Merge pull request #249 from Mesnage-Org/mainline-3-1-crosslinks

.github/workflows/release-to-pypi.yml

@@ -33,5 +33,6 @@ jobs:
       - name: Publish package to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
+          packages-dir: lib/dist/
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

CHANGELOG.md

@@ -7,6 +7,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.1.1] - 2023-11-06
+
+### Changed
+
+- Changed cross-linking modifications to read donor-acceptor (#249)
+
+## [1.1.0] - 2023-10-15
+
+### Added
+
+- Added a modification for enabling 3-1 cross-linking (#249)
+
+### Fixed
+
+- Removed the trailing space after bracketed modifications (#249)
+
 ## [1.0.3] - 2023-09-04
 
 ### Fixed
@@ -48,7 +64,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 Let there be peptidoglycan.
 
-[Unreleased]: https://github.com/Mesnage-Org/pgfinder/compare/v1.0.3...HEAD
+[Unreleased]: https://github.com/Mesnage-Org/pgfinder/compare/v1.1.1...HEAD
+[1.1.1]: https://github.com/Mesnage-Org/pgfinder/compare/v1.1.0...v1.1.1
+[1.1.0]: https://github.com/Mesnage-Org/pgfinder/compare/v1.0.3...v1.1.0
 [1.0.3]: https://github.com/Mesnage-Org/pgfinder/compare/v1.0.2...v1.0.3
 [1.0.2]: https://github.com/Mesnage-Org/pgfinder/compare/v1.0.1...v1.0.2
 [1.0.1]: https://github.com/Mesnage-Org/pgfinder/compare/v1.0.0...v1.0.1

lib/docs/installation.md

@@ -29,6 +29,8 @@ pip install pgfinder
 
 Versions are released automatically when commits on GitHub are tagged.
 
+## Development
+
 To install the most recent pre-release version, use:
 
 ``` bash

lib/pgfinder/config/allowed_modifications.txt

@@ -1,4 +1,5 @@
-Cross-Linked Multimers (=)
+3-3 and 4-3 Cross-Linked Multimers (=)
+1-3 Cross-Linked Multimers (=)
 Glycosidic Multimers (-)
 Lactyl Multimers (=Lac)
 

lib/pgfinder/config/parameters.yaml

@@ -1,5 +1,5 @@
 multimer:
-  Cross-Linked Multimers (=):
+  3-3 and 4-3 Cross-Linked Multimers (=):
     gm-AE:
       mass: 698.2858
       mult_num: 2
@@ -18,6 +18,10 @@ multimer:
     gm-AEJA=gm-AEJA:
       mass: 1864.8044
       mult_num: 3
+  1-3 Cross-Linked Multimers (=):
+    gm-A:
+      mass: 569.2433
+      mult_num: 2
   Glycosidic Multimers (-):
     gm-AE:
       mass: 696.2702

lib/pgfinder/default_config.yaml

@@ -5,7 +5,8 @@ ppm_tolerance: 10
 consolidation_ppm: 1
 time_delta: 0.5
 mod_list:
-  # - Cross-Linked Multimers (=)
+  # - 3-3 and 4-3 Cross-Linked Multimers (=)
+  # - 1-3 Cross-Linked Multimers (=)
   # - Glycosidic Multimers (-)
   # - Lactyl Multimers (=Lac)
 

lib/pgfinder/matching.py

@@ -151,7 +151,7 @@ def modification_generator(filtered_theo_df: pd.DataFrame, mod_type: str) -> pd.
     # The silly `len(s) - 2` rubbish here is to preserve the `|x` multimer number at the end of
     # each structure name
     def default_case(s):
-        return s[: len(s) - 2] + " " + mod_abbr + " " + s[len(s) - 2 : len(s)]
+        return s[: len(s) - 2] + " " + mod_abbr + s[len(s) - 2 : len(s)]
 
     structure_updater = special_cases.get(mod_type, default_case)
 

lib/pgfinder/pgio.py

@@ -171,6 +171,14 @@ def theo_masses_reader(file: Union[str, Path]) -> pd.DataFrame:
                 "columns. Have you checked the format of your database against one of the built-in databases?"
             )
         ) from e
+    # Check that all structures are followed by "|n" where n is one or more digits
+    if not theo_masses_df["Inferred structure"].str.contains(r"\|\d+$").all():
+        raise UserError(
+            (
+                "The supplied mass database contains structures missing the '|n' suffix encoding oligomerisation "
+                "state. This should be '|1' for monomers, '|2' for dimers, '|3' for trimers, and so on."
+            )
+        )
     theo_masses_df.attrs["file"] = PurePath(file).name
     LOGGER.info(f"Theoretical masses loaded from     : {file}")
     return theo_masses_df

lib/pyproject.toml

@@ -74,7 +74,6 @@ exclude = ["tests"]
 
 [tool.setuptools_scm]
 root = ".."
-write_to = "lib/pgfinder/_version.py"
 
 [tool.pytest.ini_options]
 minversion = "7.0"

web/src/lib/pgfinder.ts

@@ -17,7 +17,7 @@ let pyodide: PyodideInterface;
 	pyodide.registerJsModule('pyio', pyio);
 	await pyodide.loadPackage(['micropip', 'sqlite3']);
 	const micropip = pyodide.pyimport('micropip');
-	await micropip.install('pgfinder');
+	await micropip.install('pgfinder==1.1.1');
 	await pyodide.runPythonAsync('import pgfinder; from pgfinder.gui.shim import *');
 
 	const pgfinderVersion = await pyodide.runPythonAsync('pgfinder.__version__');

web/tests/complex_search_test.ts

@@ -9,7 +9,8 @@ test('run a complex search', async ({ page }) => {
 	await page.getByRole('option', { name: 'Complex' }).click();
 
 	await page.getByRole('button', { name: 'Advanced Options' }).click();
-	await page.getByRole('option', { name: 'Cross-Linked Multimers (=)' }).click();
+	await page.getByRole('option', { name: '3-3 and 4-3 Cross-Linked Multimers (=)' }).click();
+	await page.getByRole('option', { name: '1-3 Cross-Linked Multimers (=)' }).click();
 	await page.getByRole('option', { name: 'Glycosidic Multimers (-)' }).click();
 	await page.getByRole('option', { name: 'Lactyl Multimers (=Lac)' }).click();
 	await page.getByRole('option', { name: 'Anhydro-MurNAc (Anh)' }).click();