diff --git a/.gitignore b/.gitignore index bd99fc5..0683079 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,3 @@ -outputs/ \ No newline at end of file +outputs/ +libs/jump_smiles/CLAUDE.md +libs/jump_smiles/.claude/settings.local.json diff --git a/libs/jump_smiles/README.md b/libs/jump_smiles/README.md index d594d78..19ddbc3 100644 --- a/libs/jump_smiles/README.md +++ b/libs/jump_smiles/README.md @@ -1,100 +1,98 @@ -# JUMP-SMILES Documentation +# JUMP-SMILES -A Python library for standardizing chemical structures using RDKit. Designed to standardize SMILES strings for consistency with the [JUMP Cell Painting datasets](https://github.com/jump-cellpainting/datasets). +Python library for standardizing chemical structures using RDKit. Designed for consistency with [JUMP Cell Painting datasets](https://github.com/jump-cellpainting/datasets). ## Installation -Requires Python 3.11+ and Poetry package manager. +Requires Python 3.11 or 3.12 (RDKit 2023.9.5 constraint). ```bash +# Clone and install git clone cd jump-smiles -poetry install -poetry shell -``` +uv sync --python 3.11 -Core dependencies (managed by Poetry): -- rdkit 2023.9.5 -- pandas 2.2.2 -- numpy 2.1.1 -- fire 0.4.0+ -- tqdm 4.64.1 -- requests 2.28.2 +# Or add to your project (replace BRANCH_NAME with desired branch, or omit @BRANCH_NAME for main) +uv add "git+https://github.com/broadinstitute/monorepo.git@BRANCH_NAME#subdirectory=libs/jump_smiles" +``` ## Usage ### Command Line + ```bash -poetry run python standardize_smiles.py \ - --input molecules.csv \ - --output standardized_molecules.csv \ - --num_cpu 4 \ - --method jump_canonical +# If installed locally +uv run jump-smiles --input molecules.csv --output standardized.csv + +# Without installation (replace BRANCH_NAME with desired branch, or omit @BRANCH_NAME for main) +uvx --python 3.11 --from "git+https://github.com/broadinstitute/monorepo.git@BRANCH_NAME#subdirectory=libs/jump_smiles" jump-smiles --input molecules.csv --output standardized.csv ``` ### Python API + ```python -from smiles.standardize_smiles import StandardizeMolecule +from jump_smiles.standardize_smiles import StandardizeMolecule -# With file input +# File input standardizer = StandardizeMolecule( input="molecules.csv", - output="standardized_molecules.csv", + output="standardized.csv", num_cpu=4 ) -standardized_df = standardizer.run() +result = standardizer.run() -# With DataFrame input +# DataFrame input import pandas as pd -df = pd.DataFrame({ - 'SMILES': [ - 'CC(=O)OC1=CC=CC=C1C(=O)O', # Aspirin - 'CN1C=NC2=C1C(=O)N(C(=O)N2C)C' # Caffeine - ] -}) -standardized_df = StandardizeMolecule(input=df).run() +df = pd.DataFrame({'SMILES': ['CC(=O)OC1=CC=CC=C1C(=O)O']}) +result = StandardizeMolecule(input=df).run() ``` ## Parameters -- `input`: CSV/TSV file path or pandas DataFrame with 'SMILES'/'smiles' column +- `input`: CSV/TSV file or DataFrame with SMILES column - `output`: Output file path (optional) - `num_cpu`: Number of CPU cores (default: 1) - `limit_rows`: Maximum rows to process (optional) - `augment`: Include original columns in output (default: False) -- `method`: Standardization method (default: "jump_canonical") +- `method`: Standardization method - "jump_canonical" (default) or "jump_alternate_1" - `random_seed`: For reproducibility (default: 42) ## Standardization Methods -### jump_canonical -The default method used in JUMP Cell Painting datasets. Performs iterative steps until convergence (max 5 iterations): -- Charge parent normalization -- Isotope removal -- Stereo parent normalization -- Tautomer parent normalization -- General standardization +**jump_canonical** (default): The method used in JUMP Cell Painting datasets. Performs iterative normalization until convergence. -If no convergence, selects most common form. +**jump_alternate_1**: Sequential InChI-based standardization, recommended for tautomer-heavy datasets. -### jump_alternate_1 -Recommended for tautomer-heavy datasets. Performs sequential steps: -1. InChI-based standardization -2. Structure cleanup -3. Fragment handling -4. Charge neutralization -5. Tautomer canonicalization +See the class docstring for detailed method descriptions. ## Output Format -Returns DataFrame with columns: -- `SMILES_original`: Input SMILES -- `SMILES_standardized`: Standardized SMILES -- `InChI_standardized`: Standardized InChI -- `InChIKey_standardized`: Standardized InChIKey - -If `augment=True`, includes all original columns. - -## Limitations -1. No 3D structure processing -2. May not find most chemically relevant tautomer -3. Limited handling of complex metal-organic structures + +Returns DataFrame with standardized SMILES, InChI, and InChIKey. Use `augment=True` to include original columns. + +## Development + +```bash +# Install with dev dependencies +uv sync --python 3.11 --extra dev + +# Run tests +uv run pytest + +# Run fast tests only (skip slow idempotency tests) +uv run pytest -m "not slow" + +# Test idempotency with JUMP compounds (data already included) +uv run pytest test/test_idempotency.py -v # Tests with 100 compounds +uv run pytest test/test_idempotency.py -m "not very_slow" -v # Skip full dataset test +uv run pytest test/test_idempotency.py::test_standardizer_idempotency[all-jump_canonical] -v # Test full dataset (~115k compounds, very slow) +# To refresh/update the test data: uv run --script scripts/download_jump_compounds.py + +# Lint and format +uv run ruff check src/ +uv run ruff format src/ +``` + +## Important Notes + +- **RDKit 2023.9.5** is strictly required for reproducibility with JUMP datasets +- Must use Python 3.11 or 3.12 due to RDKit compatibility \ No newline at end of file diff --git a/libs/jump_smiles/pyproject.toml b/libs/jump_smiles/pyproject.toml index a60f179..132a087 100644 --- a/libs/jump_smiles/pyproject.toml +++ b/libs/jump_smiles/pyproject.toml @@ -1,29 +1,36 @@ -[tool.poetry] +[project] name = "jump-smiles" -version = "0.0.1" -description = "" +version = "0.0.2" +description = "Python library for standardizing chemical structures using RDKit" readme = "README.md" -authors = ["Alán F. Muñoz "] -license = "MIT" +authors = [ + {name = "Alán F. Muñoz", email = "amunozgo@broadinstitute.org"}, +] +license = {text = "MIT"} +requires-python = ">=3.11,<3.13" # RDKit 2023.9.5 only has wheels for 3.11-3.12 +dependencies = [ + "rdkit==2023.9.5", + "fire>=0.4.0", + "requests>=2.28.0,<3", + "pandas>=2.2.0,<3", + "numpy>=1.26.0,<2", + "tqdm>=4.64.1", +] -[tool.poetry.dependencies] -python = ">=3.11,<4" -rdkit = "2023.9.5" -fire = ">=0.4.0" -requests = "2.28.2" -pandas = "2.2.2" -numpy = "1.26.4" -tqdm = "4.64.1" +[project.scripts] +jump-smiles = "jump_smiles.standardize_smiles:main" -[tool.poetry.group.dev.dependencies] -jupyter = ">=1.0.0" -ipykernel = ">=6.21.2" -pytest = "8.1.1" -jupytext = "^1.15.2" -ipdb = "^0.13.13" -ruff-lsp = "^0.0.50" -ruff = "<0.2.0" +[project.optional-dependencies] +dev = [ + "jupyter>=1.0.0", + "ipykernel>=6.21.2", + "pytest>=8.1.1", + "jupytext>=1.15.2,<2", + "ipdb>=0.13.13", + "ruff-lsp>=0.0.50", + "ruff<0.2.0", +] [build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling"] +build-backend = "hatchling.build" \ No newline at end of file diff --git a/libs/jump_smiles/pytest.ini b/libs/jump_smiles/pytest.ini index 9e5553c..0b1ec63 100644 --- a/libs/jump_smiles/pytest.ini +++ b/libs/jump_smiles/pytest.ini @@ -1,3 +1,8 @@ [pytest] +markers = + slow: marks tests as slow (deselect with '-m "not slow"') + very_slow: marks tests as very slow - full dataset tests (deselect with '-m "not very_slow"') + idempotency: marks idempotency tests filterwarnings = - ignore::DeprecationWarning:fire.core \ No newline at end of file + ignore::DeprecationWarning:fire.core + ignore::DeprecationWarning:rdkit.Chem.MolStandardize \ No newline at end of file diff --git a/libs/jump_smiles/scripts/download_jump_compounds.py b/libs/jump_smiles/scripts/download_jump_compounds.py new file mode 100644 index 0000000..7c82a91 --- /dev/null +++ b/libs/jump_smiles/scripts/download_jump_compounds.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python3 +# /// script +# requires-python = ">=3.11" +# dependencies = [ +# "pandas>=2.2.0", +# "pooch>=1.8.0", +# "tqdm>=4.64.1", +# ] +# /// +""" +Download JUMP compound dataset and extract only SMILES column. + +Usage: + uv run --script scripts/download_jump_compounds.py +""" + +import pandas as pd +import pooch +from pathlib import Path + +# Configuration +CACHE_DIR = Path(__file__).parent.parent / "test/test_data/jump_compounds" +URL = "https://github.com/jump-cellpainting/datasets/refs/tags/v0.13/metadata/compound.csv.gz" +OUTPUT_FILE = CACHE_DIR / "smiles_only.csv.gz" + + +def main(): + """Download and process JUMP compounds data.""" + + # Create cache directory + CACHE_DIR.mkdir(parents=True, exist_ok=True) + + # Download with pooch (automatic caching) + print("Downloading/loading JUMP compounds data...") + file_path = pooch.retrieve( + url=URL, + known_hash=None, # Will compute on first download + path=CACHE_DIR, + fname="compound.csv.gz", + progressbar=True, + ) + + # Load and extract SMILES column + print("Extracting SMILES column...") + df = pd.read_csv( + file_path, compression="gzip", usecols=["Metadata_JCP2022", "Metadata_SMILES"] + ) + + # Clean data + original_count = len(df) + df = df[df["Metadata_SMILES"].notna()] + df = df[df["Metadata_SMILES"] != ""] + + # Save compressed + df.to_csv( + OUTPUT_FILE, compression={"method": "gzip", "compresslevel": 9}, index=False + ) + + # Report + print(f"Saved {len(df)}/{original_count} valid SMILES") + print(f" File: {OUTPUT_FILE}") + print(f" Size: {OUTPUT_FILE.stat().st_size / 1024:.1f} KB") + + +if __name__ == "__main__": + main() diff --git a/libs/jump_smiles/src/jump_smiles/standardize_smiles.py b/libs/jump_smiles/src/jump_smiles/standardize_smiles.py index ff28b93..320b5eb 100644 --- a/libs/jump_smiles/src/jump_smiles/standardize_smiles.py +++ b/libs/jump_smiles/src/jump_smiles/standardize_smiles.py @@ -24,6 +24,40 @@ class StandardizeMolecule: + """ + Standardize chemical structures for consistency with JUMP Cell Painting datasets. + + This class provides two standardization methods: + + 1. **jump_canonical** (default): The method used in JUMP Cell Painting datasets. + Performs iterative standardization until convergence (max 5 iterations): + - Charge parent normalization + - Isotope removal + - Stereo parent normalization + - Tautomer parent normalization + - General standardization + If no convergence after 5 iterations, selects the most common form. + + 2. **jump_alternate_1**: Recommended for tautomer-heavy datasets. + Performs sequential steps: + - InChI-based standardization + - Structure cleanup + - Fragment handling + - Charge neutralization + - Tautomer canonicalization + + Output includes: + - SMILES_original: Input SMILES + - SMILES_standardized: Standardized SMILES + - InChI_standardized: Standardized InChI + - InChIKey_standardized: Standardized InChIKey + + Limitations: + - No 3D structure processing + - May not find most chemically relevant tautomer + - Limited handling of complex metal-organic structures + """ + def __init__( self, input: Union[str, pd.DataFrame], @@ -43,7 +77,7 @@ def __init__( :param limit_rows: Limit the number of rows to be processed (optional) :param augment: The output is the input file augmented with the standardized SMILES, InChI, and InChIKey (default: False) :param method: Standardization method to use: "jump_canonical" or "jump_alternate_1" (default: "jump_canonical") - + :param random_seed: Random seed for reproducibility (default: 42) """ self.input = input self.output = output @@ -308,5 +342,9 @@ def run(self): return standardized_df -if __name__ == "__main__": +def main(): fire.Fire(StandardizeMolecule) + + +if __name__ == "__main__": + main() diff --git a/libs/jump_smiles/test/test_data/jump_compounds/smiles_only.csv.gz b/libs/jump_smiles/test/test_data/jump_compounds/smiles_only.csv.gz new file mode 100644 index 0000000..85fd184 Binary files /dev/null and b/libs/jump_smiles/test/test_data/jump_compounds/smiles_only.csv.gz differ diff --git a/libs/jump_smiles/test/test_idempotency.py b/libs/jump_smiles/test/test_idempotency.py new file mode 100644 index 0000000..9bb3cb9 --- /dev/null +++ b/libs/jump_smiles/test/test_idempotency.py @@ -0,0 +1,137 @@ +""" +Test idempotency of SMILES standardization using JUMP compounds data. +""" + +import pytest +import pandas as pd +from pathlib import Path +from jump_smiles.standardize_smiles import StandardizeMolecule + +# Configuration +SMILES_FILE = Path(__file__).parent / "test_data/jump_compounds/smiles_only.csv.gz" +DEFAULT_SAMPLE_SIZE = 100 # Reduced for faster testing, increase for thorough testing +RANDOM_SEED = 42 + + +def load_compounds(sample_size): + """Load JUMP compound SMILES data with specified sample size.""" + if not SMILES_FILE.exists(): + pytest.skip( + "SMILES data not found. Run: uv run --script scripts/download_jump_compounds.py" + ) + + df = pd.read_csv(SMILES_FILE, compression="gzip") + + if sample_size == "all": + return df + else: + # Sample for speed (deterministic) + actual_sample_size = min(sample_size, len(df)) + return df.sample(n=actual_sample_size, random_state=RANDOM_SEED) + + +@pytest.mark.slow +@pytest.mark.idempotency +@pytest.mark.parametrize( + "method", ["jump_canonical"] +) # Can add "jump_alternate_1" later +@pytest.mark.parametrize( + "sample_size", [100, pytest.param("all", marks=pytest.mark.very_slow)] +) +def test_standardizer_idempotency(method, sample_size): + """Test that standardization is idempotent. + + Args: + method: Standardization method to test + sample_size: Number of compounds to test (100 or "all" for full dataset) + """ + compound_smiles = load_compounds(sample_size) + + print(f"\nTesting idempotency for {len(compound_smiles)} compounds using {method}") + + # First pass: standardize original SMILES + input_df = compound_smiles[["Metadata_SMILES"]].rename( + columns={"Metadata_SMILES": "SMILES"} + ) + standardizer1 = StandardizeMolecule( + input=input_df, method=method, random_seed=RANDOM_SEED + ) + result1 = standardizer1.run() + + # Second pass: standardize the standardized SMILES + input_df2 = result1[["SMILES_standardized"]].rename( + columns={"SMILES_standardized": "SMILES"} + ) + standardizer2 = StandardizeMolecule( + input=input_df2, method=method, random_seed=RANDOM_SEED + ) + result2 = standardizer2.run() + + # Merge results with compound IDs for better error reporting + # Use reset_index to ensure proper alignment + comparison = pd.DataFrame( + { + "compound_id": compound_smiles["Metadata_JCP2022"].reset_index(drop=True), + "original": compound_smiles["Metadata_SMILES"].reset_index(drop=True), + "pass1_smiles": result1["SMILES_standardized"].reset_index(drop=True), + "pass2_smiles": result2["SMILES_standardized"].reset_index(drop=True), + "pass1_inchi": result1["InChI_standardized"].reset_index(drop=True), + "pass2_inchi": result2["InChI_standardized"].reset_index(drop=True), + "pass1_inchikey": result1["InChIKey_standardized"].reset_index(drop=True), + "pass2_inchikey": result2["InChIKey_standardized"].reset_index(drop=True), + } + ) + + # Check idempotency and track failures + failures = [] + standardization_failures = 0 + + for _, row in comparison.iterrows(): + # Track standardization failures + if pd.isna(row["pass1_smiles"]) or pd.isna(row["pass2_smiles"]): + standardization_failures += 1 + continue + + # Check for idempotency violations + if row["pass1_smiles"] != row["pass2_smiles"]: + failures.append( + f"SMILES mismatch for {row['compound_id']}: {row['original'][:50]}..." + ) + if row["pass1_inchi"] != row["pass2_inchi"]: + failures.append( + f"InChI mismatch for {row['compound_id']}: {row['original'][:50]}..." + ) + if row["pass1_inchikey"] != row["pass2_inchikey"]: + failures.append( + f"InChIKey mismatch for {row['compound_id']}: {row['original'][:50]}..." + ) + + # Report standardization failures if any + if standardization_failures > 0: + print( + f"⚠️ {standardization_failures} compounds failed standardization and were skipped" + ) + + # Report idempotency failures if any + if failures: + failure_msg = f"\n{len(failures)} idempotency failures found:\n" + failure_msg += "\n".join(failures[:10]) # Show first 10 + if len(failures) > 10: + failure_msg += f"\n... and {len(failures) - 10} more" + pytest.fail(failure_msg) + + # Count successful standardizations + successful = comparison[comparison["pass1_smiles"].notna()].shape[0] + print( + f"✅ {method}: All {successful} successfully standardized compounds passed idempotency test" + ) + + +@pytest.mark.slow +@pytest.mark.idempotency +def test_data_file_exists(): + """Test that the SMILES data file has been downloaded.""" + assert SMILES_FILE.exists(), ( + f"SMILES data file not found at {SMILES_FILE}\n" + "Run: uv run --script scripts/download_jump_compounds.py" + ) diff --git a/libs/jump_smiles/test/test_standardize_smiles.py b/libs/jump_smiles/test/test_standardize_smiles.py index 51f86a6..c68aea1 100644 --- a/libs/jump_smiles/test/test_standardize_smiles.py +++ b/libs/jump_smiles/test/test_standardize_smiles.py @@ -66,9 +66,9 @@ def test_standardize_molecule(method): assert len(inchikey) == 27, f"Invalid InChIKey length: {inchikey}" assert inchikey.count("-") == 2, f"Invalid InChIKey format: {inchikey}" parts = inchikey.split("-") - assert all( - len(part) == length for part, length in zip(parts, [14, 10, 1]) - ), f"Incorrect InChIKey sections length: {inchikey}" + assert all(len(part) == length for part, length in zip(parts, [14, 10, 1])), ( + f"Incorrect InChIKey sections length: {inchikey}" + ) # Read the expected output file expected_df = pd.read_csv(expected_output_file) diff --git a/libs/jump_smiles/uv.lock b/libs/jump_smiles/uv.lock new file mode 100644 index 0000000..88a4466 --- /dev/null +++ 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[jump\_portrait](https://github.com/broadinstitute/monorepo/tree/main/libs/jump_portrait): Fetch JUMP images from CellPainting’s AWS servers. It also contains some utilities to explore file names. - [jump\_rr](https://github.com/broadinstitute/monorepo/tree/main/libs/jump_rr): Generate browsable databases of perturbation similarities and morphological feature rankings to be explored and queried on a browser. - [trommel](https://github.com/broadinstitute/monorepo/tree/main/libs/trommel): Data-cleaning functions and pipelines to improve the signal of morphological profiles. -- [jump\_smiles](https://github.com/broadinstitute/monorepo/tree/swb/libs/smiles): Standardiser of (Chemical) SMILES. +- [jump\_smiles](https://github.com/broadinstitute/monorepo/main/libs/smiles): Standardiser of (Chemical) SMILES. ### Tools outside the monorepo