Updated README to current version

Author: brianjimenez

README.md

@@ -24,72 +24,127 @@ Several examples can be found in the `example` folder.
 |:---------------------------|
 | 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.
+
 ### 1k4c (Membrane docking)
 
-```
+```bash
 cd example/1k4c
-cp -R ../../data .
 time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire
+```
 
-...
+Output:
 
-real    3m53.851s
-user    3m52.550s
-sys     0m0.717s
+```
+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
 ```
 
 ### 1ppe (protein docking)
 
-```
+```bash
 cd example/1ppe
-cp -R ../../data .
 time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire
+```
 
-...
+Output:
 
-real    0m9.968s
-user    0m9.640s
-sys     0m0.271s
+```
+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
 ```
 
 ### 2uuy (protein docking)
 
-```
+```bash
 cd example/2uuy
-cp -R ../../data .
 time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire
+```
 
-...
+Output:
 
-real    0m18.042s
-user    0m17.123s
-sys     0m0.621s
+```
+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
 ```
 
 ### 1czy (protein-peptide docking)
 
-```
+```bash
 cd example/1czy
-cp -R ../../data .
-time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dfire
+time ../../target/release/lightdock-rust setup.json init/initial_positions_0.dat 100 dfire
+```
 
-...
+Output:
 
-real    0m20.868s
-user    0m19.692s
-sys     0m1.070s
+```
+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
 ```
 
 ### 1azp (protein-nucleic docking)
 
-```
+```bash
 cd example/1azp
 time ../../target/release/lightdock-rust setup.json initial_positions_0.dat 100 dna
+```
 
-...
+Output:
 
-real    0m30.321s
-user    0m29.219s
-sys     0m0.651s
+```
+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
 ```