Example from LightDock-Rust tutorial for version 0.9.4

Author: brianjimenez

example/1czy/analysis.sh

@@ -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/1czy/execution.sh

@@ -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