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| Name | Name | Last commit date | ||
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A Rust implementation of the LightDock macromolecular software with the DFIRE and DNA scoring functions.
git clone https://github.com/lightdock/lightdock-rust.git
cd lightdock-rust cargo build --release
Several examples can be found in the example folder.
| Setting required 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 |
Recorded times on MacBook Pro M3 Pro.
cd example/1k4c
time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfireOutput:
Reading starting positions from "initial_positions_0.dat" Swarm ID 0 Writing to swarm dir "swarm_0" Reading receptor input structure: lightdock_receptor_membrane.pdb Reading ligand input structure: lightdock_ligand.pdb Loading DFIRE scoring function Creating GSO with 200 glowworms Starting optimization (100 steps) real 1m52,132s user 1m51,808s sys 0m0,150s
cd example/1ppe
time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfireOutput:
Reading starting positions from "initial_positions_0.dat" Swarm ID 0 Writing to swarm dir "swarm_0" Reading receptor input structure: lightdock_1ppe_e.pdb Reading ligand input structure: lightdock_1ppe_i.pdb Loading DFIRE scoring function Creating GSO with 200 glowworms Starting optimization (100 steps) real 0m4,252s user 0m4,142s sys 0m0,092s
cd example/2uuy
time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfireOutput:
Reading starting positions from "initial_positions_0.dat" Swarm ID 0 Output directory does not exist for swarm 0, creating it... Writing to swarm dir "swarm_0" Reading receptor input structure: lightdock_2UUY_rec.pdb Reading ligand input structure: lightdock_2UUY_lig.pdb Loading DFIRE scoring function Creating GSO with 200 glowworms Starting optimization (100 steps) real 0m8,108s user 0m7,834s sys 0m0,261s
cd example/1czy
time ../../target/release/lightdock-rust setup.json init/initial_positions_0.dat 100 dfireOutput:
Reading starting positions from "init/initial_positions_0.dat" Swarm ID 0 Writing to swarm dir "swarm_0" Reading receptor input structure: lightdock_1czy_protein.pdb Reading ligand input structure: lightdock_1czy_peptide.pdb Loading DFIRE scoring function Creating GSO with 200 glowworms Starting optimization (100 steps) real 0m1,580s user 0m1,312s sys 0m0,248s
cd example/1azp
time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dnaOutput:
Reading starting positions from "initial_positions_0.dat" Swarm ID 0 Output directory does not exist for swarm 0, creating it... Writing to swarm dir "swarm_0" Reading receptor input structure: lightdock_protein.pdb Reading ligand input structure: lightdock_dna.pdb Loading DNA scoring function Creating GSO with 200 glowworms Starting optimization (100 steps) real 0m14,228s user 0m13,932s sys 0m0,281s
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