view-cif 0.2.3

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)
• BIRD individual lookup — auto-detects PRD_, PRDCC_, FAM_ prefixes
• 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 (uses local mirror or 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

# Individual BIRD lookups (auto-detected by prefix)
view-cif PRD_000010      # PRD definition
view-cif PRDCC_000240    # PRD chemical component
view-cif FAM_000160      # PRD family

# Bulk files
view-cif prd             # prd-all.cif.gz
view-cif prdcc           # prdcc-all.cif.gz
view-cif ccd             # components.cif.gz

Options

Option	Short	Description
--next-gen	-n	Use pdb_next_gen format

Configuration

On first run, a default config is created at ~/.config/view-cif/config.yaml. See config.example.yaml for a fully commented template.

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.prd /data/bird

Config keys

Key	Description	Example
editor	Editor command (any terminal command)	code, nvim, vim
cache_dir	Directory for cached CIF output	~/.cache/view-cif
paths.pdb_next_gen	Next-gen PDB archive root	/data/pdb_nextgen
paths.bird	BIRD bulk files (prd-all.cif.gz, prdcc-all.cif.gz)	/data/bird/prd
paths.monomers	CCD monomers (components.cif.gz)	/data/monomers
paths.chem_comp	Chemical component reference data	/data/chem_comp
paths.prd	BIRD reference root (prd/, prdcc/, family/ subdirs)	/data/refdata/bird

Directory structure expectations

Path resolution follows the PDB FTP/rsync mirror directory layout. If you maintain a local mirror, point each config path to the corresponding directory.

~ and environment variables ($HOME, $PDB_ROOT, etc.) are expanded automatically.

paths.pdb_next_gen/
  entries/divided/{ab}/pdb_{id}/pdb_{id}_xyz-enrich.cif.gz

paths.bird/
  prd-all.cif.gz
  prdcc-all.cif.gz

paths.monomers/
  components.cif.gz

paths.chem_comp/
  {X}/{ABC}/ABC.cif          # nested by first character

paths.prd/
  prd/    {N}/PRD_NNNNNN.cif
  prdcc/  {N}/PRDCC_NNNNNN.cif
  family/ {N}/FAM_NNNNNN.cif

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