molvis

A minimal web viewer for molecular trajectory/output text.

• Rust backend reads and parses output text into energy + coordinates JSON
• JavaScript frontend uses 3Dmol.js to render molecular structures and switch frames with a slider

Current parser support: ORCA .out only. Future formats (for example Gaussian / XYZ batches) can be added later.

Install

From crates.io (published package):

cargo install molvis

From local source (not published yet):

cargo install --path .

Installed binary run

molvis /path/to/your.out
molvis -H 0.0.0.0 -p 8080 /path/to/your.out
molvis --xyz /path/to/your.out
molvis -x /path/to/your.out
molvis -x -n _opt /path/to/your.out

-x / --xyz will parse the ORCA .out, take the last geometry frame, and write an XYZ file.

By default it uses the input filename stem:

<input-stem>.xyz

You can append a suffix to the input file stem with -n / --name:

<input-stem><name>.xyz

For example:

molvis -x sample.out
# writes sample.xyz

molvis --xyz sample.out
# writes sample.xyz

molvis -x -n _opt sample.out
# writes sample_opt.xyz

Server config (TOML)

molvis can read host/port defaults from config files:

• ~/.config/molvis/config.toml
• /etc/molvis/config.toml

Supported keys:

host = "127.0.0.1"
port = 3000

Priority is:

1. CLI flags (-H, -p) - highest
2. User config (~/.config/molvis/config.toml)
3. System config (/etc/molvis/config.toml)
4. Built-in defaults (127.0.0.1:3000)

Initialize user config template:

molvis --init-config

Develop (run from source)

cargo run -- /path/to/your.out

Open http://127.0.0.1:3000

cargo run -- -H 0.0.0.0 -p 8080 /path/to/your.out
cargo run -- --xyz /path/to/your.out
cargo run -- -x /path/to/your.out
cargo run -- -x -n _opt /path/to/your.out

Frontend JS loading

The frontend loads two browser libraries:

• 3Dmol-min.js for 3D molecular rendering
• plotly.min.js for interactive energy trend chart

Default behavior: local first, CDN fallback.

• If web/3Dmol-min.js / web/plotly.min.js exist, local files are used.
• If local files are absent, it automatically falls back to CDN.

Optional offline mode: place these files under web/ and they will be used first:

• web/3Dmol-min.js
• web/plotly.min.js

You can fetch them with:

scripts/fetch-web-libs.sh

Use --force to re-download:

scripts/fetch-web-libs.sh --force

Note for intranet / no-internet environments

• If external CDN access is blocked, 3D viewer or trend chart may fail to load.
• In that case, provide local files under web/ (recommended), or allowlist the CDN domains in your network policy.
• If only one library fails to load, the other feature can still work (for example, 3D works but chart fails, or vice versa).