diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 49cc383..9979385 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,12 +1,11 @@ name: CI Pipeline (PRs and pushes main) run-name: Merged to main by ${{ github.actor }} + on: push: - branches: - - main + branches: [main] pull_request: - branches: - - main + branches: [main] permissions: contents: read @@ -23,16 +22,16 @@ jobs: - name: Checkout repository uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + - name: Set up Python + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - cache: pip - - name: Install package with pip - run: | - python -m pip install --upgrade pip - pip install .[dev] + - name: Install uv + uses: astral-sh/setup-uv@v3 + + - name: Install dependencies + run: uv sync --group dev - name: Run tests - run: pytest \ No newline at end of file + run: uv run pytest diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml index cb862a3..bdab073 100644 --- a/.github/workflows/publish_pypi.yml +++ b/.github/workflows/publish_pypi.yml @@ -51,4 +51,4 @@ jobs: name: python-package-distributions path: dist/ - name: Publish distribution package to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 \ No newline at end of file + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4787e8c..6e57f55 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,19 +1,58 @@ fail_fast: true repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v6.0.0 hooks: + - id: check-ast + - id: check-builtin-literals + - id: check-case-conflict + - id: check-docstring-first + - id: check-illegal-windows-names + - id: check-merge-conflict + - id: check-shebang-scripts-are-executable + - id: check-symlinks + - id: check-toml - id: check-yaml -- repo: https://github.com/astral-sh/uv-pre-commit - rev: 0.9.5 + - id: debug-statements + - id: end-of-file-fixer + - id: mixed-line-ending + - id: trailing-whitespace +- repo: https://github.com/fpgmaas/deptry + rev: 0.24.0 hooks: - - id: uv-lock + - id: deptry + language: python + additional_dependencies: [deptry] + exclude: '^(?!.*\.py$).*$' +- repo: https://github.com/asottile/pyupgrade + rev: v3.21.2 + hooks: + - id: pyupgrade +- repo: https://github.com/asottile/add-trailing-comma + rev: v4.0.0 + hooks: + - id: add-trailing-comma - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.0 + rev: v0.14.14 hooks: - - id: ruff - args: [ --fix ] + - id: ruff-check + args: + - --fix - id: ruff-format +- repo: https://github.com/astral-sh/uv-pre-commit + rev: 0.9.28 + hooks: + - id: uv-lock +- repo: https://github.com/tombi-toml/tombi-pre-commit + rev: v0.7.25 + hooks: + - id: tombi-format + - id: tombi-lint +- repo: https://github.com/crate-ci/typos + rev: v1 + hooks: + - id: typos + exclude: "^tests/" - repo: local hooks: - id: uv-upgrade @@ -25,4 +64,4 @@ repos: name: pytest entry: uv run pytest language: system - pass_filenames: false \ No newline at end of file + pass_filenames: false diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d5d825..16c7c88 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -42,7 +42,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ### Changed - In html_json generation, changed substrate from tuple to list of tuples to visualize substrates separately -- Changed Wikidata QID checking from raise errror to log warning (frequent 403 errors) +- Changed Wikidata QID checking from raise error to log warning (frequent 403 errors) ## [1.5.1] 26-07-2025 @@ -75,7 +75,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm - Bumped `mite_schema` version to `1.7.0` - Reworked `ValidationManager` - Implemented option for intramolecular reactions (recognized from reaction SMARTS) -- Pinned RDkit version to `2024.3.6` +- Pinned RDkit version to `2024.3.6` ## [1.3.1] 02-12-2024 @@ -142,4 +142,4 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ### Added -- Initial version of `mite_extras` \ No newline at end of file +- Initial version of `mite_extras` diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f68b48e..83c7d34 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,3 +1,3 @@ # CODE OF CONDUCT -See our organization-level [Code of Conduct](https://github.com/mite-standard/.github/blob/main/CODE_OF_CONDUCT.md). \ No newline at end of file +See our organization-level [Code of Conduct](https://github.com/mite-standard/.github/blob/main/CODE_OF_CONDUCT.md). diff --git a/README.md b/README.md index 66e3f81..1ebe98a 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ mite_extras ========== -[![DOI](https://zenodo.org/badge/804997522.svg)](https://doi.org/10.5281/zenodo.13941745) +[![DOI](https://zenodo.org/badge/804997522.svg)](https://doi.org/10.5281/zenodo.13941745) [![PyPI version](https://badge.fury.io/py/mite-extras.svg)](https://badge.fury.io/py/mite-extras) @@ -59,7 +59,7 @@ Dependencies including exact versions are specified in the [pyproject.toml](./py ## Quick Start -To validate MITE entries or update them to a new schema versiom, run: +To validate MITE entries or update them to a new schema version, run: - `mite_extras -i -o ` @@ -87,7 +87,7 @@ This work was supported by the Netherlands Organization for Scientific Research ### With `uv` from GitHub -*Note: assumes that `uv` is installed locally - see the methods described [here](https://docs.astral.sh/uv/getting-started/installation/).* +*Note: assumes that `uv` is installed locally - see the methods described [here](https://docs.astral.sh/uv/getting-started/installation/).* ```commandline git clone https://github.com/mite-standard/mite_extras diff --git a/src/mite_extras/__init__.py b/mite_extras/__init__.py similarity index 100% rename from src/mite_extras/__init__.py rename to mite_extras/__init__.py diff --git a/src/mite_extras/cli/__init__.py b/mite_extras/cli/__init__.py similarity index 100% rename from src/mite_extras/cli/__init__.py rename to mite_extras/cli/__init__.py diff --git a/src/mite_extras/cli/cli_manager.py b/mite_extras/cli/cli_manager.py similarity index 100% rename from src/mite_extras/cli/cli_manager.py rename to mite_extras/cli/cli_manager.py diff --git a/src/mite_extras/main.py b/mite_extras/main.py similarity index 99% rename from src/mite_extras/main.py rename to mite_extras/main.py index a4f2315..7b3fa18 100644 --- a/src/mite_extras/main.py +++ b/mite_extras/main.py @@ -46,8 +46,8 @@ def config_logger(verboseness: str) -> logging.Logger: console_handler = logging.StreamHandler(sys.stdout) console_handler.setFormatter( coloredlogs.ColoredFormatter( - "%(asctime)s - %(name)s - %(levelname)s - %(message)s" - ) + "%(asctime)s - %(name)s - %(levelname)s - %(message)s", + ), ) logger.addHandler(console_handler) return logger diff --git a/src/mite_extras/processing/__init__.py b/mite_extras/processing/__init__.py similarity index 100% rename from src/mite_extras/processing/__init__.py rename to mite_extras/processing/__init__.py diff --git a/src/mite_extras/processing/data_classes.py b/mite_extras/processing/data_classes.py similarity index 98% rename from src/mite_extras/processing/data_classes.py rename to mite_extras/processing/data_classes.py index 8aabd6a..ecfa574 100644 --- a/src/mite_extras/processing/data_classes.py +++ b/mite_extras/processing/data_classes.py @@ -168,7 +168,7 @@ def to_json(self: Self) -> dict: if self.databaseIds.to_json() == {}: raise RuntimeError( - "At least one of 'uniprot' and 'genpept' IDs must be provided." + "At least one of 'uniprot' and 'genpept' IDs must be provided.", ) else: json_dict["databaseIds"] = self.databaseIds.to_json() @@ -271,7 +271,8 @@ def validate_ids(self): try: if self.uniprot and self.genpept: self._id_validator.cleanup_ids( - genpept=self.genpept, uniprot=self.uniprot + genpept=self.genpept, + uniprot=self.uniprot, ) elif self.uniprot: data = self._id_validator.cleanup_ids(uniprot=self.uniprot) @@ -336,8 +337,8 @@ def cleanup_smarts(self): cleaned_smarts = ( self._reaction_validator.reaction_cleaner.clean_ketcher_format( self._reaction_validator.molecule_validator._clean_string( - self.reactionSMARTS - ) + self.reactionSMARTS, + ), ) ) @@ -372,7 +373,7 @@ def validate_reactions(self): ) except Exception as e: raise ValueError( - f"Reaction SMARTS #{reaction_id} - reaction example #{reaction}: Validation failed for substrate {reaction.substrate}: {e!s}" + f"Reaction SMARTS #{reaction_id} - reaction example #{reaction}: Validation failed for substrate {reaction.substrate}: {e!s}", ) from e return self @@ -460,13 +461,13 @@ def validate_smiles(self): try: # Clean substrate SMILES self.substrate = self._molecule_validator.canonicalize_smiles( - self._molecule_validator._clean_string(self.substrate) + self._molecule_validator._clean_string(self.substrate), ) # Clean product SMILES self.products = [ self._molecule_validator.canonicalize_smiles( - self._molecule_validator._clean_string(prod) + self._molecule_validator._clean_string(prod), ) for prod in self.products ] @@ -476,7 +477,7 @@ def validate_smiles(self): cleaned_forbidden = [] for prod in self.forbidden_products: cleaned = self._molecule_validator.canonicalize_smiles( - self._molecule_validator._clean_string(prod) + self._molecule_validator._clean_string(prod), ) # Split composite SMILES into individual molecules cleaned_forbidden.extend(cleaned.split(".")) @@ -505,7 +506,7 @@ def to_json(self: Self) -> dict: def to_html(self: Self) -> dict: def _smiles_to_svg(smiles: str) -> str: - """Generates a base64 encoded SVG strin""" + """Generates a base64 encoded SVG string""" m = MolFromSmiles(smiles) for atom in m.GetAtoms(): @@ -538,7 +539,7 @@ def _smiles_to_svg(smiles: str) -> str: ] except Exception as e: logger.warning( - f"Error during splitting substrate SMILES for rendering: {e!s}" + f"Error during splitting substrate SMILES for rendering: {e!s}", ) html_dict["substrate"] = [(self.substrate, _smiles_to_svg(self.substrate))] diff --git a/src/mite_extras/processing/file_manager.py b/mite_extras/processing/file_manager.py similarity index 97% rename from src/mite_extras/processing/file_manager.py rename to mite_extras/processing/file_manager.py index 60efcd7..89cd8d7 100644 --- a/src/mite_extras/processing/file_manager.py +++ b/mite_extras/processing/file_manager.py @@ -60,19 +60,19 @@ def validate_exists(self): def read_files_indir(self: Self) -> None: """Read files in the indir, store to self""" logger.debug( - f"FileManager: started reading file in input directory '{self.indir.name}'." + f"FileManager: started reading file in input directory '{self.indir.name}'.", ) for infile in self.indir.iterdir(): if infile.suffix != ".json": logger.warning( - f"FileManager: file '{infile.name}' does not apprear to be in .json-format - SKIP." + f"FileManager: file '{infile.name}' does not appear to be in .json-format - SKIP.", ) continue self.infiles.append(infile) logger.debug( - f"FileManager: completed reading file in input directory '{self.indir.name}'." + f"FileManager: completed reading file in input directory '{self.indir.name}'.", ) def write_json(self: Self, outfile_name: str, payload: dict) -> None: diff --git a/src/mite_extras/processing/mite_parser.py b/mite_extras/processing/mite_parser.py similarity index 97% rename from src/mite_extras/processing/mite_parser.py rename to mite_extras/processing/mite_parser.py index 643278f..86a6d44 100644 --- a/src/mite_extras/processing/mite_parser.py +++ b/mite_extras/processing/mite_parser.py @@ -123,7 +123,7 @@ def get_databaseids_reaction( return ReactionDatabaseIds(**data) def get_reactions(self: Self, reactions: list) -> list: - """Extract reactions infor and converts into internal data structure + """Extract reactions info and converts into internal data structure Args: reactions: list with reaction data @@ -166,11 +166,11 @@ def parse_mite_json(self: Self, data: dict): description=data.get("enzyme", {}).get("description"), databaseIds=EnyzmeDatabaseIds(**data["enzyme"]["databaseIds"]), auxiliaryEnzymes=self.get_auxenzymes( - auxenzymes=data.get("enzyme", {}).get("auxiliaryEnzymes") + auxenzymes=data.get("enzyme", {}).get("auxiliaryEnzymes"), ), references=data.get("enzyme", {}).get("references"), cofactors=self.get_cofactors( - cofactors=data.get("enzyme", {}).get("cofactors") + cofactors=data.get("enzyme", {}).get("cofactors"), ), ), reactions=self.get_reactions(reactions=data.get("reactions")), @@ -178,7 +178,7 @@ def parse_mite_json(self: Self, data: dict): ) except Exception as e: msg = str(e).split("For further information visit")[0].rstrip() - msg = f"Error in parsing entry {data.get("accession")}: {msg}" + msg = f"Error in parsing entry {data.get('accession')}: {msg}" raise ValueError(msg) from e logger.debug("MiteParser: completed creating Entry object.") diff --git a/src/mite_extras/processing/validation_manager.py b/mite_extras/processing/validation_manager.py similarity index 96% rename from src/mite_extras/processing/validation_manager.py rename to mite_extras/processing/validation_manager.py index 2f4c87c..034910f 100644 --- a/src/mite_extras/processing/validation_manager.py +++ b/mite_extras/processing/validation_manager.py @@ -51,7 +51,8 @@ class IdValidator(BaseModel): @staticmethod def cleanup_ids( - genpept: str | None = None, uniprot: str | None = None + genpept: str | None = None, + uniprot: str | None = None, ) -> dict[str, str]: """Cleans up IDs using the UniProt SPARQL endpoint. @@ -77,7 +78,7 @@ def fetch_result(query: str) -> str: ) if not response.ok: raise ValueError( - f"HTTP Error while querying Uniprot: {response.status_code}" + f"HTTP Error while querying Uniprot: {response.status_code}", ) response_json = response.json() @@ -89,7 +90,7 @@ def fetch_result(query: str) -> str: protein_data = bindings[0].get("protein") if not protein_data or "value" not in protein_data: raise ValueError( - "'protein' key or its 'value' is missing in the Uniprot response" + "'protein' key or its 'value' is missing in the Uniprot response", ) protein_uri = protein_data["value"] @@ -101,7 +102,7 @@ def build_genpept_query(genpept: str) -> str: PREFIX up: SELECT ?protein WHERE {{ - VALUES ?target {{}} + VALUES ?target {{}} ?protein a up:Protein . ?protein rdfs:seeAlso ?target. }} @@ -130,7 +131,7 @@ def build_uniprot_query(uniprot: str) -> str: if genpept and uniprot and genpept_result != uniprot: raise ValueError( - f"The provided Genpept ID '{genpept}' and Uniprot ID '{uniprot}' do not correspond to each other!" + f"The provided Genpept ID '{genpept}' and Uniprot ID '{uniprot}' do not correspond to each other!", ) return { @@ -168,7 +169,7 @@ def fetch_result(query: str) -> str | bool: ) if not response.ok: logger.warning( - f"HTTP Error while querying Wikidata: {response.status_code}" + f"HTTP Error while querying Wikidata: {response.status_code}", ) return False @@ -177,7 +178,7 @@ def fetch_result(query: str) -> str | bool: if not fetch_result(query=build_query(qid=qid)): raise ValueError( - f"Wikidata QID '{qid}' does not exist or has no statements." + f"Wikidata QID '{qid}' does not exist or has no statements.", ) @@ -196,7 +197,7 @@ def canonicalize_smiles(self, smiles: str) -> str: mol = MolFromSmiles(self._clean_string(smiles)) if mol is None: raise ValueError( - f"RDKit rejected SMILES string - is it a valid SMILES?\n" f"{smiles}" + f"RDKit rejected SMILES string - is it a valid SMILES?\n{smiles}", ) for atom in mol.GetAtoms(): atom.SetAtomMapNum(0) @@ -207,7 +208,7 @@ def canonicalize_smarts(self, smarts: str) -> str: mol = MolFromSmarts(self._clean_string(smarts)) if mol is None: raise ValueError( - f"RDKit rejected SMARTS string - is it a valid pattern?\n" f"{smarts}" + f"RDKit rejected SMARTS string - is it a valid pattern?\n{smarts}", ) for i, atom in enumerate(mol.GetAtoms()): atom.SetAtomMapNum(i) @@ -290,7 +291,7 @@ def enumerate_smarts(self, smarts: str) -> set[str]: mol = MolFromSmarts(smarts) if mol is None: raise ValueError( - f"RDKit rejected SMARTS string - is it a valid pattern?\n" f"{smarts}" + f"RDKit rejected SMARTS string - is it a valid pattern?\n{smarts}", ) enumerated_mols = self.enumerate_molecule(mol) return {MolToSmarts(m) for m in enumerated_mols if m is not None} @@ -366,13 +367,15 @@ def validate_reaction( if overlap := forbidden_smiles & expected_smiles: raise ValueError( f"Overlap between expected and forbidden products:\n" - f"{'\n'.join(overlap)}\n" + f"{'\n'.join(overlap)}\n", ) # Generate reaction variants and validate reactions = self._get_reaction_variants(reaction_smarts) predicted_products = self._run_reactions( - reactions, substrate_smiles, intramolecular + reactions, + substrate_smiles, + intramolecular, ) # Validate predictions @@ -388,13 +391,13 @@ def validate_reaction( f"Expected products:\n" f"{'\n'.join(expected_smiles)}\n" f"Generated products:\n" - f"{'\n'.join(predicted_smiles)}\n" + f"{'\n'.join(predicted_smiles)}\n", ) if overlap := forbidden_smiles & predicted_smiles: raise ValueError( f"Reaction product(s) belong(s) to the specified forbidden product(s):\n" - f"{'\n'.join(overlap)}\n" + f"{'\n'.join(overlap)}\n", ) logger.debug("Successfully validated reaction SMARTS") @@ -440,7 +443,7 @@ def _run_reactions( if substrate is None: raise ValueError( f"RDKit rejected SMILES string - is it a valid SMILES?\n" - f"{substrate_smiles}" + f"{substrate_smiles}", ) substrate_variants = self.enumerator.enumerate_molecule(substrate) diff --git a/pyproject.toml b/pyproject.toml index e0f447e..b1a8950 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,101 +3,84 @@ name = "mite_extras" version = "1.6.5" description = "Parsing, conversion, and validation functionality for Minimum Information about a Tailoring Enzyme (MITE) files." readme = "README.md" -requires-python = ">=3.12.0,<3.13.0" # because of rdkit 2024 -license-files = { paths = ["LICENSE"] } +requires-python = ">=3.12.0,<3.13.0" # because of rdkit 2024 +license-files = ["LICENSE"] authors = [ - { name = "Mitja M. Zdouc", email = "zdoucmm@gmail.com" }, - { name = "Adriano Rutz", email = "adafede@gmail.com" } -] -keywords = [ - "cheminformatics", - "genomics" + { name = "Mitja M. Zdouc", email = "zdoucmm@gmail.com" }, + { name = "Adriano Rutz", email = "adafede@gmail.com" } ] +keywords = ["cheminformatics", "genomics"] classifiers = [ - "Programming Language :: Python :: 3.12", - "License :: OSI Approved :: MIT License", - "Operating System :: POSIX :: Linux", - "Development Status :: 4 - Beta", - "Topic :: Scientific/Engineering :: Bio-Informatics", - "Topic :: Scientific/Engineering :: Chemistry" + "Development Status :: 4 - Beta", + "License :: OSI Approved :: MIT License", + "Operating System :: POSIX :: Linux", + "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Topic :: Scientific/Engineering :: Chemistry" ] dependencies = [ - "argparse~=1.4", - "coloredlogs~=15.0", - "json-repair~=0.51", - "jsonschema~=4.25", - "mite-schema", - "pydantic~=2.11", - "rdkit==2024.3.6", - "requests~=2.32", + "coloredlogs~=15.0", + "json-repair~=0.51", + "mite-schema>=1.8.4", + "pydantic~=2.11", + "rdkit==2024.3.6", + "requests~=2.32", ] [project.urls] -Homepage = "https://mite.bioinformatics.nl/" Github = "https://github.com/mite-standard/mite_extras" +Homepage = "https://mite.bioinformatics.nl/" Issues = "https://github.com/mite-standard/mite_extras/issues" [project.scripts] mite_extras = "mite_extras.main:main_cli" -[build-system] -requires = ["hatchling"] -build-backend = "hatchling.build" - -[project.optional-dependencies] +[dependency-groups] dev = [ - "pre-commit~=4.3", - "pytest~=8.4", - "ruff~=0.13" + "pre-commit~=4.3", + "pytest~=8.4", + "ruff~=0.13", ] -[tool.pytest.ini_options] -minversion = "6.0" -addopts = "-ra -q" -testpaths = [ - "tests", -] -pythonpath = [ - "src/mite_extras" -] +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" [tool.ruff] line-length = 88 [tool.ruff.lint] select = [ - # flake8-bugbear - "B", - # flake8-comprehensions - "C4", - # flake8-eradicate/eradicate - "ERA", - # isort - "I", - # pep8-naming - "N", - # flake8-pie - "PIE", - # pygrep - "PGH", - # ruff checks - "RUF", - # flake8-simplify - "SIM", - # flake8-type-checking - "TCH", - # flake8-tidy-imports - "TID", - # pyupgrade - "UP", + # flake8-bugbear + "B", + # flake8-comprehensions + "C4", + # flake8-eradicate/eradicate + "ERA", + # isort + "I", + # pep8-naming + "N", + # flake8-pie + "PIE", + # pygrep + "PGH", + # ruff checks + "RUF", + # flake8-simplify + "SIM", + # flake8-tidy-imports + "TID", + # pyupgrade + "UP", ] ignore = [ - # whitespace-before-punctuation - "E203", - # percent-format-invalid-format - "E501", - # mixed-case-variable-in-class-scope - "N815", - # needless-boool - "SIM103" + # whitespace-before-punctuation + "E203", + # percent-format-invalid-format + "E501", + # mixed-case-variable-in-class-scope + "N815", + # needless-boool + "SIM103" ] diff --git a/tests/test_processing/example_indir_mite/example_valid.json b/tests/test_processing/example_indir_mite/example_valid.json index 244694b..bbea421 100644 --- a/tests/test_processing/example_indir_mite/example_valid.json +++ b/tests/test_processing/example_indir_mite/example_valid.json @@ -73,4 +73,4 @@ } } ] -} \ No newline at end of file +} diff --git a/tests/test_processing/test_data_classes.py b/tests/test_processing/test_data_classes.py index cc2af26..877fe2f 100644 --- a/tests/test_processing/test_data_classes.py +++ b/tests/test_processing/test_data_classes.py @@ -1,6 +1,7 @@ from copy import deepcopy import pytest + from mite_extras.processing.data_classes import ( Changelog, Cofactors, diff --git a/tests/test_processing/test_file_manager.py b/tests/test_processing/test_file_manager.py index c750af8..89afaa7 100644 --- a/tests/test_processing/test_file_manager.py +++ b/tests/test_processing/test_file_manager.py @@ -2,6 +2,7 @@ from pathlib import Path import pytest + from mite_extras.processing.file_manager import FileManager diff --git a/tests/test_processing/test_mite_parser.py b/tests/test_processing/test_mite_parser.py index 6bd1516..038c504 100644 --- a/tests/test_processing/test_mite_parser.py +++ b/tests/test_processing/test_mite_parser.py @@ -1,9 +1,10 @@ import json import pytest +from mite_schema import SchemaManager + from mite_extras.processing.data_classes import Cofactors, EnzymeAux, Reaction from mite_extras.processing.mite_parser import MiteParser -from mite_schema import SchemaManager @pytest.fixture @@ -22,7 +23,7 @@ def test_get_cofactors(mite_json): def test_get_auxenzymes_valid(mite_json): parser = MiteParser() log = parser.get_auxenzymes( - auxenzymes=mite_json.get("enzyme").get("auxiliaryEnzymes") + auxenzymes=mite_json.get("enzyme").get("auxiliaryEnzymes"), ) assert len(log) == 1 assert isinstance(log[0], EnzymeAux) @@ -31,7 +32,7 @@ def test_get_auxenzymes_valid(mite_json): def test_get_databaseids_reaction_valid(mite_json): parser = MiteParser() log = parser.get_databaseids_reaction( - data=mite_json.get("reactions")[0].get("databaseIds") + data=mite_json.get("reactions")[0].get("databaseIds"), ) assert log.ec == "1.2.3.4" diff --git a/tests/test_processing/test_validation_manager/test_canonicalize_smarts.py b/tests/test_processing/test_validation_manager/test_canonicalize_smarts.py index ccc50b5..6378596 100644 --- a/tests/test_processing/test_validation_manager/test_canonicalize_smarts.py +++ b/tests/test_processing/test_validation_manager/test_canonicalize_smarts.py @@ -1,5 +1,4 @@ import pytest -from mite_extras.processing.validation_manager import MoleculeValidator from rdkit.Chem import ( CanonSmiles, MolFromSmarts, @@ -8,6 +7,8 @@ MolToSmiles, ) +from mite_extras.processing.validation_manager import MoleculeValidator + @pytest.fixture def _molecule_validator(): @@ -22,7 +23,7 @@ def test_canonicalize_smarts_valid(_molecule_validator): for i, atom in enumerate(mol.GetAtoms()): atom.SetAtomMapNum(i) expected_canonical_smarts = MolToSmarts( - MolFromSmiles(CanonSmiles(MolToSmiles(mol))) + MolFromSmiles(CanonSmiles(MolToSmiles(mol))), ) assert canonical_smarts == expected_canonical_smarts @@ -36,7 +37,7 @@ def test_canonicalize_smarts_complex(_molecule_validator): for i, atom in enumerate(mol.GetAtoms()): atom.SetAtomMapNum(i) expected_canonical_smarts = MolToSmarts( - MolFromSmiles(CanonSmiles(MolToSmiles(mol))) + MolFromSmiles(CanonSmiles(MolToSmiles(mol))), ) assert canonical_smarts == expected_canonical_smarts @@ -49,6 +50,6 @@ def test_canonicalize_smarts_with_aromatic(_molecule_validator): for i, atom in enumerate(mol.GetAtoms()): atom.SetAtomMapNum(i) expected_canonical_smarts = MolToSmarts( - MolFromSmiles(CanonSmiles(MolToSmiles(mol))) + MolFromSmiles(CanonSmiles(MolToSmiles(mol))), ) assert canonical_smarts == expected_canonical_smarts diff --git a/tests/test_processing/test_validation_manager/test_canonicalize_smiles.py b/tests/test_processing/test_validation_manager/test_canonicalize_smiles.py index 9102908..4665089 100644 --- a/tests/test_processing/test_validation_manager/test_canonicalize_smiles.py +++ b/tests/test_processing/test_validation_manager/test_canonicalize_smiles.py @@ -1,5 +1,4 @@ import pytest -from mite_extras.processing.validation_manager import MoleculeValidator from rdkit.Chem import ( CanonSmiles, MolFromSmarts, @@ -8,6 +7,8 @@ MolToSmiles, ) +from mite_extras.processing.validation_manager import MoleculeValidator + @pytest.fixture def _molecule_validator(): diff --git a/tests/test_processing/test_validation_manager/test_cleanup_ids.py b/tests/test_processing/test_validation_manager/test_cleanup_ids.py index 1c84941..bea7f8a 100644 --- a/tests/test_processing/test_validation_manager/test_cleanup_ids.py +++ b/tests/test_processing/test_validation_manager/test_cleanup_ids.py @@ -1,6 +1,8 @@ +import re from unittest.mock import patch import pytest + from mite_extras.processing.validation_manager import IdValidator @@ -19,9 +21,13 @@ def json(self): { "results": { "bindings": [ - {"protein": {"value": "http://purl.uniprot.org/uniprot/Q8KND5"}} - ] - } + { + "protein": { + "value": "http://purl.uniprot.org/uniprot/Q8KND5", + }, + }, + ], + }, }, 200, ) @@ -30,9 +36,13 @@ def json(self): { "results": { "bindings": [ - {"protein": {"value": "http://purl.uniprot.org/uniprot/Q8KND4"}} - ] - } + { + "protein": { + "value": "http://purl.uniprot.org/uniprot/Q8KND4", + }, + }, + ], + }, }, 200, ) @@ -43,11 +53,11 @@ def json(self): "bindings": [ { "protein": { - "value": "http://purl.uniprot.org/embl-cds/AAM70353.1" - } - } - ] - } + "value": "http://purl.uniprot.org/embl-cds/AAM70353.1", + }, + }, + ], + }, }, 200, ) @@ -58,11 +68,11 @@ def json(self): "bindings": [ { "protein": { - "value": "http://purl.uniprot.org/embl-cds/AAM70354.1" - } - } - ] - } + "value": "http://purl.uniprot.org/embl-cds/AAM70354.1", + }, + }, + ], + }, }, 200, ) @@ -94,7 +104,9 @@ def test_cleanup_ids_both_ok(mock_get): def test_cleanup_ids_both_fail_1(mock_get): with pytest.raises( ValueError, - match="The provided Genpept ID 'CAA71118.1' and Uniprot ID 'Q8KND5' do not correspond to each other!", + match=re.escape( + "The provided Genpept ID 'CAA71118.1' and Uniprot ID 'Q8KND5' do not correspond to each other!", + ), ): IdValidator().cleanup_ids(genpept="CAA71118.1", uniprot="Q8KND5") @@ -103,7 +115,9 @@ def test_cleanup_ids_both_fail_1(mock_get): def test_cleanup_ids_both_fail_2(mock_get): with pytest.raises( ValueError, - match="The provided Genpept ID 'AAM70353.1' and Uniprot ID 'Q8KND4' do not correspond to each other!", + match=re.escape( + "The provided Genpept ID 'AAM70353.1' and Uniprot ID 'Q8KND4' do not correspond to each other!", + ), ): IdValidator().cleanup_ids(genpept="AAM70353.1", uniprot="Q8KND4") @@ -111,14 +125,18 @@ def test_cleanup_ids_both_fail_2(mock_get): @patch("requests.get", side_effect=mock_requests_get) def test_cleanup_ids_none(mock_get): with pytest.raises( - ValueError, match="Please provide one of NCBI Genpept or Uniprot IDs." + ValueError, + match=re.escape("Please provide one of NCBI Genpept or Uniprot IDs."), ): IdValidator().cleanup_ids() @patch("requests.get", side_effect=mock_requests_get) def test_cleanup_ids_invalid(mock_get): - with pytest.raises(ValueError, match="HTTP Error while querying Uniprot: 404"): + with pytest.raises( + ValueError, + match=re.escape("HTTP Error while querying Uniprot: 404"), + ): IdValidator().cleanup_ids(genpept="invalidID") diff --git a/tests/test_processing/test_validation_manager/test_cleanup_reaction_smarts.py b/tests/test_processing/test_validation_manager/test_cleanup_reaction_smarts.py index ebac16f..3bc31af 100644 --- a/tests/test_processing/test_validation_manager/test_cleanup_reaction_smarts.py +++ b/tests/test_processing/test_validation_manager/test_cleanup_reaction_smarts.py @@ -1,4 +1,5 @@ import pytest + from mite_extras.processing.validation_manager import ( MoleculeValidator, ReactionValidator, @@ -19,6 +20,6 @@ def test_cleanup_reaction_smarts_valid(_molecule_validator, _reaction_validator) """Test cleanup of a valid reaction SMARTS string""" reaction_smarts = "[C:1][O:2]>>[C:1]=[O:2]" result = _reaction_validator.reaction_cleaner.clean_ketcher_format( - _reaction_validator.molecule_validator._clean_string(reaction_smarts) + _reaction_validator.molecule_validator._clean_string(reaction_smarts), ) assert result == reaction_smarts diff --git a/tests/test_processing/test_validation_manager/test_remove_ketcher_flavor_smarts.py b/tests/test_processing/test_validation_manager/test_remove_ketcher_flavor_smarts.py index dc81acf..aa67eed 100644 --- a/tests/test_processing/test_validation_manager/test_remove_ketcher_flavor_smarts.py +++ b/tests/test_processing/test_validation_manager/test_remove_ketcher_flavor_smarts.py @@ -1,4 +1,5 @@ import pytest + from mite_extras.processing.validation_manager import ReactionCleaner @@ -16,7 +17,7 @@ def test_chloride_wo_indexing(): def test_chloride_substitute_w_indexing(): assert ReactionCleaner.clean_ketcher_format( - "[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2]-[#6:3]=1-Cl:7>>[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2](-Cl)-[#6:3]=1-Cl:7" + "[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2]-[#6:3]=1-Cl:7>>[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2](-Cl)-[#6:3]=1-Cl:7", ) == ( "[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2]-[#6:3]=1-[Cl:7]>>[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2](-[Cl])-[#6:3]=1-[Cl:7]" ) @@ -24,7 +25,7 @@ def test_chloride_substitute_w_indexing(): def test_chloride_substitute_wo_indexing(): assert ReactionCleaner.clean_ketcher_format( - "[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2]-[#6:3]=1>>[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2]-[#6:3]=1-Cl" + "[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2]-[#6:3]=1>>[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2]-[#6:3]=1-Cl", ) == ( "[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2]-[#6:3]=1>>[#6:1]1-[#6:5]=[#6:6]-[#6:4]=[#6:2]-[#6:3]=1-[Cl]" ) @@ -32,7 +33,7 @@ def test_chloride_substitute_wo_indexing(): def test_nitrogen_heterocycle_1(): assert ReactionCleaner.clean_ketcher_format( - "[#7:1;h1]1:[#6:3]:[#6:2]:[#6:4](-[#7]-[#6]):[#6:5]:1>>[#7:1;h1]1:[#6:5]:[#6:4]:[#6:2](-[#7]-[#6]):[#6:3]:1" + "[#7:1;h1]1:[#6:3]:[#6:2]:[#6:4](-[#7]-[#6]):[#6:5]:1>>[#7:1;h1]1:[#6:5]:[#6:4]:[#6:2](-[#7]-[#6]):[#6:3]:1", ) == ( "[nH1:1]1:[#6:3]:[#6:2]:[#6:4](-[#7]-[#6]):[#6:5]:1>>[nH1:1]1:[#6:5]:[#6:4]:[#6:2](-[#7]-[#6]):[#6:3]:1" ) @@ -40,7 +41,7 @@ def test_nitrogen_heterocycle_1(): def test_nitrogen_heterocycle_2(): assert ReactionCleaner.clean_ketcher_format( - "[#7;h1]1:[#6:3]:[#6:2]:[#6:4](-[#7]-[#6]):[#6:5]:1>>[#7;h1]1:[#6:5]:[#6:4]:[#6:2](-[#7]-[#6]):[#6:3]:1" + "[#7;h1]1:[#6:3]:[#6:2]:[#6:4](-[#7]-[#6]):[#6:5]:1>>[#7;h1]1:[#6:5]:[#6:4]:[#6:2](-[#7]-[#6]):[#6:3]:1", ) == ( "[nH1]1:[#6:3]:[#6:2]:[#6:4](-[#7]-[#6]):[#6:5]:1>>[nH1]1:[#6:5]:[#6:4]:[#6:2](-[#7]-[#6]):[#6:3]:1" ) @@ -48,7 +49,7 @@ def test_nitrogen_heterocycle_2(): def test_numbered_charges_1(): assert ReactionCleaner.clean_ketcher_format( - "[#6:1]1:[#6:5]:[#6:6]:[#6:4]:[#6:2](-[#6:7]):[#6:3]:1-[#7:8;+](=[#8:10])-[#8:9;-]>>[#6:1]1:[#6:5]:[#6:6]:[#6:4]:[#6:2](-[#6:7]-[#8]):[#6:3]:1-[#7:8;+](=[#8:10])-[#8:9;-]" + "[#6:1]1:[#6:5]:[#6:6]:[#6:4]:[#6:2](-[#6:7]):[#6:3]:1-[#7:8;+](=[#8:10])-[#8:9;-]>>[#6:1]1:[#6:5]:[#6:6]:[#6:4]:[#6:2](-[#6:7]-[#8]):[#6:3]:1-[#7:8;+](=[#8:10])-[#8:9;-]", ) == ( "[#6:1]1:[#6:5]:[#6:6]:[#6:4]:[#6:2](-[#6:7]):[#6:3]:1-[#7;+:8](=[#8:10])-[#8;-:9]>>[#6:1]1:[#6:5]:[#6:6]:[#6:4]:[#6:2](-[#6:7]-[#8]):[#6:3]:1-[#7;+:8](=[#8:10])-[#8;-:9]" ) @@ -57,7 +58,7 @@ def test_numbered_charges_1(): def test_expl_hydro_valid(): assert ( ReactionCleaner.detect_undesired_smarts( - "[#6:1]1-[#6:2]-[#6:3]-[#6:4]-[#6:5]-[#6:6]-1>>[#6:1]1-[#6:6]-[#6:5](-[#8])-[#6:4]-[#6:3]-[#6:2]-1" + "[#6:1]1-[#6:2]-[#6:3]-[#6:4]-[#6:5]-[#6:6]-1>>[#6:1]1-[#6:6]-[#6:5](-[#8])-[#6:4]-[#6:3]-[#6:2]-1", ) is None ) @@ -66,14 +67,14 @@ def test_expl_hydro_valid(): def test_expl_hydro_invalid(): with pytest.raises(ValueError): assert ReactionCleaner.detect_undesired_smarts( - "[#6:1]-[#6:2]-[#6:3]-[#7:4]>>[#6:2](-[#6@:3](-[#7:4])(/[H])\\[#8])-[#6:1]" + "[#6:1]-[#6:2]-[#6:3]-[#7:4]>>[#6:2](-[#6@:3](-[#7:4])(/[H])\\[#8])-[#6:1]", ) def test_cxsmarts_valid(): assert ( ReactionCleaner.detect_undesired_smarts( - "[#6:1]1-[#6:2]-[#6:3]-[#6:4]-[#6:5]-[#6:6]-1>>[#6:1]1-[#6:6]-[#6:5](-[#8])-[#6:4]-[#6:3]-[#6:2]-1" + "[#6:1]1-[#6:2]-[#6:3]-[#6:4]-[#6:5]-[#6:6]-1>>[#6:1]1-[#6:6]-[#6:5](-[#8])-[#6:4]-[#6:3]-[#6:2]-1", ) is None ) @@ -82,5 +83,5 @@ def test_cxsmarts_valid(): def test_cxsmarts_invalid(): with pytest.raises(ValueError): assert ReactionCleaner.detect_undesired_smarts( - "[NH2:1][C@@H:2]([CH2:3][c:4]1[cH:5][n:6][c:7]2[cH:8][cH:9][cH:10][cH:11][c:12]12)[C:13]([OH:14])=[O:15].[ClH:16]>>[NH2:1][C@@H:2]([CH2:3][c:4]1[cH:5][nH:6][c:7]2[cH:8][cH:9][cH:10][c:11]([Cl:12])[c:13]12)[C:14]([OH:15])=[O:16] |r,Sg:n:2:1-2:ht|" + "[NH2:1][C@@H:2]([CH2:3][c:4]1[cH:5][n:6][c:7]2[cH:8][cH:9][cH:10][cH:11][c:12]12)[C:13]([OH:14])=[O:15].[ClH:16]>>[NH2:1][C@@H:2]([CH2:3][c:4]1[cH:5][nH:6][c:7]2[cH:8][cH:9][cH:10][c:11]([Cl:12])[c:13]12)[C:14]([OH:15])=[O:16] |r,Sg:n:2:1-2:ht|", ) diff --git a/tests/test_processing/test_validation_manager/test_unescape_string.py b/tests/test_processing/test_validation_manager/test_unescape_string.py index 0cfcee1..b0e75fb 100644 --- a/tests/test_processing/test_validation_manager/test_unescape_string.py +++ b/tests/test_processing/test_validation_manager/test_unescape_string.py @@ -1,4 +1,5 @@ import pytest + from mite_extras.processing.validation_manager import MoleculeValidator diff --git a/tests/test_processing/test_validation_manager/test_validate_reaction_smarts.py b/tests/test_processing/test_validation_manager/test_validate_reaction_smarts.py index 8d5495e..e643cb3 100644 --- a/tests/test_processing/test_validation_manager/test_validate_reaction_smarts.py +++ b/tests/test_processing/test_validation_manager/test_validate_reaction_smarts.py @@ -1,4 +1,5 @@ import pytest + from mite_extras.processing.validation_manager import ( ReactionValidator, ) @@ -16,7 +17,10 @@ def test_validate_reaction_valid(_reaction_validator): expected_products = ["C=O"] forbidden_products = [] result = _reaction_validator.validate_reaction( - reaction_smarts, substrate_smiles, expected_products, forbidden_products + reaction_smarts, + substrate_smiles, + expected_products, + forbidden_products, ) assert result == None @@ -29,7 +33,10 @@ def test_validate_reaction_forbidden_in_expected(_reaction_validator): forbidden_products = ["C=O"] # Forbidden product is also in expected products with pytest.raises(ValueError): _reaction_validator.validate_reaction( - reaction_smarts, substrate_smiles, expected_products, forbidden_products + reaction_smarts, + substrate_smiles, + expected_products, + forbidden_products, ) @@ -42,7 +49,10 @@ def test_validate_reaction_unexpected_products(_reaction_validator): predicted_smiles_set = {"O=CO"} # Assume this is what the reaction predicts with pytest.raises(ValueError): _reaction_validator.validate_reaction( - reaction_smarts, substrate_smiles, expected_products, forbidden_products + reaction_smarts, + substrate_smiles, + expected_products, + forbidden_products, ) @@ -54,7 +64,10 @@ def test_validate_reaction_forbidden_products(_reaction_validator): forbidden_products = ["O=CCO"] # Forbidden product is also expected with pytest.raises(ValueError): _reaction_validator.validate_reaction( - reaction_smarts, substrate_smiles, expected_products, forbidden_products + reaction_smarts, + substrate_smiles, + expected_products, + forbidden_products, ) @@ -66,7 +79,10 @@ def test_validate_reaction_empty_expected_products(_reaction_validator): forbidden_products = [] with pytest.raises(ValueError): _reaction_validator.validate_reaction( - reaction_smarts, substrate_smiles, expected_products, forbidden_products + reaction_smarts, + substrate_smiles, + expected_products, + forbidden_products, ) @@ -78,7 +94,10 @@ def test_validate_reaction_invalid_expected_product(_reaction_validator): forbidden_products = [] with pytest.raises(ValueError): _reaction_validator.validate_reaction( - reaction_smarts, substrate_smiles, expected_products, forbidden_products + reaction_smarts, + substrate_smiles, + expected_products, + forbidden_products, ) @@ -90,7 +109,10 @@ def test_validate_reaction_invalid_forbidden_product(_reaction_validator): forbidden_products = ["INVALID_SMILES"] # Invalid forbidden product with pytest.raises(ValueError): _reaction_validator.validate_reaction( - reaction_smarts, substrate_smiles, expected_products, forbidden_products + reaction_smarts, + substrate_smiles, + expected_products, + forbidden_products, ) @@ -102,7 +124,10 @@ def test_validate_reaction_valid_composite_pass(_reaction_validator): expected_products = ["Clc1cccc2[nH]ccc12"] forbidden_products = [] result = _reaction_validator.validate_reaction( - reaction_smarts, substrate_smiles, expected_products, forbidden_products + reaction_smarts, + substrate_smiles, + expected_products, + forbidden_products, ) assert result == None @@ -117,7 +142,10 @@ def test_validate_reaction_halogenation(_reaction_validator): ] forbidden_products = [] result = _reaction_validator.validate_reaction( - reaction_smarts, substrate_smiles, expected_products, forbidden_products + reaction_smarts, + substrate_smiles, + expected_products, + forbidden_products, ) assert result == None @@ -128,7 +156,7 @@ def test_validate_intramolecular_macrolactam(_reaction_validator): "C[C@H](NC(=O)[C@H](CCC(=O)O)NC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)CN)C(=O)O" ) expected_products = [ - "C[C@H](NC(=O)[C@@H]1CCC(=O)ONCC(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N1)C(=O)O" + "C[C@H](NC(=O)[C@@H]1CCC(=O)ONCC(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N1)C(=O)O", ] forbidden_products = [] result = _reaction_validator.validate_reaction( @@ -145,7 +173,7 @@ def test_validate_cheatoglobosin_1(_reaction_validator): r_smarts = "[#6:1]1(:[#6:36]:[#7:35;h1]:[#6:30]2:[#6:31]:[#6:32]:[#6:33]:[#6:34]:[#6:29]:1:2)-[#6:2]\\[#6@:3]1-[#6@:13]2-[#6@@:7]3(-[#6:27](=[#8:28])-[#6:26]=[#6:25]-[#6:24]-[#6:23]-[#6:21](-[#6:22])=[#6:20]-[#6@@:18](/[#6:19])-[#6:17]-[#6:16]=[#6:15]/[#6@:8]-3-[#6:9]=[#6:10](-[#6:14])-[#6@:11]/2/[#6:12])/[#6:5](=[#8:6])-[#7:4]-1>>[#6:1]1(:[#6:36]:[#7:35;h1]:[#6:30]2:[#6:31]:[#6:32]:[#6:33]:[#6:34]:[#6:29]:1:2)-[#6:2]\\[#6@:3]1-[#6@:13]2-[#6@@:7]3(-[#6:27](=[#8:28])-[#6:26]=[#6:25]-[#6:24]-[#6:23]-[#6:21](-[#6:22])=[#6:20]-[#6@@:18](/[#6:19])-[#6:17]-[#6:16]=[#6:15]/[#6@:8]-3-[#6@@:9]3\\[#8]-[#6@:10]-3(/[#6:14])-[#6@:11]/2/[#6:12])/[#6:5](=[#8:6])-[#7:4]-1" substr = "c1(C[C@@H]2NC(=O)[C@@]34[C@H](C=C([C@@H](C)C23)C)C=CC[C@H](C)C=C(C)CCC=CC4=O)c2c(cccc2)[nH]c1 |c:21,t:16,26|" prods = [ - "c1(C[C@H]2C3[C@H](C)[C@]4(C)[C@@H](O4)[C@H]4[C@@]3(C(N2)=O)C(C=CCCC(C)=C[C@H](CC=C4)C)=O)c2c(cccc2)[nH]c1" + "c1(C[C@H]2C3[C@H](C)[C@]4(C)[C@@H](O4)[C@H]4[C@@]3(C(N2)=O)C(C=CCCC(C)=C[C@H](CC=C4)C)=O)c2c(cccc2)[nH]c1", ] result = _reaction_validator.validate_reaction( r_smarts, @@ -157,7 +185,7 @@ def test_validate_cheatoglobosin_1(_reaction_validator): assert result == None substr = "c1(C[C@@H]2NC(=O)[C@@]34[C@H](C=C([C@@H](C)C23)C)C=CC[C@H](C)C=C(C)[C@@H](O)[C@@H](O)C=CC4=O)c2c(cccc2)[nH]c1 |c:21,t:16,28|" prods = [ - "c1(C[C@@H]2NC(=O)[C@@]34[C@H]([C@H]5[C@]([C@@H](C)C23)(C)O5)C=CC[C@H](C)C=C(C)[C@@H](O)[C@@H](O)C=CC4=O)c2c(cccc2)[nH]c1" + "c1(C[C@@H]2NC(=O)[C@@]34[C@H]([C@H]5[C@]([C@@H](C)C23)(C)O5)C=CC[C@H](C)C=C(C)[C@@H](O)[C@@H](O)C=CC4=O)c2c(cccc2)[nH]c1", ] result = _reaction_validator.validate_reaction( r_smarts, @@ -169,7 +197,7 @@ def test_validate_cheatoglobosin_1(_reaction_validator): assert result == None substr = "c1(C[C@@H]2NC(=O)[C@@]34[C@H](C=C([C@@H](C)C23)C)C=CC[C@H](C)C=C(C)[C@@H](O)C(=O)C=CC4=O)c2c(cccc2)[nH]c1 |c:21,t:16,28|" prods = [ - 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