+ fi
+
+ # auto bonds
+ if [ "$ab" != "0" ]; then
+ ((cnt=1))
+ while [ $cnt -le $ab ]; do
+ anr=${anr[$cnt]}
+
+ ((tmp=anr+1))
+ line="`sed -n ${tmp}p $file`"
+ aX=`echo $line | awk '{ print $2 }'`
+ aY=`echo $line | awk '{ print $3 }'`
+ aZ=`echo $line | awk '{ print $4 }'`
+ export aX aY aZ cutoff mirror
+ cat $file | grep -v '#' | awk '\
+ BEGIN {
+ x=ENVIRON["aX"]; y=ENVIRON["aY"]; z=ENVIRON["aZ"];
+ co=ENVIRON["cutoff"]; dist=0; bcr=ENVIRON["bcr"];
+ mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"];
+ mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"];
+ my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"];
+ mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"];
+ mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"];
+ }
+ {
+ dist=sqrt((x-$2)^2+(y-$3)^2+(z-$4)^2);
+ if((dist<=co)&&(dist>0.01)) {
+ print "cylinder {";
+ print "<"x","z","y">,";
+ print "<"$2","$4","$3">, "bcr;
+ print "pigment { color Blue }";
+ print "}";
+ }
+
+ if(mirror) {
+ nx=$2-mx1; ny=$3-mx2; nz=$4-mx3;
+ dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2)
+ if((dist<=co)&&(dist>0.01)) {
+ print "cylinder {";
+ print "<"x","z","y">,";
+ print "<"nx","nz","ny">, "bcr;
+ print "pigment { color Blue }";
+ print "}";
+ }
+ nx=$2-my1; ny=$3-my2; nz=$4-my3;
+ dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2)
+ if((dist<=co)&&(dist>0.01)) {
+ print "cylinder {";
+ print "<"x","z","y">,";
+ print "<"nx","nz","ny">, "bcr;
+ print "pigment { color Blue }";
+ print "}";
+ }
+ nx=$2-mz1; ny=$3-mz2; nz=$4-mz3;
+ dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2)
+ if((dist<=co)&&(dist>0.01)) {
+ print "cylinder {";
+ print "<"x","z","y">,";
+ print "<"nx","nz","ny">, "bcr;
+ print "pigment { color Blue }";
+ print "}";
+ }
+ }
+
+ }' >> temp.pov
+
+ ((cnt+=1))
+ done
+ fi