csdb2snfg

Convert CSDB linear notation to SNFG (Symbol Nomenclature for Glycans) diagrams.

Features

• Parse CSDB linear strings into structured AST (JSON output)
• Render SNFG diagrams as PNG/SVG images
• Export PowerPoint (PPTX) with vector shapes
• Supports branching, repeating units (/n=N/, expanded or compact [unit]n display), modifiers (Me, Ac)

Current Limitations

• Only standard CSDB syntax and repeating units (/n=N/) are supported. Fuzzy/XOR alternatives (<...|...>, <<...|...>>) are not yet supported.
• Only orthogonal (horizontal/vertical) chain layout is supported. Diagonal or angled linkages are not available.

Installation

From PyPI (stable):

pip install glyco-csdb2snfg

With uv:

# Install as a global CLI tool
uv tool install glyco-csdb2snfg

# Or run directly without installing
uvx --from glyco-csdb2snfg csdb2snfg parse -c="-4)βDGlcp(1-4)αDGlcp(1-"

From source:

pip install git+https://github.com/sosyphe/glyco-csdb2snfg.git

Development (uv)

This project uses uv for dependency management (pyproject.toml + uv.lock).

git clone https://github.com/sosyphe/glyco-csdb2snfg.git
cd glyco-csdb2snfg

# Create .venv and install all dependencies (including dev extras)
uv sync --extra dev

# Run the CLI inside the project environment
uv run csdb2snfg --version

Quick Start

# Render to PNG
csdb2snfg image -c="-4)βDGlcp(1-4)βDGlcp(1-4)αDGlcp(1-" --format png -o output/

# Export to PowerPoint
csdb2snfg pptx -c="-4)βDGalp(1-4)βDGalp(1-3)αDGalp(1-" -o output/

# Parse to JSON AST
csdb2snfg parse -c="-4)βDGlcp(1-4)αDGlcp(1-"

# Repeating unit in compact mode ([unit]n instead of expanding)
csdb2snfg image -c="-4)βDGalp(1-4)/βDGalp(1-4)/n=3/βDGalp(1-4)αDGlcp(1-" --compact-repeat -o output/

# Batch processing (one CSDB string per line, # for comments)
csdb2snfg image -f glycans.txt --format png -o output/

Note: Use -c="..." (with =) to prevent argparse from treating the leading - as a flag.

Python API

from csdb2snfg import parse_csdb_linear, draw_snfg, generate_snfg_pptx

tree = parse_csdb_linear("-4)βDGlcp(1-4)αDGlcp(1-")

# Render to matplotlib figure
fig, ax = draw_snfg(tree)
fig.savefig("glycan.png", dpi=300, bbox_inches="tight")

# Save SVG directly
draw_snfg(tree, save_svg="glycan.svg")

# Export to PowerPoint
buf = generate_snfg_pptx(["-4)βDGlcp(1-4)αDGlcp(1-"])
with open("glycans.pptx", "wb") as f:
    f.write(buf.read())

Examples

Simple linear chain

-4)βDGlcp(1-4)βDGlcp(1-4)βDGlcp(1-4)αDGlcp(1-

Branched unit

-4)[βDGalp(1-6)]αDManp(1-4)[βDGalp(1-3)]αDManp(1-4)βDGlcNAcp(1-4)βDGlcNAcp(1-

Repeating unit (/n=3/)

-4)βDGalp(1-4)/βDGalp(1-4)/n=3/βDGalp(1-4)αDGlcp(1-

The image above shows the compact display: the repeat unit is drawn once with an n= annotation. The CLI expands the unit N times by default — pass --compact-repeat for the compact display (which is the default in the Python API: draw_snfg(tree, compact_repeat=True)).

With modifiers (Me, Ac)

-4)[Me(1-3)]αDGalp(1-6)[Ac(1-3)]αDGalp(1-6)αDGalp(1-

Complex multi-branched

-3)[[αDGalp(1-6)]αLArap(1-3)αLAraf(1-6)]βDGalp(1-3)[Me(1-4)βDGalp(1-4)βDGalp(1-6)]βDGalp(1-3)[αLAraf(1-4)βDXylp(1-6)]βDGalp(1-3)[αLAraf(1-4)βDManp(1-6)]βDGalp(1-3)βDGalp(1-3)βDGlcp(1-

License

MIT License - see LICENSE for details.