Implementation of fetch_pdb() #4943

jauy123 · 2025-03-03T18:28:48Z

Changes made in this Pull Request:

This is a still work in progress, but here's a implementation of @BradyAJohnston 's code wrapped into classes. I still need to write tests and docs for the entire thing.

Added two classes: DownloaderBase and 'PDBDownloader' in order to implement downloading structure file from online sources such as the PDB databank.
Added requests as a dependency
mda.fetch_pdb() is implemented as a wrapper to commonly used option in 'PDBDownloader'

PR Checklist

Issue raised/referenced?
Tests updated/added?
Documentation updated/added?
package/CHANGELOG file 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.

📚 Documentation preview 📚: https://mdanalysis--4943.org.readthedocs.build/en/4943/

jauy123 · 2025-03-03T18:31:48Z

I'm not sure where to put this code in the codebase, so I create a new folder for it right now. I'm open to it being moved somewhere

Some stuff which I like to still add (besides tests and docs):

Verbose option for PdbDownloader.download() (I think tqdm was a dependency last time I saw?)
Integration with Mdanalysis' logger
Probably could wrap the cache logic into a separate function

BradyAJohnston · 2025-03-04T01:20:19Z

I think others will have to confirm, but likely we'll want to have requests be an optional dependency to reduce core library dependencies (as the fetching of structures won't be something that lot of users will be doing).

Additional it's not finalised yet but if the mmcif reader in #2367 gets finalised then the default download shouldn't be .pdb (but can remain for now).

codecov · 2025-03-04T20:44:31Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.02%. Comparing base (5c7c480) to head (31a8f7b).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4943      +/-   ##
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+ Coverage    92.68%   93.02%   +0.34%     
===========================================
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  Lines        22452    22473      +21     
  Branches      3186     3190       +4     
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jauy123 · 2025-03-05T02:49:30Z

I'm ok with that. I can make the code raise an exception if requests is not in the environment.

jauy123 · 2025-03-10T17:41:23Z

Assuming that requests will be optional dependency, how would I exactly specify in the build files? Right now, I'm just hard coding it in, so that the github CLI tests can build successfully and run.

BradyAJohnston · 2025-03-19T12:36:18Z

You've added it to one of the optional dependency categories which is all that should be required. For the actual files where it is used you'll need to have something setup like the usage of biopython:

mdanalysis/package/MDAnalysis/analysis/align.py

Lines 200 to 207 in dcaa087

    
           try: 
        
               import Bio.AlignIO 
        
               import Bio.Align 
        
               import Bio.Align.Applications 
        
           except ImportError: 
        
               HAS_BIOPYTHON = False 
        
           else: 
        
               HAS_BIOPYTHON = True

I'm not an expert on the pipelines so someone else would have to pitch in more on that.

jauy123 · 2025-03-19T23:14:58Z

Thanks for the comment!

jauy123 · 2025-03-19T23:15:52Z

I happen to have another question!

Is it normal for some of the tests to not be consistent across each commit? From what I understand, each github CLI has to get and build each MDAnalysis from source, and this instance can potentially timeout from what I observe across each commit.

The macOS (of the latest commit) failed at 97% of test because it reached the max wall time of two hours.

Even then the latest Azure tests failed because of other tests in the source code which I didn't write (namely due to other tests)

From Azure_Tests Win-Python310-64bit-full (commit 651bf267076d2d7da6491608b1b5136915caf2e2)

FAIL MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_open_filestream - Issue #2884
XFAIL MDAnalysisTests/coordinates/test_h5md.py::TestH5MDWriterWithRealTrajectory::test_write_with_drivers[core] - occasional PermissionError on windows
XFAIL MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_frame_collect_all_same - reason: memoryreader allows independent coordinates
XFAIL MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_values[slice0] - reason: MemoryReader uses deprecated stop inclusive indexing, see Issue #3893
XFAIL MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_values[slice1] - reason: MemoryReader uses deprecated stop inclusive indexing, see Issue #3893
XFAIL MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_values[slice2] - reason: MemoryReader uses deprecated stop inclusive indexing, see Issue #3893
XFAIL MDAnalysisTests/core/test_topologyattrs.py::TestResids::test_set_atoms
XFAIL MDAnalysisTests/lib/test_util.py::test_which - util.which does not get right binary on Windows
XFAIL MDAnalysisTests/converters/test_rdkit.py::TestRDKitFunctions::test_order_independant_issue_3339[C-[N+]#N] - Not currently tackled by the RDKitConverter
XFAIL MDAnalysisTests/converters/test_rdkit.py::TestRDKitFunctions::test_order_independant_issue_3339[C-N=[N+]=[N-]] - Not currently tackled by the RDKitConverter
XFAIL MDAnalysisTests/converters/test_rdkit.py::TestRDKitFunctions::test_order_independant_issue_3339[C-[O+]=C] - Not currently tackled by the RDKitConverter
XFAIL MDAnalysisTests/converters/test_rdkit.py::TestRDKitFunctions::test_order_independant_issue_3339[C-[N+]#[C-]] - Not currently tackled by the RDKitConverter
XFAIL MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_frame_collect_all_same - reason: DCDReader allows independent coordinates.This behaviour is deprecated and will be changedin 3.

orbeckst · 2025-03-20T18:17:46Z

In principle, tests should pass everywhere.

The Azure tests time out in the test

_________________________ Test_Fetch_Pdb.test_timeout _________________________

which looks like something that you added. I haven't looked at your code but it might simply be the case that some stuff needs to be written differently for windows.

orbeckst · 2025-06-12T16:18:16Z

@jauy123 do you have time to pick up this PR again? Would be great to have the feature in 2.10!

jauy123 · 2025-06-12T21:25:55Z

I have time again. I was busy starting the end of spring break with comps, classes, and you know what.

…xt files

…since text files are just binary files with special encoding

This reverts commit f09115a.

jauy123 · 2025-10-21T21:25:20Z

@IAlibay @BradyAJohnston @orbeckst

I added the test, and github's machines are now returning 100% coverage. I also refilled out the changelog. I believe this PR should be okay to merge with the dev branch.

p-j-smith

Nice work @jauy123! I've made some non-blocking suggestions. The only blocking one is to explicitly document all supported formats for file_format in the docstring

package/MDAnalysis/topology/PDBParser.py

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

package/MDAnalysis/topology/PDBParser.py

Still need to add to docstring. sphinx, and probably also still write test as well.

p-j-smith

looks good to me, thanks @jauy123!

orbeckst

Looks all good in principle, but I have a few major requests:

Have the output shape be the same as in the input shape, i.e., str -> str and list -> list and NOT "list of length 1" -> str, "list of length > 1" -> list.
Update docs; you can accept my suggestions, for others you have to write a bit more. Look at it from a user's perspective: what do you want to/need to know?
You need to follow our code style and you can use darker to format only your changes. Do not run black on all of the topology/PDBParser.py file because at the moment @RMeli has this file excluded from format checking (he wants to avoid collisions with active PRs). Do run black test_fetch_pdb.py because this is a completely new file.

See comments for other minor things.

Looking good, you're almost there!

orbeckst · 2025-10-22T21:11:47Z

package/MDAnalysis/topology/PDBParser.py

+    Download multiple PDB files and converting them to a universe:
+
+    >>> [mda.Universe(mda.fetch_pdb(PDB_ID), file_format="pdb.gz") for PDB_ID in ("1AKE", "4BWZ")]
+    [<Universe with 3816 atoms>, <Universe with 2824 atoms>]


Why is downloading one-by-one in a loop preferred over downloading all at once (shown above), i.e.,

universes = [mda.Universe(pdb) for pdb in mda.fetch_pdb(["1AKE", "4BWZ"], progressbar=True)]

If you want an example with multiple files then I'd use the one that uses fetch_pdb 's capability to download multiple files at once.

orbeckst · 2025-10-22T21:13:00Z

package/MDAnalysis/topology/PDBParser.py

+    ----------
+    PDB_IDS : str or sequence of str
+        A single PDB ID as a string, or a sequence of PDB IDs to fetch.
+    cache_path : str or pathlib.Path


Explain what the default None does.

Reading the code I see that it enables a default cache. Need to explain that and how to manage the default cache. Possibly link to relevant pooch docs.

User would want to know where data are saved, how they can clean up the data, etc.

orbeckst · 2025-10-22T21:14:41Z

package/MDAnalysis/topology/PDBParser.py

+    Returns
+    -------
+    str or list of str
+        The path(s) to the downloaded file(s). Returns a single string if one PDB ID is given,


What happens when I ask for a list with a single ID?

fetch_pdb(["1ake"])

I hope it returns a list of length 1 as this will make it so much easier to write code that works seamlessly with any number of inputs.

orbeckst · 2025-10-22T21:24:43Z

package/MDAnalysis/topology/PDBParser.py

+    
+    Notes
+    -----
+    This function downloads using the API established here at https://www.rcsb.org/docs/programmatic-access/file-download-services.


Do not use "here" for links — that's really bad for accessibility. Instead integrate into language:

Suggested change

This function downloads using the API established here at https://www.rcsb.org/docs/programmatic-access/file-download-services.

This function uses the `RCSB File Download Services`_ for directly downloading

structure files via https.

.. _`RCSB File Download Services`:

https://www.rcsb.org/docs/programmatic-access/file-download-services

I wouldn't call it an API (the RCSB Web API is a real programmatic API).

Also, keep the text within 79 characters for easier readability.

orbeckst · 2025-10-22T21:27:25Z

package/MDAnalysis/topology/PDBParser.py

+    -----
+    This function downloads using the API established here at https://www.rcsb.org/docs/programmatic-access/file-download-services.
+
+    Currently supported file formats (per the API) are ('cif', 'cif.gz', 'bcif', 'bcif.gz', 'xml', 'xml.gz', 'pdb', 'pdb.gz', 'pdb1', 'pdb1.gz')


Be clear that not all of these formats can be read:

Suggested change

Currently supported file formats (per the API) are ('cif', 'cif.gz', 'bcif', 'bcif.gz', 'xml', 'xml.gz', 'pdb', 'pdb.gz', 'pdb1', 'pdb1.gz')

The RCSB currently provides data in 'cif', 'cif.gz', 'bcif', 'bcif.gz', 'xml',

'xml.gz', 'pdb', 'pdb.gz', 'pdb1', 'pdb1.gz' file formats and can therefore be

downloaded. Not all of these formats can be currently read with MDAnalysis.

orbeckst · 2025-10-22T21:34:09Z

package/MDAnalysis/topology/PDBParser.py

+    if isinstance(PDB_IDS, str):
+        PDB_IDS = (PDB_IDS,)
+
+    if cache_path is None:


document what happens for None

Where is the cache located? Perhaps link to pooch docs

How do I clear the cache?

How do I force re-fetching?

orbeckst · 2025-10-22T21:38:58Z

package/MDAnalysis/topology/PDBParser.py

+    cache_path : str or pathlib.Path
+        Directory where downloaded file(s) will be cached.
+    file_format : str
+        The file extension/format to download (e.g., "cif", "pdb")


Need to document allowed values.

Suggested change

The file extension/format to download (e.g., "cif", "pdb")

The file extension/format to download (e.g., "cif", "pdb").

See the Notes section below for a list of all supported file formats.

orbeckst · 2025-10-22T21:44:01Z

package/MDAnalysis/topology/PDBParser.py

+    if len(PDB_IDS) == 1:
+        return str(
+            downloader.fetch(
+                fname=tuple(registry_dictionary.keys())[0],
+                progressbar=progressbar,
+            )
+        )


I dislike this approach where a length 1 list always returns a string. It makes it very frustrating to write code that can process arbitrary lists because I have to check if I get back a single file, then it's a string, but if I gave multiple ones, it's a list. It's MUCH SANER if the ''output shape = input shape''.

If input is a str, make output a str.

If input is a sequence, make output a sequence.

package/MDAnalysis/topology/PDBParser.py

orbeckst · 2025-10-22T21:53:41Z

package/CHANGELOG

+* Added new function `PDBParser.fetch_pdb` to download structure files from wwPDB
+   using `pooch` as optional dependency. This can be used to interactively create
+   `Universe` classes on the fly. (Issue #4907, PR #4943)  


indent properly

and shorten

Suggested change

* Added new function `PDBParser.fetch_pdb` to download structure files from wwPDB

using `pooch` as optional dependency. This can be used to interactively create

`Universe` classes on the fly. (Issue #4907, PR #4943)

* Added function `topology.PDBParser.fetch_pdb` (accessible as

`MDAnalysis.fetch_pdb()`) to download structure files from wwPDB using

`pooch` as optional dependency (Issue #4907, PR #4943)

If you use a length 1 iterator for pdb_id, you get back a rank 1 list

Docstring changed Shortened really long comment in fetch_pdb

orbeckst · 2025-10-22T23:42:23Z

package/MDAnalysis/topology/PDBParser.py

+    if type(pdb_ids) is str:
+        return str(
+            downloader.fetch(
+                fname=tuple(registry_dictionary.keys())[0],
+                progressbar=progressbar,
+            )
+        )
+    else:
+        return [
+            str(
+                downloader.fetch(fname=file_name, progressbar=progressbar)
+                for file_name in registry_dictionary.keys()
+            )


Is there a way to simplify the code so that you only downloader.fetch(fname=...) once? Along the lines of

paths = [downloader.fetch(fname=file_name, progressbar=progressbar) for file_name in registry_dictionary.keys()] if type(pdb_ids) is str: return paths[0] return paths

or even more concise with the Python ternary operator:

paths = [downloader.fetch(fname=file_name, progressbar=progressbar) for file_name in registry_dictionary.keys()] return paths if type(pdb_ids) is not str else paths[0]

orbeckst · 2025-10-22T23:45:48Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

+class TestDocstringExamples:
+    """This class tests all the examples found in fetch_pdb's docstring"""
+
+    @pytest.mark.parametrize("pdb_id", [("1AKE"), ("4BWZ")])


Also test a list with a single entry ["1AKE"]. Check that it returns a list of paths.

orbeckst · 2025-10-22T23:46:39Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

+        list_of_path_strings = mda.fetch_pdb(
+            ["1AKE", "4BWZ"], cache_path=tmp_path, progressbar=True
+        )
+        assert all(isinstance(PDB_ID, str) for PDB_ID in list_of_path_strings)


also test the actual names not just types

orbeckst · 2025-10-22T23:49:30Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

+    reason="Pooch is installed.",
+)
+def test_pooch_installation(tmp_path):
+    with pytest.raises(ModuleNotFoundError):


also check the error message of the exception, there's an additional argument like

with pytest.raises(ModuleNotFoundError, match="pooch is needed as a dependency for fetch_pdb()"):

orbeckst · 2025-10-22T23:51:36Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

+)
+@pytest.mark.parametrize("pdb_id", [("1AKE"), ("4BWZ")])
+def test_no_cache_path(pdb_id):
+    assert isinstance(mda.fetch_pdb(pdb_id, cache_path=None), str)


It would be good practice to clean up the default cache afterwards because if I run this test myself, the cache persists somewhere in my system. Tests should not leave anything behind.

orbeckst · 2025-10-23T21:35:45Z

package/MDAnalysis/topology/PDBParser.py

+    paths = [downloader.fetch(fname=file_name, progressbar=progressbar)
+             for file_name in registry_dictionary.keys()]
+
+    return paths if type(pdb_ids) is not str else paths[0]


is not isinstance(pdb_ids, str) as you used above is probably safer than using type.

orbeckst · 2025-10-23T21:37:11Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py


 if HAS_POOCH:
    from requests.exceptions import HTTPError
+    from pooch import os_cache


I'd avoid importing into the namespace. When reading code below it's not clear where os_cache is from. It's much clearer to just import pooch and then later use pooch.os_cache.

orbeckst · 2025-10-23T21:40:38Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

 class TestDocstringExamples:
    """This class tests all the examples found in fetch_pdb's docstring"""

    @pytest.mark.parametrize("pdb_id", [("1AKE"), ("4BWZ")])


The parentheses don't do anything so remove:

@pytest.mark.parametrize("pdb_id", ["1AKE", "4BWZ"])

orbeckst · 2025-10-23T21:50:44Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

-            mda.fetch_pdb(
-                pdb_ids="1AKE", cache_path=tmp_path, file_format="barfoo"
-            )
+@pytest.fixture()


very nice to create it as a fixture

orbeckst · 2025-10-23T21:53:00Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

+@pytest.fixture()
+def clean_up_default_cache():
+    yield
+    rmtree(os_cache("MDAnalysis_pdbs"))


For this to work one must know that "MDAnalysis_pdbs" is hard-coded into fetch_pdb. It would be safer to define the name in PDBParser.py ad

DEFAULT_POOCH_CACHE_NAME = "MDAnalysis_pdbs"

and then use DEFAULT_POOCH_CACHE_NAME everywhere else. In particular, here you can then use

import MDAnalysis.topology.PDBParser ... def clean_up_default_cache(): yield rmtree(os_cache(MDAnalysis.topology.PDBParser.DEFAULT_POOCH_CACHE_NAME))

More typing initially but cleaner and more robust because the hard-coded name exists in exactly one location only.

orbeckst · 2025-10-23T21:54:49Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

 from MDAnalysis.topology.PDBParser import HAS_POOCH

 from urllib import request
+from shutil import rmtree


Personally I'd import the packages instead of functions.

(However, these are all standard library packages so people may know where rmtree etc come from so I'll leave it to you.)

orbeckst · 2025-10-23T22:01:39Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

+class TestExpectedErrors:
+
+    def test_invalid_pdb(self, tmp_path):
+        with pytest.raises(HTTPError):


match="..." error output (when you test an exception you want to make sure it is "your" exception)

In this particular case, this wouldn't be my exception. It's requests.exceptions.HTTPError - a third party pooch dependency. I don't think I would need to match in that case?

orbeckst · 2025-10-23T22:01:45Z

testsuite/MDAnalysisTests/topology/test_fetch_pdb.py

+            mda.fetch_pdb(pdb_ids="foobar", cache_path=tmp_path)
+
+    def test_invalid_file_format(self, tmp_path):
+        with pytest.raises(ValueError):


match="..." error output (when you test an exception you want to make sure it is "your" exception)

BradyAJohnston self-assigned this Mar 4, 2025

jauy123 added 18 commits June 23, 2025 10:25

Added requests as a dependency

7899f3d

Inital download code

44393be

fixed typo

b1f6002

cleaner convert_to_universe()

9c6e87a

Added abc module and allowed closing of file stream for downloaded te…

aecefc9

…xt files

Fixed __all__ -- should fixed pull request test on github

9510cc6

refactored cache logic

8c1a196

Initial tests

f0e30ed

Added __init.py to make tests work

1c7d909

typos fixed

eb23ed1

Refactored Tests -- put them in classes!

b0c7f5a

PdbDownloader().download() now downloads in binary rather than text (…

f2ec203

…since text files are just binary files with special encoding

Updated Tests to comply with pdb.gz

a21fd94

Added Progress bar to PdbDownloader().download()

d58bed9

Added a few clarifications to _requests_progress_bar

1147b6d

Added filename attribute() to BaseDownloader()

91feb16

made _requests_progress_bar a private method of PdbDownloader

ddcef9e

minor comments

bf3e07f

jauy123 added 4 commits October 21, 2025 13:31

merged with upstream

e2141a8

Revert "Added no cache test"

bf81128

This reverts commit f09115a.

Copy and Pasted from old changelog

934eda3

uunrevert commit bf81128

9b8da31

p-j-smith requested changes Oct 21, 2025

View reviewed changes

jauy123 added 3 commits October 22, 2025 09:30

Split pytest fixtures into two

0b80840

renamed pdb_cache to MDAnalysis_pdbs

a7519af

Added supported file_formats to code.

72c24e0

Still need to add to docstring. sphinx, and probably also still write test as well.

jauy123 force-pushed the downloads branch from c982474 to bcd8ba1 Compare October 22, 2025 18:13

Added documentation and update test for file formats

ffcc270

jauy123 force-pushed the downloads branch from bcd8ba1 to ffcc270 Compare October 22, 2025 18:17

p-j-smith approved these changes Oct 22, 2025

View reviewed changes

jauy123 requested a review from orbeckst October 22, 2025 20:10

orbeckst requested changes Oct 22, 2025

View reviewed changes

jauy123 added 4 commits October 22, 2025 15:38

post darker pre flake8

b07a16d

Updated fetch_pdb return types

a2aff4c

If you use a length 1 iterator for pdb_id, you get back a rank 1 list

Manual flake 8 on fetch_pdb

98fa75b

Addressing obeckset's fetch_pdb's docstring changes

1e635c4

Docstring changed Shortened really long comment in fetch_pdb

orbeckst reviewed Oct 22, 2025

View reviewed changes

jauy123 added 5 commits October 22, 2025 16:54

Changed 'Multiple PDBs example in docstring

447de56

wrote tests for str/tuple arguement -- need to refactor however

c28110f

Updated PDBParser.py and applied flake8

02d81a3

Modified Tests per orbeckst's requests

adbfabb

Modified fetch_pdb()'s logic and added cache docs

31a8f7b

orbeckst requested changes Oct 23, 2025

View reviewed changes

-    This function downloads using the API established here at https://www.rcsb.org/docs/programmatic-access/file-download-services.
+    This function uses the `RCSB File Download Services`_ for directly downloading
+    structure files via https.
+    .. _`RCSB File Download Services`:
+       https://www.rcsb.org/docs/programmatic-access/file-download-services

-    Currently supported file formats (per the API) are ('cif', 'cif.gz', 'bcif', 'bcif.gz', 'xml', 'xml.gz', 'pdb', 'pdb.gz', 'pdb1', 'pdb1.gz')
+    The RCSB currently provides data in 'cif', 'cif.gz', 'bcif', 'bcif.gz', 'xml',
+    'xml.gz', 'pdb', 'pdb.gz', 'pdb1', 'pdb1.gz' file formats and can therefore be
+    downloaded. Not all of these formats can be currently read with MDAnalysis.

	The file extension/format to download (e.g., "cif", "pdb")
	The file extension/format to download (e.g., "cif", "pdb").
	See the Notes section below for a list of all supported file formats.

Implementation of fetch_pdb() #4943

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Implementation of fetch_pdb() #4943

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