#!/bin/sh
#
#  import a CATH database into Kpax ...
#
#  YOU WILL NEED TO EDIT THIS SCRIPT TO MAKE IT WORK!
#
#  This script assumes you have downloaded the chopped CATH PDB files
#  and that you have also downloaded the CATH file called CathDomainList
#  and copied it to a folder called "kpax_database". The CATH data is 
#  available here:

#  http://release.cathdb.info/v3.4.0/CathDomainList
#  http://release.cathdb.info/v3.4.0/CathDomainPdb.S35.v3_4_0.tgz

#  Assume you have something like: KPAX_DATABASE=/home/dritchie/kpax_database

if [ -z "${KPAX_DATABASE}" ]; then
   echo "Please define the variable KPAX_DATABASE first!"
   exit
fi

#  remove previous database

rm -rf ${KPAX_DATABASE}/cath_kpax

# assume the above CATH data is here (EDIT THIS!)

CATH_ROOT=/data/Cath

# make the import follow the style for Cath

if [ ! -f "${KPAX_DATABASE}/CathDomainList" ]; then

   ln -s ${CATH_ROOT}/CathDomainList  ${KPAX_DATABASE}/CathDomainList
fi

# load the PDB files from /home/ritchied/Cath/dompdb and make a
# CATH-flavoured database in ${KPAX_DATABASE}/cath_kpax
# (this assumes the presence of ${KPAX_DATABASE}/CathDomainList).

kpax -cath -build=cath -stats -source=${CATH_ROOT}/dompdb
    

#
#  You can now query the database using:
#
#  kpax -db=cath  query-file.pdb
#