#!/bin/bash
if [ $# -lt 2 ]; then
    echo "USAGE: cluster_decoys.sh <silent file> <cluster radius, A>"
    exit
fi
silent=$1
radius=$2
mkdir clusters
cd clusters
../../../../../../main/source/bin/cluster.static.linuxgccrelease \
-in:file:silent_struct_type binary \
-in::file:silent ../$1 \
-ignore_unrecognized_res \
-in:path:database ../../../../../../main/database \
-in:file:fullatom \
-limit_clusters 20 \
-sort_groups_by_size \
-cluster:radius $2 > cluster_log.out
cd ..
./top10-clusters.sh
cp -p clusters/cluster_log.out cluster_log.out
grep "Cluster:" cluster_log.out