little_helpers/tikz/dmol2sketch.sh

   1 #!/bin/bash -eu
   2 #------------------------------------------------
   3 #    dmol2sketch.sh
   4 #    Helper script that turns dmol file into points in syntax that can be
   5 #    used in a sketch input file.
   6 #    Sketch lives at http://www.frontiernet.net/~eugene.ressler/
   7 #
   8 #    Copyright (C) Max J. Hoffmann 2009 mjhoffmann@gmail.com
   9 #
  10 #    This program is free software: you can redistribute it and/or modify
  11 #    it under the terms of the GNU General Public License as published by
  12 #    the Free Software Foundation, either version 3 of the License, or
  13 #    (at your option) any later version.
  14 #
  15 #    This program is distributed in the hope that it will be useful,
  16 #    but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18 #    GNU General Public License for more details.
  19 #
  20 #    You should have received a copy of the GNU General Public License
  21 #    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  22 #
  23 #------------------------------------------------
  24
  25 #Initialize variables
  26 dmol=""
  27
  28
  29 while getopts "i:h" optionName
  30 do
  31   case "${optionName}" in
  32     h) echo "Usage: ${0} -i DMOL_FILE > SKETCH_FILE" ;
  33        exit;;
  34     i) dmol=${OPTARG} ;;
  35   esac
  36 done
  37
  38
  39 #Exit with usage message if no input file is provided
  40 if [ "${dmol}" = "" ]
  41 then
  42    ${0} -h
  43    exit
  44 fi
  45
  46 #Find lines where atomic coordinates are stored
  47 start_line=$(expr "$(grep -rin coordinates ${dmol} | cut -d ":" -f 1) + 1" | bc -l)
  48 end_line=$(expr "$(wc -l ${dmol} | awk '{print $1}' ) -1 " | bc -l)
  49
  50 #Determine starting species
  51 species=$(sed -n ${start_line}p ${dmol} | awk '{print $1}')
  52 #Initialize atom counter
  53 atom_nr=0
  54
  55 for line in $(seq ${start_line} ${end_line})
  56 do
  57   if [  "$(sed -n ${line}p ${dmol} | awk '{print $1}')" = "${species}" ]
  58   then
  59     atom_nr="$(expr "${atom_nr}+1" | bc -l)"
  60   else
  61     atom_nr=1
  62     species="$(sed -n ${line}p ${dmol} | awk '{print $1}')"
  63   fi
  64
  65
  66   sed -n ${line}p ${dmol}| sed -e "s/\([^ ]*\)\s*\([0-9.-]*\)\s*\([0-9.-]*\)\s*\([0-9.-]*\)/def \1${atom_nr} (\2,\3,\4)/"
  67 done
  68