ciffy 0.5.5

Fast CIF file parsing for molecular structures

Overview

ciffy is a fast CIF file parser for molecular structures, with a C backend and Python interface. It supports both NumPy and PyTorch backends for array operations.

Performance

ciffy is 50-90x faster than BioPython and Biotite for parsing CIF files:

Structure	Atoms	ciffy	BioPython	Biotite
3SKW	2,874	0.47 ms	31 ms (66x)	28 ms (59x)
9GCM	4,466	0.71 ms	40 ms (56x)	36 ms (51x)
9MDS	102,216	14 ms	1266 ms (93x)	911 ms (67x)

_{Benchmarked on Apple M1 Max. Run python tests/profile.py to reproduce.}

Installation

From PyPI

pip install ciffy

From Source

git clone https://github.com/hmblair/ciffy.git
cd ciffy
pip install -r requirements.txt
pip install -e .

Backends

ciffy supports two array backends:

• NumPy: Lightweight, no additional dependencies required
• PyTorch: For GPU support and integration with deep learning workflows

Specify the backend when loading structures:

import ciffy

# Load with NumPy backend (recommended for general use)
polymer = ciffy.load("structure.cif", backend="numpy")

# Load with PyTorch backend (for deep learning workflows)
polymer = ciffy.load("structure.cif", backend="torch")

Polymers can be converted between backends:

# Convert to PyTorch tensors
torch_polymer = polymer.torch()

# Convert to NumPy arrays
numpy_polymer = polymer.numpy()

Note: The default backend will change from "torch" to "numpy" in v0.6.0. Specify the backend explicitly to avoid deprecation warnings.

Usage

import ciffy

# Load a structure from a CIF file
polymer = ciffy.load("structure.cif", backend="numpy")

# Basic information
print(polymer)  # Summary of chains, residues, atoms

# Access coordinates and properties
coords = polymer.coordinates      # (N, 3) array/tensor
atoms = polymer.atoms             # (N,) array/tensor of atom types
sequence = polymer.str()          # Sequence string

# Geometric operations
centered, means = polymer.center(ciffy.MOLECULE)
aligned, Q = polymer.align(ciffy.CHAIN)
distances = polymer.pd(ciffy.RESIDUE)

# Selection
rna_chains = polymer.subset(ciffy.RNA)
backbone = polymer.backbone()

# Iterate over chains
for chain in polymer.chains(ciffy.RNA):
    print(chain.id(), chain.str())

# Compute RMSD between structures
rmsd = ciffy.rmsd(polymer1, polymer2, ciffy.MOLECULE)

Saving Structures

# Save to CIF format (supports all molecule types)
polymer.write("output.cif")

# Save only polymer atoms (excludes water, ions, ligands)
polymer.poly().write("polymer_only.cif")

Module Structure

ciffy/
├── backend/        # NumPy/PyTorch abstraction layer
├── types/          # Scale, Molecule enums
├── biochemistry/   # Element, Residue, nucleotide definitions
├── operations/     # Reduction, alignment operations
├── io/             # File loading and writing
└── utils/          # Helper functions and base classes

Testing

pip install pytest
pytest tests/