mogura: A molecular graphic toy visualizer in Rust

--> Try demo with WASM using WebGPU <--

Warning

RAM $\geq$ 8GB, CPU $\geq$ 8cores and GPU are desirable.

Do not load too large structure files.

There are some limitation for WASM version. See Feature

Quick Start

Install

cargo install --git https://github.com/mogura-rs/mogura mogura --locked

Run mogura

# start mogura
mogura

# show help
mogura -h

# visualize PDB: 8GNG (Or you can load them after staring mogura)
mogura 8gng.pdb

# visualize MD simulation of chignolin (Or you can load them after staring mogura)
mogura init.gro input.mol.compact.xtc

Gallery

Input files are available here

Feature

• Visualize PDB, GRO format
  • stick, stick&ball, ball, tube(catmull-rom), line mode are supported
  • WASM does not support line (because WebGPU)
• Visualize MD simulation using XTC format
  • topology must be PDB or GRO format
  • WASM does not support this (because of groan_rs, this crate depends internally on libc)
• Atom selection language
  • resname, resid, name, index, protein, water, backbone, sidechain, ion, all, (), and, or, not are reserved words
  • support complex syntax
    • e.g. protein and name C CA N, (resname TYR PRO) and protein or not water
• Multiple selection panel
  • multiple atom selection are possible for a single structure file.
• Fetch PDB
  • dirty pdb file will cause parse error because of pdbtbx.

TODO

• Lv1: Change configuration of selected atoms (e.g. Color, Radius, Opacity)
• Lv1: Load multiple structure files
• Lv1: Morphing by specifying two structures
• Lv2: Pick up atoms and highlight them with their name
• Lv2: Allow more flexible configuration of plugins
• Lv3: Secondary structure prediction using DSSP or STRIDE
• Lv3: Visualize structure as Cartoon and NewCartoon
• Lv4: Path tracing using bevy-hikari(but no more developed) or developing default feature

About the name

$$ \text{Molecular Graphic Visualizer} \rightarrow \text{Mole + graphic} \rightarrow \text{Mo + gra} \rightarrow \text{mogura} $$

mogura also means "Mole".

Useful Reference

References

• bevy
  • https://bevy-cheatbook.github.io/
  • https://github.com/qu1x/bevy_trackball
  • https://github.com/bytestring-net/bevy_lunex
• graphics
  • https://github.com/RayTracing
    • https://github.com/RayTracing/gpu-tracing
    • https://github.com/RayTracing/raytracing.github.io
  • https://github.com/NotCamelCase/RasterizationInOneWeekend
  • https://github.com/svenstaro/bvh
  • https://github.com/pannapudi/voidin
  • https://github.com/BLaZeKiLL/webray
  • https://github.com/servo/pathfinder
• egui
  • https://github.com/vladbat00/bevy_egui
• wgpu
  • https://sotrh.github.io/learn-wgpu/
  • https://github.com/jack1232/wgpu-step-by-step
  • https://github.com/jinleili/simuverse
• pdb, gro, xtc
  • https://github.com/douweschulte/pdbtbx
  • https://github.com/Ladme/groan_rs
• other great visualizer
  • PyMol
  • VMD
  • ChimeraX
  • molstar
    • VSCoding-Sequence
  • Cuemol
  • ngl
• other visualizer in Rust
  • ferricyanide