PartialAAMs

PartialAAMs is a library designed to provide a benchmarking framework for evaluating effectiveness of Partial Atom-Atom Mappings (AAMs) extension. It simplifies the generation, manipulation, and testing of AAMs for chemical reactions.

Installation

Follow the steps below to set up the environment and install the library:

1. Create a conda environment with Python 3.11.10:

   conda create -n partialaams python=3.11.10 -y

2. Activate the environment:

   conda activate partialaams

3. Clone the GranMapache repository:

   git clone https://github.com/MarcosLaffitte/GranMapache.git

4. Navigate to the GranMapache directory:

   cd GranMapache

5. Install GranMapache:

   pip install .

6. Return to the original directory:

   cd ..

7. Remove the GranMapache directory:

   rm -rf GranMapache

8. Install additional requirements:

   pip install -r requirements.txt

Usagebenchmark

Python Interface

Extend a partial atom-atom mapping (AAM) directly from reaction SMILES. Choose one of five strategies:

from partialaams.aam_expand import partial_aam_extension_from_smiles

# Define your (partial) reaction SMILES
rsmi = "[CH3][CH:1]=[CH2:2].[H:3][H:4]>>[CH3][CH:1]([H:3])[CH2:2][H:4]"

# Expected fully-mapped SMILES
expected = (
    "[CH2:1]=[CH:2][CH3:3].[H:4][H:5]>>"
    "[CH2:1]([CH:2]([CH3:3])[H:5])[H:4]"
)

# Try all five extension methods:
for method in ("ilp", "gm", "syn", "extend", "extend_g"):
    result = partial_aam_extension_from_smiles(rsmi, method=method)
    print(f"{method:8} →", result)
    # You can validate with AAMValidator, e.g.:
    # assert AAMValidator.smiles_check(result, expected)

Supported methods

• gm  Graph-matching extension. Please refer to https://github.com/MarcosLaffitte/GranMapache
• ilp  ILP-based extension
• syn  Gluing Graph extension
• extend  Color reorder extension
• extend_g  Color reorder extension using gm isomorphism

Command-Line Interface

Once you’ve installed partialaams (e.g. via pip install . in your project root), you can run the CLI with:

python -m partialaams [OPTIONS] [RSMI]

Options

Flag	Description	Default
-i, --input	Path to a file with one reaction SMILES per line, or a single SMILES string if the file does not exist.	—
RSMI	Reaction SMILES string (partial AAM). Use this instead of -i when processing a single reaction directly.	—
-m, --method	Extension strategy. One of: gm, ilp, syn, extend, extend_g.	gm
-o, --output	File path to write the extended SMILES to. If omitted, results stream to stdout.	stdout
-l, --list-methods	List all supported extension methods and exit.	—

Examples

$ python -m partialaams -i "CC[CH2:3][Cl:1].[N:2]>>CC[CH2:3][N:2].[Cl:1]"
>> [Cl:1][CH2:5][CH2:4][CH3:3].[N:2]>>[Cl:1].[N:2][CH2:5][CH2:4][CH3:3]

Benchmarking

$ python benchmarking.py

Publication

Extension of Partial Atom-to-Atom Maps: Uniqueness and Algorithms

Citation

TODO

Contributing

• Marcos E. González Laffitte
• Tieu-Long Phan

License

This project is licensed under MIT License - see the License file for details.

Acknowledgments

This project has received funding from the European Unions Horizon Europe Doctoral Network programme under the Marie-Skłodowska-Curie grant agreement No 101072930 (TACsy -- Training Alliance for Computational)