getPNGofVMD

#!/bin/bash

# If VMD was a personalizate installation, please find the library of tachyon_LINUXAMD64 or equivalent 
# 		and put the path and command for using VMD in the next two lines
# Authorship, support, and maintenance of this script is attributed to
# Luis Alfredo Nunez Meneses
# luis.alfredo.nu@gmail.com

path_of_tachyon="/usr/local/lib/vmd/tachyon_LINUXAMD64"
vmd_line_command="vmd"

#####################################################################
#--------------------------------------------------------------   Fdx
#####################################################################
#--------------------------------------------------------------   Fdx
#####################################################################

the_prog_name=$(echo "$0" | sed -e 's;\(.*\)/\(.*\);\2;')
cmdl_argv=($@)
cmdl_argc=${#cmdl_argv[@]}

help_and_syntax()
{
   the_prog_name=$1
echo -e "\n    Script syntax: \033[1m$the_prog_name\033[0m [\033[0;4moption(s)\033[0m \
[\033[4margument(s)\033[0m]] [\033[4minputname.xyz\033[0m]"
#Here you may put a description of the script. The text between 'END_USAGE_TEXT'
#will be displayed as it is.
cat << END_USAGE_TEXT

This script will create a images in png format from file with format VMD using VMD program

Tip:
	If you want a different view of your molecule, please open the file "name_file.vmd" with VMD like this

	vmd -e name_file.vmd

	Save the visualization how you like to look your molecule in the same file and run this script again.

Description of options. For instance:
   -h               Display the help menu.
   -b color         Color of background. "black" or "white". Default white
   -x ####          Size wight image. Default 800.
   -y ####          Size height image. Default 680.

END_USAGE_TEXT
}
#####################################################################
prove_if_exist_tachyon_lib(){
	path=$1
	if [[ -f $path ]]
	then
		echo $path
	else
		echo -e " Error: Missing the tachyon_LINUXAMD64 \n Search where is the lib of vmd"
		exit 2
	fi
}
#####################################################################
generate_png_from_vmd(){
	file_name=$1
	res_x=$2
	res_y=$3
	backgroud_color=$4

	base_file_name=${file_name%.*}
	file_name_vmd_view="$base_file_name.vmd"
	file_name_for_render="$base_file_name.render"
	file_name_png="$base_file_name.png"
	file_name_tga="$base_file_name.tga"

	tachyon=$(prove_if_exist_tachyon_lib $path_of_tachyon)
	vmd_commands="axes location off \n render Tachyon $file_name_for_render"
	echo -e $vmd_commands | $vmd_line_command -e $file_name_vmd_view  -size $res_x $res_y -dispdev text -eofexit
	$tachyon -V -aasamples 12 -trans_max_surfaces 1 -rescale_lights 2.0 -add_skylight 0.0 $file_name_for_render -o $file_name_tga 
	convert  $file_name_tga $file_name_png
	
	rm $file_name_for_render
	rm $file_name_tga
}
#####################################################################
#     Corpus of the Script
#####################################################################

file_name_vmd="${@: -1}"

size_in_x=800
size_in_y=800
backgroud_color="white"

#Checks the consistency of the argument list
if [ $# -lt 1 ]; then
	echo "Error: input filename missing (Try -h for more information.)."
	exit 2
fi

while getopts ":hb:x:y:" opt; do
  case $opt in
  	 b)
	 	backgroud_color="$OPTARG"
	 	;;
  	 x)
	 	size_in_x=$OPTARG
	 	;;
	 y)
	 	size_in_y=$OPTARG
	 	;;
    h)
      help_and_syntax $prog_name
      exit 0
      ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      ;;
    :)
      echo "Option -$OPTARG requires an argument." >&2
      exit 1
      ;;
  esac
done
if [ ! -f $file_name_vmd ]; then
	echo "Error: input filename missing (Try -h for more information.)."
	exit 2
fi

echo " Create image in png of $file_name_vmd"
generate_png_from_vmd $file_name_vmd $size_in_x $size_in_y $backgroud_color
echo