#!/bin/sh
#------------------------------------------------------------------------------
#$Author: antanas $
#$Date: 2021-04-28 19:35:53 +0300 (Wed, 28 Apr 2021) $
#$Revision: 8738 $
#$URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/tags/v3.8.0/scripts/cif_CODify $
#------------------------------------------------------------------------------
#*
#* Extract essential data from the input CIF file and format it
#* using the rules of the Crystallography Open Database (COD).
#*
#* USAGE:
#*   $0 1000000.cif
#*   $0 4000042.cif --options
#**

set -ue
# set -x

CIF_FILTER="cif_filter"
CIF_FILE=""
ARGS=""

while [ $# -gt 0 ]
do
  case $1 in
      --options|--option|--optio|--opti|--opt|--op|--o)
          echo "$(basename "$0"):: The '--options' option is a placeholder."
          echo "$(basename "$0"):: It should be replaced by one of the following options:"
          awk '/#\* OPTIONS:/,/#\*\*/ {
                  sub("OPTIONS:", "");
                  sub("^ *#[*]?[*]?", "");
                  gsub("\\$0","'"$0"'");
                  print $0
              }' $(dirname $0)/${CIF_FILTER}
          echo "$0:: NOTE, the option list was retrieved from the '${CIF_FILTER}' script."
          exit
          ;;
      --help|--hel|--he|--h|--usage)
          gawk '/^#\*/,/^#\*\*/ {
                  sub("^ *#[*]?[*]?", "");
                  gsub("\\$0","'"$0"'");
                  print $0
              }' "$0"
          awk '/#\* OPTIONS:/,/#\*\*/ {
                  sub("^ *#[*]?[*]?", "");
                  gsub("\\$0","'"$0"'");
                  print $0
              }' "$(dirname "$0")"/${CIF_FILTER}
          echo "$0:: NOTE, the option list was retrieved from the '${CIF_FILTER}' script."
          exit
          ;;
      --version)
          $(dirname $0)/cod-tools-version
          exit
          ;;
      *)
          if [ -z "${CIF_FILE}" ];
          then
             CIF_FILE=$1
          else
             ARGS="${ARGS} $1"
          fi
          ;;
    esac
    shift
done

if [ -z "${CIF_FILE}" ];
then
    echo "$0:: ERROR, the mandatory input CIF file was not provided." 1>&2
    exit 1;
fi

if head "${CIF_FILE}" | grep -q '^#' > /dev/null 2>&1
then
    awk '{if( match( $0, "^#" )) print; else exit}' "${CIF_FILE}"
else
    cat <<EOF
#------------------------------------------------------------------------------
#\$Date\$
#\$Revision\$
#\$URL\$
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/
#
# All data on this site have been placed in the public domain by the
# contributors.
#
EOF
fi

NUMBER=`basename "${CIF_FILE}" .cif | sed -e 's/[^0-9]//g'`

${CIF_FILTER} \
    --renumber \
    --start-data="${NUMBER}" \
    --exclude-empty-non-loop-tags \
    --estimate-spacegroup \
    --reformat-spacegroup \
    --keep-unrecognised-spacegroup \
    --parse-formula-sum \
    --calculate-cell-volume \
    --use-all-datablocks \
    "${CIF_FILE}" ${ARGS}
