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
1 maintainer
Metadata
1 maintainer
Release files for view-cif 0.2.3
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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|---|---|---|---|---|
| view_cif-0.2.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 40.7 kB
Release files / view_cif-0.2.3.tar.gz
| Download URL | view_cif-0.2.3.tar.gz |
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| Size | 31.7 kB |
| Tags | Source |
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| Tags | Python 3 |
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| Uploaded via |
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