getPNGofXYZ

#!/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 XYZ 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
}
#####################################################################
print_vmd_script(){

file_name=$1
backgroud_color=$2

cat << END_VMD_SCRIPT
#!/usr/local/bin/vmd

#VMD script written by save_state \$Revision: 1.47 $
#VMD version: 1.9.3
set viewplist {}
set fixedlist {}
# Display settings
display projection   Orthographic
display height       4.000000
display distance     -2.000000
display nearclip set 0.000000
display depthcue   off
display shadows off
display ambientocclusion off
display aoambient 0.800000
display aodirect 0.300000
display dof off
display dof_fnumber 64.000000
display dof_focaldist 0.700000
mol new $file_name type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol delrep 0 top
mol representation CPK 1.000000 0.400000 150.000000 150.000000
mol color Element
mol selection {all}
mol material Opaque
mol addrep top
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol rename $file_name
# done with molecule 0
proc vmdrestoremycolors {} {
  set colorcmds {
    {color Display {Background} $backgroud_color}
    {color Display {BackgroundTop} black}
    {color Display {BackgroundBot} blue2}
    {color Display {FPS} black}
    {color Element {X} cyan}
    {color Element {Ac} ochre}
    {color Element {Ag} ochre}
    {color Element {Al} ochre}
    {color Element {Am} ochre}
    {color Element {Ar} ochre}
    {color Element {As} ochre}
    {color Element {At} ochre}
    {color Element {Au} ochre}
    {color Element {B} ochre}
    {color Element {Ba} ochre}
    {color Element {Be} ochre}
    {color Element {Bh} ochre}
    {color Element {Bi} ochre}
    {color Element {Bk} ochre}
    {color Element {Br} ochre}
    {color Element {Ca} ochre}
    {color Element {Cd} ochre}
    {color Element {Ce} ochre}
    {color Element {Cf} ochre}
    {color Element {Cl} green}
    {color Element {Cm} ochre}
    {color Element {Co} ochre}
    {color Element {Cr} ochre}
    {color Element {Cs} ochre}
    {color Element {Cu} ochre}
    {color Element {Db} ochre}
    {color Element {Ds} ochre}
    {color Element {Dy} ochre}
    {color Element {Er} ochre}
    {color Element {Es} ochre}
    {color Element {Eu} ochre}
    {color Element {F} ochre}
    {color Element {Fe} ochre}
    {color Element {Fm} ochre}
    {color Element {Fr} ochre}
    {color Element {Ga} ochre}
    {color Element {Gd} ochre}
    {color Element {Ge} ochre}
    {color Element {He} ochre}
    {color Element {Hf} ochre}
    {color Element {Hg} ochre}
    {color Element {Ho} ochre}
    {color Element {Hs} ochre}
    {color Element {I} ochre}
    {color Element {In} ochre}
    {color Element {Ir} ochre}
    {color Element {K} ochre}
    {color Element {Kr} ochre}
    {color Element {La} ochre}
    {color Element {Li} ochre}
    {color Element {Lr} ochre}
    {color Element {Lu} ochre}
    {color Element {Md} ochre}
    {color Element {Mg} ochre}
    {color Element {Mn} ochre}
    {color Element {Mo} ochre}
    {color Element {Mt} ochre}
    {color Element {Na} ochre}
    {color Element {Nb} ochre}
    {color Element {Nd} ochre}
    {color Element {Ne} ochre}
    {color Element {Ni} ochre}
    {color Element {No} ochre}
    {color Element {Np} ochre}
    {color Element {Os} ochre}
    {color Element {Pa} ochre}
    {color Element {Pb} ochre}
    {color Element {Pd} ochre}
    {color Element {Pm} ochre}
    {color Element {Po} ochre}
    {color Element {Pr} ochre}
    {color Element {Pt} ochre}
    {color Element {Pu} ochre}
    {color Element {Ra} ochre}
    {color Element {Rb} ochre}
    {color Element {Re} ochre}
    {color Element {Rf} ochre}
    {color Element {Rg} ochre}
    {color Element {Rh} ochre}
    {color Element {Rn} ochre}
    {color Element {Ru} ochre}
    {color Element {Sb} ochre}
    {color Element {Sc} ochre}
    {color Element {Se} ochre}
    {color Element {Sg} ochre}
    {color Element {Si} ochre}
    {color Element {Sm} ochre}
    {color Element {Sn} ochre}
    {color Element {Sr} ochre}
    {color Element {Ta} ochre}
    {color Element {Tb} ochre}
    {color Element {Tc} ochre}
    {color Element {Te} ochre}
    {color Element {Th} ochre}
    {color Element {Ti} ochre}
    {color Element {Tl} ochre}
    {color Element {Tm} ochre}
    {color Element {U} ochre}
    {color Element {V} ochre}
    {color Element {W} ochre}
    {color Element {Xe} ochre}
    {color Element {Y} ochre}
    {color Element {Yb} ochre}
    {color Element {Zr} ochre}
  }
  foreach colcmd \$colorcmds {
    set val [catch {eval \$colcmd}]
  }
}
vmdrestoremycolors
END_VMD_SCRIPT
}
#####################################################################
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"

	if [[ -f $file_name_vmd_view ]]
	then
		echo " The file $file_name_vmd_view for viewing in VMD already exist"
	else
		print_vmd_script $file_name $backgroud_color > $file_name_vmd_view
	fi

	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_xyz="${@: -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_xyz ]; then
	echo "Error: input filename missing (Try -h for more information.)."
	exit 2
fi

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