe4

applied flake8 where it made sense

d0e494e

applied black

2d7c289

removed not needed pass statement

1d1c8c4

Merge remote-tracking branch 'origin/Fetcher_Class' into fetcher_alph…

f493c7f

…afold

working tests

040a965

linters

39384a8

applied linter and black

800d7bb

jauy123 changed the title ~~Fetcher alphafold~~ Implementation of from_alphafold Aug 12, 2026

jauy123 added 3 commits August 11, 2026 23:43

hand written docs done

c9feafe

LLM Pass for syntax

823a9cd

post black

d7eefc8

orbeckst requested changes Sep 1, 2026

View reviewed changes

orbeckst mentioned this pull request Sep 1, 2026

Implementation of from_DOI() #5454

Open

4 tasks

orbeckst added GSoC GSoC project fetcher labels Sep 1, 2026

orbeckst mentioned this pull request Sep 1, 2026

StaticFetcher() Implementation + from_pdb() refactor #5436

Open

6 tasks


		Download a single AlphaFold file and convert it to a universe:

		>>> mda.Universe(from_ALPHAFOLD("Q9I1F6"), files_format="pdb")

Uh oh!

Conversation

jauy123 commented Aug 12, 2026

LLM / AI generated code disclosure

PR Checklist

Developers Certificate of Origin

Uh oh!

jauy123 commented Aug 12, 2026

Uh oh!

jauy123 commented Aug 12, 2026

Uh oh!

read-the-docs-community Bot commented Aug 12, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Documentation build overview

Uh oh!

codecov Bot commented Aug 12, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

jauy123 commented Aug 12, 2026

Uh oh!

orbeckst left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

read-the-docs-community Bot commented Aug 12, 2026 •

edited

Loading

codecov Bot commented Aug 12, 2026 •

edited

Loading