#!/bin/sh
#
# xmlconv,v 1.1 2003/07/30 00:25:42 dsg Exp
# unix shell script to run the convert mmcif files to xml format
#
# Copyright 2001 Douglas S. Greer
#

# set local variable definitions
execname=`echo $0`
execdir=`dirname ${execname}`
. ${execdir}/_vars.sh

#  public static void main class
rclass=org.rcsb.openmms.apps.xconv.XmlConvert

# defaults
dictionary1=${DICTIONARY_DIR}/mmcif_pdbx_2.dic
data_dir="${TEST_CIF_DATA_DIR}"
file_list=${TEST_DATA_DIR}/lists/StructureIDs.list
#xml_dir=`pwd`
xml_dir=${TEST_DATA_DIR}/xml
vm_size=512M
verbosity=7

# process command line
while getopts d:l:m:n:s:v:x: option
do
    case "${option}"
    in
	d)   data_dir=${OPTARG};;
	l)   file_list=${OPTARG};;
	m)   dictionary1=${OPTARG};;
	s)   vm_size=${OPTARG};;
	v)   verbosity=${OPTARG};;
	x)   xml_dir=${OPTARG};;
	\?)  echo "Usage: cif2xmc [-d ddir] [-l list ] [-n|m dictionary]"
		echo "    [-x xml_dir] [-s vm_size] [-v verbosity]"
		echo "\tddir = mmcif data directory"
		echo "\tlist = file containing structure ids to process"
		echo "\t-n = do not write DTD file"
		echo "\tdict = mmCIF dictionary\c"
		echo " (default = ${CIF_MM_DICTIONARY_NAME})"
		echo "\txml_dir = directory where xmc files will be\c"
		echo " written"
		echo "\t  (default = ${xml_dir})"
		echo "\tvm_size = java virtual machine memory size\c"
		echo " (default = 512M)"
		echo "\tverbosity = message verbosity level (default = 3)"
		exit 1;;
    esac
done

cmd_line="${RUN_JAVA} -Xmx${vm_size} ${rclass}
	    dct=${dictionary1} \
	    filelist=${file_list} data=${data_dir} \
	    xmldir=${xml_dir} debug=${verbosity}"

if [ ${verbosity} -ge 4 ]
then
    echo ${cmd_line}
fi

${cmd_line}
