#!/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;