Merge pull request #18 from lightdock/issue_17

Issue 17

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

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+CORES=4
+
+### Calculate the number of swarms ###
+s=`ls -d ./swarm_* | wc -l`
+swarms=$((s-1))
+
+### Create files for Ant-Thony ###
+for i in $(seq 0 $swarms)
+  do
+    echo "cd swarm_${i}; lgd_generate_conformations.py ../1czy_protein.pdb ../1czy_peptide.pdb  gso_100.out 200 > /dev/null 2> /dev/null;" >> generate_lightdock.list;
+  done
+
+for i in $(seq 0 $swarms)
+  do
+    echo "cd swarm_${i}; lgd_cluster_bsas.py gso_100.out > /dev/null 2> /dev/null;" >> cluster_lightdock.list;
+  done
+
+### Generate LightDock models ###
+ant_thony.py -c ${CORES} generate_lightdock.list;
+
+### Clustering BSAS (rmsd) within swarm ###
+ant_thony.py -c ${CORES} cluster_lightdock.list;
+
+### Generate ranking files for filtering ###
+lgd_rank.py $s 100;
+
+### Generate top predictions ###
+mkdir top;
+lgd_top.py 1czy_protein.pdb 1czy_peptide.pdb rank_by_scoring.list 10;
+mv top_*.pdb top/
+
+### Clean ###
+rm -rf swarm_*/*.pdb solutions.list generate_lightdock.list cluster_lightdock.list rank_by_luciferin.list rank_by_rmsd.list;
+

example/1azp/gso_10.out renamed to example/1azp/swarm_0/gso_10.out

@@ -4,7 +4,7 @@
 NUM_CORES=4
 
 # LightDock setup
-lightdock3_setup.py 1czy_protein.pdb 1czy_peptide.pdb 400 200 --noxt --noh -anm -rst restraints.list
+lightdock3_setup.py 1czy_protein.pdb 1czy_peptide.pdb --noxt --noh -anm -rst restraints.list -spr 10
 
 # Convert ANM data
 lgd_flatten.py lightdock_rec.nm.npy rec_nm.npy
@@ -14,14 +14,14 @@ lgd_flatten.py lightdock_lig.nm.npy lig_nm.npy
 s=`ls -d swarm_* | wc -l`
 swarms=$((s-1))
 
-# Copy binary
+# Copy lightdock-rust binary
 cp ../../target/release/lightdock-rust .
 
 # Create a task.list file for ant_thony
-for i in `seq 0 $swarms`;do echo "cd swarm_${i}; cp ../lightdock_1czy_protein.pdb .; cp ../lightdock_1czy_peptide.pdb .;cp ../rec_nm.npy .;cp ../lig_nm.npy .;cp -R ../../../data .;../lightdock-rust ../setup.json ../init/initial_positions_${i}.dat 10 dfire; rm -rf lightdock_*.pdb *.npy data;" >> task.list; done
+for i in `seq 0 $swarms`;do echo "./lightdock-rust setup.json init/initial_positions_${i}.dat 100 dfire;" >> task.list; done
 
 # Let ant_thony run
-ant_thony.py --cores ${NUM_CORES} task.list
+time ant_thony.py --cores ${NUM_CORES} task.list
 
 # Clean task.list
 rm -rf task.list