POMS - Portable Molecular Surface

An implementation of Molecular Surface generation and rendering, following the approach by Hermosilla et al. [1]. It is designed to be highly portable across platforms through the use of wgpu. In addition to molecular surface visualization, the application also offers a simpler space-filling model for molecules and basic post-processing.

[1] Hermosilla, Pedro, et al. "Interactive GPU-based generation of solvent-excluded surfaces." The Visual Computer 33.6 (2017): 869-881.

Screenshots

Requirements

• Rust toolchain (recommended installation via rustup.rs).

The Minimum Supported Rust Version (MSRV) is defined in rust-toolchain.toml. Should match the MSRV required by wgpu.

🛠️️ Building (MacOS, Windows)

cargo run

Features

• no-vsync: uncaps the FPS, useful for performance testing:

  cargo run --features no-vsync

For optimal performance, also include the --release flag.

️🌐 Building for the Web

To build the application for the web, we use Trunk, a tool for building WebAssembly (WASM) applications in Rust.

First install Trunk (if you haven't already):

cargo install --version ^0.16 trunk

This might take a few minutes as it is built from source.

After that, to build the application for the web, run:

trunk build --release

This will generate a dist directory with the necessary files to host the application on a web server.

Alternatively, to build and run the application on a local web server, run:

trunk serve --release --public-url "/"

which installs Trunk and runs it with necessary configuration. This should build our WASM code and start a web server that hosts the application at localhost:8080.

What happens behind the scenes?

Trunk takes care of several things, which would have to be done manually otherwise:

• Builds our Rust code to WASM bytecode using wasm32-unknown-unknown platform target, generating a .wasm file.
• Optimizes the WASM code using wasm-opt.
• Generates necessarry glue between WASM and JavaScript using wasm-bindgen, generating a .js file.
• Compiles an index.html file that loads the WASM code and JavaScript glue.
• Places all generated files in dist directory (you may use --dist argument to change the output directory).
• Starts a simple dev web server that hosts the application from this directory (in case of trunk serve).

🐧 Building on Linux

On linux, you might need to install some additional supporting libraries to build and run. On Ubuntu 22.04, the following packages are required:

sudo apt install libgtk-3-dev libglib2.0-dev libssl-dev