#!/bin/sh
#
#  import a SCOP database into Kpax ...
#
#  YOU WILL NEED TO EDIT THIS SCRIPT TO MAKE IT WORK!
#
#  This script assumes you have downloaded the SCOP PDB files
#  and that you have also downloaded the SCOP list of domain names. 
#
#  For example, the files for version 1.75 (40% sequence identity filter)
#  are available here:
#
#  http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.75
#  http://astral.berkeley.edu/pdbstyle-sel-gs-bib-40-1.75.tgz
#  
#  This script assumes you have a folder called "kpax_database". 
#  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}/scop_kpax

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

SCOP_ROOT=/data/Scop

# make the import follow the style for Cath

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

   ln -s ${SCOP_ROOT}/dir.cla.scop.txt_1.75 ${KPAX_DATABASE}/ScopDomainList
fi

# make a list of PDB file names

ls -1 ${SCOP_ROOT}/pdbstyle-1.75/*/*.ent > ${KPAX_DATABASE}/ScopFiles

# load the PDB files from from this list and make a SCOP-flavoured database 
# in ${KPAX_DATABASE}/scop_kpax

kpax -scop -build=scop -stats -source=${KPAX_DATABASE}/ScopFiles

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