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
 ```
 

example/1azp/gso_1.out renamed to example/1azp/swarm_0/gso_1.out

@@ -10,7 +10,7 @@
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 (-22.1418797, -33.5086673, 29.9539405, 0.7809790, 0.5439619, -0.3066130, 0.0128764)    0    0   -36.82874685  0 0.600 -98.32186713
 (-16.7365785, -31.5086717, 32.1487729, 0.7602509, 0.6258322, -0.1685662, -0.0440229)    0    0   -54.88718087  0 0.600 -143.46795217
-(-25.5301263, -27.3836750, 25.0291598, 0.7449746, 0.4214678, -0.4251852, 0.2942709)    0    0   -59.18552960  0 0.600 -154.21382399
+(-25.5301263, -27.3836750, 25.0291598, 0.7449746, 0.4214678, -0.4251852, 0.2942709)    0    0   -59.17997422  0 0.600 -154.19993556
 (-29.4816370, -28.6374774, 30.3858118, 0.7129152, 0.4511820, -0.4660982, 0.2663441)    0    0   -41.63931310  0 0.600 -110.34828275
 (-16.0003010, -27.6427375, 32.9661799, 0.8353202, 0.5410787, -0.0973262, -0.0013138)    0    0   -59.53150859  0 0.600 -155.07877148
 (-27.2067309, -40.8585632, 25.8267275, 0.7911516, 0.4157794, -0.3548484, -0.2743888)    0    0   -19.18193282  0 0.600 -54.20483206
@@ -116,7 +116,7 @@
 (-19.3551357, -30.9937869, 36.0004658, 0.7930446, 0.5668957, -0.2220465, 0.0201198)    0    0   -38.41298538  0 0.600 -102.28246346
 (-24.9088770, -31.6379649, 31.8825485, 0.7328232, 0.3548958, -0.5528999, -0.1769771)    0    0   -46.91566395  0 0.600 -123.53915989
 (-16.9197285, -31.8008088, 36.6296484, 0.8425447, 0.4695503, -0.2462905, -0.0947734)    0    0   -25.49259793  0 0.600 -69.98149483
-(-21.4004621, -30.7178551, 23.8641083, 0.8193449, 0.4908916, -0.2558362, 0.1491553)    0    0   -46.12530494  0 0.600 -121.56326234
+(-21.4004621, -30.7178551, 23.8641083, 0.8193449, 0.4908916, -0.2558362, 0.1491553)    0    0   -46.12520287  0 0.600 -121.56300718
 (-27.0405723, -35.1097514, 28.4868323, 0.7816531, 0.5034896, -0.3399186, 0.1413221)    0    0   -23.76988176  0 0.600 -65.67470440
 (-21.6197268, -39.4445540, 25.3468374, 0.8769884, 0.4477154, -0.1728926, -0.0234600)    0    0   -16.41646353  0 0.600 -47.29115883
 (-24.7689842, -25.8813356, 26.6340309, 0.7947572, 0.3778753, -0.4201682, 0.2214273)    0    0   -48.23562318  0 0.600 -126.83905796
@@ -143,7 +143,7 @@
 (-23.7879644, -34.0248183, 28.9418041, 0.8029878, 0.5212465, -0.2576739, 0.1308315)    0    0   -33.80571592  0 0.600 -90.76428980
 (-28.5972063, -40.6273585, 28.1006114, 0.8534442, 0.4309361, -0.2923565, 0.0213248)    0    0   -14.89638989  0 0.600 -43.49097474
 (-26.0602780, -32.3473791, 20.3702072, 0.9376027, 0.2441658, -0.2301248, 0.0912510)    0    0   -4.03733551  0 0.600 -16.34333876
-(-18.9159067, -31.2112698, 32.9735593, 0.7735966, 0.6078552, -0.1713763, 0.0518707)    0    0   -39.45838975  0 0.600 -104.89597438
+(-18.9159067, -31.2112698, 32.9735593, 0.7735966, 0.6078552, -0.1713763, 0.0518707)    0    0   -39.45885151  0 0.600 -104.89712877
 (-19.6290111, -41.7594229, 29.7685251, 0.7947379, 0.5848534, -0.1568295, -0.0417452)    0    0   -18.53158048  0 0.600 -52.57895120
 (-29.3359223, -27.6040373, 27.7218337, 0.7251576, 0.3967608, -0.4795739, 0.2945102)    0    0   -43.02405606  0 0.600 -113.81014014
 (-30.3267199, -32.1674862, 27.9427460, 0.7686364, 0.3862519, -0.5087392, 0.0345259)    0    0   -18.79908001  0 0.600 -53.24770003