pycchem
Python bindings for cchem - a high-performance cheminformatics library.
Features
- Fast SMILES canonicalization - 2-3x faster than RDKit
- 1600+ molecular descriptors - Comprehensive descriptor set
- Molecular sanitization - Salt removal, neutralization, aromatization
- Pure C backend - No heavy dependencies
Installation
pip install pycchem
From Source
git clone https://github.com/Vitruves/cchem.git
cd cchem/pycchem
pip install .
Quick Start
Canonicalization
import pycchem
# Canonicalize a SMILES
canon = pycchem.canonicalize("C(C)O")
print(canon) # CCO
# Check if two SMILES are equivalent
pycchem.are_equivalent("CCO", "OCC") # True
# Validate SMILES
pycchem.validate("CCO") # True
pycchem.validate("invalid") # False
Sanitization
import pycchem
# Remove salts and neutralize
clean = pycchem.sanitize("[Na+].CC(=O)[O-]")
print(clean) # CC(=O)O
# Specific operations
pycchem.sanitize("C1=CC=CC=C1", operations=["aromatize"]) # c1ccccc1
Molecular Descriptors
import pycchem
# Create a molecule
mol = pycchem.Molecule("CCO")
# Compute all descriptors (1600+)
descriptors = mol.descriptors()
print(descriptors["MolecularWeight"]) # 46.069
print(descriptors["CarbonCount"]) # 2
# Compute specific descriptors
selected = mol.descriptors(["MolecularWeight", "WCLogP", "TPSA"])
# List available descriptors
names = pycchem.list_descriptors()
print(len(names)) # ~1600
Batch Processing
import pycchem
smiles_list = ["CCO", "c1ccccc1", "CC(=O)O"]
results = pycchem.canonicalize_batch(smiles_list)
Command-Line Interface
After installation, the cchem command is available:
# Canonicalize SMILES
cchem canonicalize -S "C(C)O"
# Output: CCO
# Validate SMILES
cchem validate -S "CCO"
# Output: CCO: valid
# Compute descriptors
cchem compute -S "CCO" -d MolecularWeight
# Output: MolecularWeight: 46.069000
# Compute all descriptors
cchem compute -S "CCO" --all -o descriptors.csv
# List available descriptors
cchem compute --list
# Sanitize SMILES
cchem sanitize -S "[Na+].CC(=O)[O-]"
# Output: CC(=O)O
# Compare two SMILES
cchem compare "CCO" "OCC"
# Output: equivalent
# Show version
cchem --version
CLI Commands
| Command | Description |
|---|---|
canonicalize |
Canonicalize SMILES strings |
validate |
Validate SMILES syntax |
compute |
Compute molecular descriptors |
sanitize |
Sanitize SMILES (remove salts, neutralize, etc.) |
compare |
Check if two SMILES are equivalent |
API Reference
Functions
| Function | Description |
|---|---|
canonicalize(smiles) |
Canonicalize SMILES string |
canonicalize_batch(list) |
Batch canonicalization |
sanitize(smiles, operations) |
Sanitize molecule |
validate(smiles) |
Check SMILES validity |
are_equivalent(s1, s2) |
Check if SMILES are equivalent |
compute_descriptor(smiles, name) |
Compute single descriptor |
compute_descriptors(smiles, names) |
Compute multiple descriptors |
list_descriptors() |
List all descriptor names |
version() |
Get library version |
Molecule Class
mol = pycchem.Molecule(smiles)
mol.canonical_smiles # Canonical form
mol.descriptors() # All descriptors
mol.descriptor(name) # Single descriptor
Sanitization Operations
| Operation | Description |
|---|---|
complete |
Full sanitization (default) |
unsalt |
Remove salts/counter-ions |
aromatize |
Perceive aromaticity |
kekulize |
Convert to Kekule form |
neutralize |
Neutralize charges |
normalize |
Normalize functional groups |
remove_stereo |
Remove stereochemistry |
remove_isotopes |
Remove isotope labels |
remove_h |
Remove explicit hydrogens |
Performance
Benchmarks on MacBook Air M3 (8-core, 16GB RAM):
| Library | Throughput | vs RDKit |
|---|---|---|
| pycchem | 28,311/s | 2.52x |
| RDKit | 11,229/s | 1.00x |
Requirements
- Python 3.9+
- cffi >= 1.15.0
License
Apache License 2.0
1 maintainer
Metadata
1 maintainer
Release files for pycchem 1.1.0
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