X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=visualize;h=ab6e374ebd551c65074c3bd89b28df2bf9efe36e;hb=95cfeec6fbbfa975d5ac5b99ec3f7386ca3d6071;hp=b5d8f74f2a6a86c59c081e66c9c0ab0201090efd;hpb=c40d54eb3e319b17b2f6174c4eddcfd6ee3a407b;p=physik%2Fposic.git

diff --git a/visualize b/visualize
index b5d8f74..ab6e374 100755
--- a/visualize
+++ b/visualize
@@ -14,6 +14,14 @@ pigment { color White }
 }
 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"
@@ -23,8 +31,10 @@ x0=""; y0=""; z0="";
 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
@@ -39,6 +49,7 @@ while [ "$1" ]; do
 		-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 "########"
@@ -49,6 +60,7 @@ while [ "$1" ]; do
 				echo "  -h <height>"
 				echo "atom size:"
 				echo "  -r <radius>"
+				echo "  -B <bond cylinder radius>"
 				echo "visualization volume:"
 				echo "  -nll <x> <y> <z> (near lower left)"
 				echo "  -fur <x> <y> <z> (far upper right)"
@@ -125,14 +137,11 @@ EOF
 	if [ -z "$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
@@ -171,6 +180,38 @@ EOF
 
 	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 {