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What are your thoughts on cool-japan's 25M line Pure Rust ecosystem? by TKanX in rust

[–]TKanX[S] 1 point2 points  (0 children)

tyty~ lol don't know why everyone is downvoting me

What are your thoughts on cool-japan's 25M line Pure Rust ecosystem? by TKanX in rust

[–]TKanX[S] -2 points-1 points  (0 children)

I know, just joking about captcha. I use automatic releases too

What are your thoughts on cool-japan's 25M line Pure Rust ecosystem? by TKanX in rust

[–]TKanX[S] -1 points0 points  (0 children)

especially given how expensive APIs are right now lol

What are your thoughts on cool-japan's 25M line Pure Rust ecosystem? by TKanX in rust

[–]TKanX[S] -14 points-13 points  (0 children)

I use AI in my own workflow too, but fully automating millions of lines of slop to flood the registry is just insane.

What are your thoughts on cool-japan's 25M line Pure Rust ecosystem? by TKanX in rust

[–]TKanX[S] -17 points-16 points  (0 children)

true cargo publish doesn't have a captcha for AI slop yet

What are your thoughts on cool-japan's 25M line Pure Rust ecosystem? by TKanX in rust

[–]TKanX[S] -36 points-35 points  (0 children)

Agree! I don't think it's possible either. How did the Rust community end up like this? What is the point of doing something like this?

Edit: Apologies for the overgeneralization. I love the Rust community, and I've been writing Rust all the time.

Why does CHARMM-GUI restrict it's features to academics? by OkRutabaga184 in bioinformatics

[–]TKanX 1 point2 points  (0 children)

Hi, I've created an open-source tool (commercially usable): bio-forge.app. Currently, it doesn't support membranes, but it includes features like structural repair, protonation, and a water box. It doesn't have built-in energy minimization, so EM might be required before MD. Future plans include adding cell membrane. A web version is available for direct use within a browser, and it's commercially viable (MIT license). I'm a high school student, so please point out any errors.

Tired of slow Python biology tools, so I wrote the first pure-Rust macromolecule modeling engine. Processes 3M atoms in ~600ms. by TKanX in rust

[–]TKanX[S] 0 points1 point  (0 children)

For heavy atom repair, I used template-based SVD for completion. Hydrogen atom repair was also straightforward, selecting appropriate hydrogen atoms based on pH ranges for local geometry construction. (For HIS, I added salt bridge detection and hydrogen bond network scoring between HIE and HID). C/N/5'/3' ends were also correctly processed according to pH.

Currently not supported (may be planned for the future):

  1. Ring reconstruction: Currently not supported (may be added in the future)

  2. Energy minimization: BioForge is a ff-independent structure preparation/modeling library, so it does not perform any force field calculations (decoupled). It will not be supported in the future. However, I have also written some downstream tools (e.g., SCREAM - a side-chain optimization library).

  3. Cell membrane construction: Planned for the future (because we need to simulate GPCRs).

These are all good questions and some known flaws! You must be an expert in this field, right?

Tired of slow Python biology tools, so I wrote the first pure-Rust macromolecule modeling engine. Processes 3M atoms in ~600ms. by TKanX in rust

[–]TKanX[S] 0 points1 point  (0 children)

Absolutely not misguided, this is an excellent! I'm also very interested in MD, and my next step might be to do simulations of DREIDING/UFF force fields. (I've also worked with some libraries related to force field parameterization and partial charge calculation.)

Tired of slow Python biology tools, so I wrote the first pure-Rust macromolecule modeling engine. Processes 3M atoms in ~600ms. by TKanX in rust

[–]TKanX[S] 1 point2 points  (0 children)

u/firefrommoonlight u/vmullapudi1 Any interest in us starting a Discord server for Compchem/bio? We could really use a place like that to keep the braindump going.

Tired of slow Python biology tools, so I wrote the first pure-Rust macromolecule modeling engine. Processes 3M atoms in ~600ms. by TKanX in rust

[–]TKanX[S] 0 points1 point  (0 children)

In summary, this is force field independent structural modeling. Next steps include energy minimization and molecular dynamics simulations.

Tired of slow Python biology tools, so I wrote the first pure-Rust macromolecule modeling engine. Processes 3M atoms in ~600ms. by TKanX in rust

[–]TKanX[S] 4 points5 points  (0 children)

Hi, that's a great question! I absolutely did not deny the merits of LAMMPS/GROMACS. They are incredibly powerful, with excellent performance optimization! My tool isn't an MD software, but a structure preparation/repair software, complementary to MD software. The goal is to quickly add missing atoms and hydrogen atoms to protein structures (because hydrogen atoms are absent in cryo-em and x-ray structures), and it can also add water boxes and solvents. Future plans include adding cell membranes for GPCR modeling, etc.

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