chiralipy 0.1.0

Pure Python chemistry library with zero dependencies

chiralipy

Chiralipy is a pure Python library for SMILES/SMARTS parsing, canonicalization, and molecular manipulation.

Installation

pip install -e .

Quick Start

from chiralipy import parse, canonical_smiles

# Parse and canonicalize
mol = parse("C(C)CC")
print(canonical_smiles(mol))  # CCCC

# Substructure matching
from chiralipy.match import substructure_search
mol = parse("c1ccccc1CCO")
pattern = parse("[OH]")
matches = substructure_search(mol, pattern)  # [(7,)]

# BRICS decomposition
from chiralipy.decompose import brics_decompose
mol = parse("CCOc1ccc(CC)cc1")
fragments = brics_decompose(mol)
print(sorted(fragments))
# ['[16*]c1ccc([16*])cc1', '[3*]O[4*]', '[4*]CC', '[8*]CC']

Features

• SMILES/SMARTS parsing with full stereochemistry support
• Canonical SMILES generation
• Substructure matching (RDKit-compatible)
• BRICS decomposition for retrosynthetic fragmentation
• Aromaticity perception based on Hückel's 4n+2 rule
• Ring detection (SSSR algorithm)
• Zero dependencies — pure Python

Core API

from chiralipy import parse, canonical_smiles, to_smiles

from chiralipy.match import substructure_search, has_substructure
from chiralipy.decompose import brics_decompose, get_scaffold
from chiralipy.rings import find_sssr
from chiralipy.transform import kekulize

Benchmark: BRICS Decomposition

Comparison against RDKit (C++ implementation):

Molecule            Atoms  Bonds   RDKit ms  chiralipy ms    Ratio
----------------------------------------------------------------
small_ether             5      4     0.37       0.60      1.62x
medium_drug            15     15     0.88       1.89      2.13x
drug_like              37     41     3.54       5.05      1.43x
large_complex          84     98     5.04      13.33      2.64x

Average: ~2x slower than RDKit

License

MIT