inc0/lightdock-rust

A Rust implementation of the LightDock macromolecular docking software

LightDock-Rust

A Rust implementation of the LightDock macromolecular software with the DFIRE and DNA scoring functions.

Installation

1. Clone this repository:

git clone https://github.com/lightdock/lightdock-rust.git

2. Compile it with Rust (you may install Rust using rustup):

cd lightdock-rust
cargo build --release

Examples

Several examples can be found in the example folder.

ℹ️ Data Path
You may set an environment variable LIGHTDOCK_DATA to point to the data folder included in this repository to avoid copying it: export LIGHTDOCK_DATA=/path/to/lightdock-rust/data

1k4c (Membrane docking)

cd example/1k4c
cp -R ../../data .
time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire

...

real    3m53.851s
user    3m52.550s
sys     0m0.717s

1ppe (protein docking)

cd example/1ppe
cp -R ../../data .
time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire

...

real    0m9.968s
user    0m9.640s
sys     0m0.271s

2uuy (protein docking)

cd example/2uuy
cp -R ../../data .
time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire

...

real    0m18.042s
user    0m17.123s
sys     0m0.621s

1czy (protein-peptide docking)

cd example/1czy
cp -R ../../data .
time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire

...

real    0m20.868s
user    0m19.692s
sys     0m1.070s

1azp (protein-nucleic docking)

cd example/1azp
time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dna

...

real    0m30.321s
user    0m29.219s
sys     0m0.651s