aded visual atoms script ...

diff --git a/visual_atoms_script b/visual_atoms_script
new file mode 100755 (executable)
index 0000000..2b7f55f
--- /dev/null
+++ b/visual_atoms_script
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+rm -f $5/va_*.*
+
+((count=0))
+
+./search_bonds $1 $2 $3 $4 | grep ' # atoms' | while read a b c d e f; do
+
+       ca=`echo $c | awk -F/ '{ print $1}'`
+       ma=`echo $d | awk -F/ '{ print $1}'`
+
+       ./visual_atoms $1 $ca 12.0 5.429 $ma | \
+               grep ^[A-Z] > $5/va_${count}.xyz
+
+       which povray
+       ret=$?
+       if [ "$ret" = "0" ]; then
+               ./visualize -w 640 -h 480 -d $5/va_${count}.xyz \
+                            -nll -0.76 -0.76 -0.76 -fur 0.76 0.76 0.76 \
+                            -b -0.5 -0.5 -0.5 0.5 0.5 0.5 \
+                            -c -0.2 -2.0 0.6 -L 0 0 -0.1 \
+                            -r 0.6 -B 0.1
+       fi
+
+       echo -en "$count "
+
+       ((count+=1))
+done
+
+echo "done"
+
+qiv $5/va_*.png
+