view-cif 0.2.1

CLI tool to view CIF files from various sources in your editor

view-cif

CLI tool to view CIF files from various sources in your preferred editor.

Features

• Open CIF files by file path, PDB code, or compound name
• Automatic download from PDB (including next-gen format)
• CCD and PRD/PRDCC bulk file support
• Configurable editor and data paths via YAML config
• Cache-based viewing (no blocking --wait)

Installation

Requires Python 3.12+.

# From PyPI
pip install view-cif

# Or with uv
uv tool install view-cif

Usage

# Open a local CIF file
view-cif /path/to/structure.cif

# Open by PDB code (auto-downloads)
view-cif 1abc

# Open next-gen PDB format
view-cif 1abc --next-gen

# Open from a specific directory
view-cif ABC /path/to/cif/dir

# Open CCD chemical component
view-cif ATP

# Open PRD definition
view-cif prd --ccd-definition

Options

Option	Short	Description
--ccd-definition	-d	Use CCD definition file type
--next-gen	-n	Use pdb_next_gen format

Configuration

On first run, a default config is created at ~/.config/view-cif/config.yaml.

Managing config via CLI

# Show current configuration
view-cif config show

# Change editor
view-cif config set editor nvim

# Set data paths
view-cif config set paths.chem_comp /data/chem_comp
view-cif config set paths.monomers /data/monomers

Config keys

Key	Description
editor	Editor command to open CIF files (e.g., code, nvim, emacs)
cache_dir	Directory for cached CIF output
paths.pdb_next_gen	Root directory for next-gen PDB files
paths.bird	Root directory for BIRD (PRD) data
paths.monomers	Directory containing components.cif.gz
paths.chem_comp	Directory for chemical component CIF files
paths.prd	Directory for PRD definition CIF files

Development

# Install with dev dependencies
uv sync --group dev

# Run tests
uv run pytest --cov=view_cif -v

# Lint
uv run ruff check .

License

MIT