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A Rust implementation of the LightDock macromolecular docking software

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lightdock/lightdock-rust

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

Installation

  1. Clone this repository:
git clone https://github.com/lightdock/lightdock-rust.git
  1. Compile it with Rust (you may install Rust usingrustup):
cd lightdock-rustcargo build --release

Examples

Several examples can be found in theexample folder.

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

Recorded times on MacBook Pro M3 Pro.

1k4c (Membrane docking)

cd example/1k4ctime ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire

Output:

Reading starting positions from "initial_positions_0.dat"Swarm ID 0Writing to swarm dir "swarm_0"Reading receptor input structure: lightdock_receptor_membrane.pdbReading ligand input structure: lightdock_ligand.pdbLoading DFIRE scoring functionCreating GSO with 200 glowwormsStarting optimization (100 steps)real    1m52,132suser    1m51,808ssys     0m0,150s

1ppe (protein docking)

cd example/1ppetime ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire

Output:

Reading starting positions from "initial_positions_0.dat"Swarm ID 0Writing to swarm dir "swarm_0"Reading receptor input structure: lightdock_1ppe_e.pdbReading ligand input structure: lightdock_1ppe_i.pdbLoading DFIRE scoring functionCreating GSO with 200 glowwormsStarting optimization (100 steps)real    0m4,252suser    0m4,142ssys     0m0,092s

2uuy (protein docking)

cd example/2uuytime ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire

Output:

Reading starting positions from "initial_positions_0.dat"Swarm ID 0Output directory does not exist for swarm 0, creating it...Writing to swarm dir "swarm_0"Reading receptor input structure: lightdock_2UUY_rec.pdbReading ligand input structure: lightdock_2UUY_lig.pdbLoading DFIRE scoring functionCreating GSO with 200 glowwormsStarting optimization (100 steps)real    0m8,108suser    0m7,834ssys    0m0,261s

1czy (protein-peptide docking)

cd example/1czytime ../../target/release/lightdock-rust setup.json init/initial_positions_0.dat 100 dfire

Output:

Reading starting positions from "init/initial_positions_0.dat"Swarm ID 0Writing to swarm dir "swarm_0"Reading receptor input structure: lightdock_1czy_protein.pdbReading ligand input structure: lightdock_1czy_peptide.pdbLoading DFIRE scoring functionCreating GSO with 200 glowwormsStarting optimization (100 steps)real    0m1,580suser    0m1,312ssys    0m0,248s

1azp (protein-nucleic docking)

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

Output:

Reading starting positions from "initial_positions_0.dat"Swarm ID 0Output directory does not exist for swarm 0, creating it...Writing to swarm dir "swarm_0"Reading receptor input structure: lightdock_protein.pdbReading ligand input structure: lightdock_dna.pdbLoading DNA scoring functionCreating GSO with 200 glowwormsStarting optimization (100 steps)real    0m14,228suser    0m13,932ssys     0m0,281s

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