- Notifications
You must be signed in to change notification settings - Fork5
A Rust implementation of the LightDock macromolecular docking software
License
NotificationsYou must be signed in to change notification settings
lightdock/lightdock-rust
Folders and files
| Name | Name | Last commit message | Last commit date | |
|---|---|---|---|---|
Repository files navigation
A Rust implementation of theLightDock macromolecular software with the DFIRE and DNA scoring functions.
- Clone this repository:
git clone https://github.com/lightdock/lightdock-rust.git- Compile it with Rust (you may install Rust usingrustup):
cd lightdock-rustcargo build --releaseSeveral 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.
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 0m0,150scd 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 0m0,092scd 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 0m0,261scd 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 0m0,248scd 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 0m0,281sAbout
A Rust implementation of the LightDock macromolecular docking software
Topics
Resources
License
Stars
Watchers
Forks
Sponsor this project
Packages0
No packages published