Biopython update by pipaj97 · Pull Request #157 · volkamerlab/opencadd

pipaj97 · 2023-06-25T12:10:13Z

Description

In the latest version of biopython, some functionalities do not work anymore in OpenCADD.
This PR fixes this problem.

Todos

Notable points that this PR has either accomplished or will accomplish.

Update sequence functionalities to work with the latest biopython version
add a test for the newly implemented gap function
Check and solve CI failures

Status

Ready to go

AAriam

There were some apparent mistakes that I commented on the opencadd/structure/superposition/sequences.py file.

However, more importantly, the fasta2select function (i.e. the only part of the code being changed in this PR) does not have any explicit unit tests. Therefore, even after resolving these comments, we can't be sure of the correctness of the function until we write some explicit test-cases.

AAriam · 2024-01-30T12:17:30Z

        s = np.zeros((nseq, alignment.get_alignment_length()), dtype=object)
        for iseq, a in enumerate(alignment):
-            GAP = a.seq.alphabet.gap_char
+            print(a.seq)


Leftover from debugging?

AAriam · 2024-01-30T12:45:08Z

    ref_selection = " or ".join(sel[0])
    target_selection = " or ".join(sel[1])
-    return {"reference": ref_selection, "mobile": target_selection}
+    return {"reference": ref_selection, "mobile": target_selection}


add end-of-file newline

AndreaVolkamer · 2024-01-30T13:04:12Z

@pipaj97 can you have a look at these comments please?

AndreaVolkamer · 2024-01-30T13:23:08Z

@dominiquesydow can you please have a look in the CI failures realted to the kliffs package:

 =========================== short test summary info ============================
  FAILED opencadd/tests/databases/test_klifs_local_remote.py::TestsAllQueries::test_all_interactions - bravado.exception.HTTPURITooLong: 414 Request-URI Too Long: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
  <html><head>
  <title>414 Request-URI Too Long</title>
  </head><body>
  <h1>Request-URI Too Long</h1>
  <p>The requested URL's length exceeds the capacity
  limit for this server.<br />
  </p>
  <hr>
  <address>Apache/2.4.38 (Debian) Server at klifs.net Port 443</address>
  </body></html>
  FAILED opencadd/tests/databases/test_klifs_local_remote.py::TestsAllQueries::test_all_conformations - bravado.exception.HTTPURITooLong: 414 Request-URI Too Long: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
  <html><head>
  <title>414 Request-URI Too Long</title>
  </head><body>
  <h1>Request-URI Too Long</h1>
  <p>The requested URL's length exceeds the capacity
  limit for this server.<br />
  </p>
  <hr>
  <address>Apache/2.4.38 (Debian) Server at klifs.net Port 443</address>
  </body></html>

dominiquesydow · 2024-02-25T17:34:21Z

Hi @AndreaVolkamer,

I fixed the following two items:

1. A future deprecation warning for pandas, e.g. here:

/Users/dominique/Documents/GitHub/opencadd/opencadd/databases/klifs/core.py:147: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
  The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.
  
  For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.
  
  
    dataframe["ligand_allosteric.expo_id"].replace(0, "-", inplace=True)

We are doing now instead:

dataframe["ligand_allosteric.expo_id"] = dataframe["ligand_allosteric.expo_id"].replace(0, "-")

2. Two instances of HTTPURITooLong errors when querying KLIFS.

In these two cases we are pulling all interactions and all conformations - part of that query is that we pull all structure IDs from KLIFS, to then build a URL with all of them to retrieve interactions and conformations. This URL is naturally too long (I guess they rightfully added a limit). I am now chunking over the list of structure IDs instead.

codecov-commenter · 2024-02-25T17:35:50Z

Codecov Report

Merging #157 (cb3a39f) into master (c76e87c) will increase coverage by 0.10%.
The diff coverage is 91.42%.

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

dominiquesydow · 2024-02-25T17:36:17Z

@AndreaVolkamer I did not touch any KLIFS-unrelated issues.

dominiquesydow · 2024-02-25T17:40:09Z

@AndreaVolkamer ok could not resist & applied black to the full package --- can someone look into Python 3.12, which seems to fail with conda.

AndreaVolkamer · 2025-02-24T14:23:13Z

@AAriam since this was stale for a while (1.5 years) can you please check if we need further fixes, so we can merge the PR.

AAriam · 2025-02-26T10:07:41Z

So this PR now contains two unrelated changes: one is fixes to the KLIFS subpackage by Dominique, and the other is updating the Biopython version. For the latter, I had already left a review pointing to some problems, which are not yet resolved. Also, as we discussed in our last meeting, the Biopython problem is only a part of the problem with the superposition subpackage.
I think the best approach is to separate these two fixes, and first apply the KLIFS fix, which is already working. Also, depending on your decision on how to proceed with separating the two subpackages, there are other updates that need to be done, but first we need to decide on our strategy.
As I mentioned earlier, the best approach in my opinion is to release a new version of the KLIFS subpackage as a standalone package on PyPI. This way the updated KLIFS part will be immediately available to downstream users. I can do this in a couple of hours if you want.

AndreaVolkamer · 2025-03-13T20:39:04Z

@AAriam in the interest of getting the whole infrastructure running again, let's keep the package as is, implement the fixes, and do the separation, if needed, later. Could you have a look at the CI failure, please?

AAriam · 2025-03-14T14:25:48Z

@AndreaVolkamer I added the updates to the CI pipeline in #164. Please squash-merge into main, then we can pull here.

…vour of rcsb.fetch

fix: deprecate mmtf.fetch in favour of rcsb.fetch

pipaj97 added 3 commits June 25, 2023 13:32

use own function to find gap chars

9493f88

remove version for biopython

3472a94

rename test env to

7ca2b37

pipaj97 added the enhancement New feature or request label Jun 25, 2023

pipaj97 requested a review from AAriam June 25, 2023 12:10

pipaj97 added the module-structure-superposition Concerns opencadd.structure.superposition module label Jun 25, 2023

AAriam changed the base branch from dev to master January 30, 2024 09:17

AAriam closed this Jan 30, 2024

AAriam reopened this Jan 30, 2024

AAriam added 2 commits January 30, 2024 12:32

Update ci.yaml

ad552f4

Update ci.yaml

fb35568

AAriam reviewed Jan 30, 2024

View reviewed changes

AndreaVolkamer requested a review from dominiquesydow January 30, 2024 13:20

dominiquesydow added 2 commits February 25, 2024 17:27

future deprectation pandas: do not use inplace on copy

00260a1

fix: chunk list of IDs in request to avoid HTTPURITooLong

00a497a

chore: fix formatting with black

cb3a39f

AndreaVolkamer requested a review from AAriam February 24, 2025 14:22

AndreaVolkamer reviewed Mar 13, 2025

View reviewed changes

Comment thread .github/workflows/ci.yaml Outdated

Update .github/workflows/ci.yaml

7aa1f6a

AndreaVolkamer mentioned this pull request Mar 13, 2025

superposition still needs fixing! #163

Open

AndreaVolkamer reviewed Mar 13, 2025

View reviewed changes

Comment thread opencadd/structure/superposition/sequences.py Outdated

Update opencadd/structure/superposition/sequences.py

b6ec5c2

Update ci.yaml

9aaf3ce

AAriam mentioned this pull request Mar 18, 2025

Update GHA actions in CI pipeline #164

Merged

gph82 and others added 2 commits October 2, 2025 11:21

[structure.core.Structure.from_pdbid] fix: deprecate mmtf.fetch in fa…

0f2d2c9

…vour of rcsb.fetch

Merge pull request #166 from gph82/ditch_mmtf

7bc9bc9

fix: deprecate mmtf.fetch in favour of rcsb.fetch

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pipaj97 commented Jun 25, 2023 •

edited by AndreaVolkamer

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