}
EOF
}
+draw_bond() {
+ cat >> temp.pov <<-EOF
+cylinder {
+<$1, $3, $2>, <$4, $6, $5>, $7
+pigment { color Blue }
+}
+EOF
+}
directory="doesnt_exist____for_sure"
width="640"
x1=""; y1=""; z1="";
cx=""; cy=""; cz="";
lx="0"; ly="-100"; lz="100";
+ortographic=""
bx0=""; by0=""; bz0="";
bx1=""; by1=""; bz1="";
+bcr="";
while [ "$1" ]; do
case "$1" in
-o) ortographic=1; shift 1;;
-b) bx0=$2; by0=$3; bz0=$4;
bx1=$5; by1=$6; bz1=$7; shift 7;;
+ -B) bcr=$2; shift 2;;
*)
echo "options:"
echo "########"
echo " -h <height>"
echo "atom size:"
echo " -r <radius>"
+ echo " -B <bond cylinder radius>"
echo "visualization volume:"
echo " -nll <x> <y> <z> (near lower left)"
echo " -fur <x> <y> <z> (far upper right)"
if [ -z "$bx0" ]; then
if [ -z "$x0" ]; then
+
cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
- cat >> temp.pov <<-EOF
-cylinder {
-<$x1, $z1, $y1>, <$x2, $z2, $y2>, 0.05
-pigment { color White }
-}
-EOF
+ draw_cyl $x1 $z1 $y1 $x2 $z2 $y2 0.05
done
+
else
# manually drawing the 3x4 boundaries ...
draw_cyl $x0 $y0 $z0 $x1 $y0 $z0
fi
+ # bonds
+ if [ -n "$bcr" ]; then
+
+ if [ -z "$x0" ]; then
+
+ cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
+ draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr
+ done
+
+ else
+
+ export x0 y0 z0 x1 y1 z1 bcr
+ cat $file | grep '# \[B\]' | awk '\
+ BEGIN {
+ x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
+ x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
+ bcr=ENVIRON["bcr"];
+ }
+ {
+ if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\
+ ($3<=x1)&&($4<=y1)&&($5<=z1)) {
+ print "cylinder {";
+ print "<"$3","$5","$4">,";
+ print "<"$6","$8","$7">, "bcr;
+ print "pigment { color Blue }";
+ print "}";
+ }
+ }' >> temp.pov
+
+ fi
+ fi
+
# add camera and light source
cat >> temp.pov <<-EOF
camera {