SynRFP — Graph-based, mapping-free reaction fingerprints

SynRFP (Synthesis Reaction FingerPrint) is a mapping-free, permutation-invariant framework for representing chemical transformations as fixed-length fingerprints.
It explicitly factorises the fingerprint pipeline into three modular operators:

• Ψ (extractor) — isomorphism-invariant subgraph/token extraction from each reaction side;
• Φ (combination) — algebraic reparameterisation producing the signed net change Δ and total counts U per token;
• 𝒮 (sketcher) — randomized compression of (Δ,U) into a fixed-dimensional fingerprint f ∈ 𝓕.

---

⚙️ Installation

# 1) Clone the repository
git clone https://github.com/TieuLongPhan/synrfp.git
cd synrfp

# 2) Install the package (with optional extras)
pip install .                  # core functionality
pip install .[all]             # with datasketch and pynauty support

or can install via pip

pip install synrfp

🔧 Quick Start

1. Single‐reaction fingerprint

from synrfp.graph.reaction import Reaction
from synrfp import SynRFP
from synrfp.tokenizers.wl import WLTokenizer
from synrfp.sketchers.parity_fold import ParityFold

# Parse RSMI into GraphData
reactant_G, product_G = Reaction.from_rsmi("CCO>>C=C.O")

# Build engine: WL at radius 1 + 1024-bit parity-fold
fp_engine = SynRFP(
    tokenizer=WLTokenizer(),
    radius=1,
    sketch=ParityFold(bits=1024, seed=42),
)

# Compute fingerprint
res = fp_engine.fingerprint(reactant_G, product_G)
print(res)               # SynRFPResult(tokens_R=3 tokens, tokens_P=3 tokens, support=0, sketch_type=bytearray)
bits = res.to_binary()   # [0,1,0,0, …]

2. One‐line wrapper

from synrfp import synrfp

# Generate a 1024-bit binary fingerprint in one call
bits = synrfp(
    "CCO>>C=C.O",
    tokenizer="wl",
    radius=1,
    sketch="parity",
    bits=1024,
    seed=42,
)
print(len(bits), bits[:16])  # e.g. 1024 [0, 1, 0, 0, …]

3. Batch encoding

from synrfp import BatchEncoder

rxn_smiles = [
    "CO.O[C@@H]1CCNC1.[C-]#[N+]CC(=O)OC>>[C-]#[N+]CC(=O)N1CC[C@@H](O)C1",
    "CCOC(=O)C(CC)c1cccnc1.Cl.O>>CCC(C(=O)O)c1cccnc1",
]

# Encode two reactions into a 2×1024 array of bits
fps = BatchEncoder.encode(
    rxn_smiles,
    tokenizer="wl",
    radius=1,
    sketch="parity",
    bits=1024,
    seed=42,
    batch_size=2
)

print(fps.shape)    # (2, 1024)
print(fps[0][:16])  # first 16 bits of the first fingerprint

Contributing

• 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)