New structures default to (0,0) and some work on info dict

Atom.coffee

@@ -39,4 +39,3 @@ class Atom extends Element
 
 	asArray: => [@x, @y, @z]
 
-

CanvasContext.coffee

@@ -22,15 +22,18 @@ class CanvasContext
 			el.init()
 
 		@canvas.addEventListener 'mousewheel', @changeZoom
-		@zoom_prev = 1
-		@zoom = 1
-		console.log @.findBestZoom()
-
-		@x_origin = @canvas.width/2 
+		@zoom = @.findBestZoom()
+		@zoom_prev = @zoom
+		center = @.avgCenterOfAllElements()
+
+		for el in @elements
+			el.translateTo(center)
+
+		@x_origin = @canvas.width/2
 		@y_origin = @canvas.height/2
 		@.clear()
 		@canvas.addEventListener 'dblclick', @translateOrigin
-
+		
 		@.drawAll()
 
 	findBestZoom: =>
@@ -42,7 +45,7 @@ class CanvasContext
 					max_x = Math.abs(a.x)
 				if Math.abs(a.y) > max_y
 					max_y = Math.abs(a.y)
-		@zoom = if max_x > max_y then @canvas.width/max_x else @canvas.width/max_y
+		if max_x > max_y then @canvas.width/(2*max_x) else @canvas.width/(2*max_y)
 
 	drawGridLines: =>
 		"""
@@ -80,6 +83,7 @@ class CanvasContext
 	clear: => 
 		@canvas.width = @canvas.width
 		@context.translate @x_origin, @y_origin
+		@.drawGridLines()
 
 	mousedown: (e) =>
 		@mouse_x_prev = e.x
@@ -134,19 +138,18 @@ class CanvasContext
 		htmlInfo = (index, oldhtml) =>
 			el_info = ("<p>#{el.writeContextInfo()}</p>" for el in @elements)
 			el_info.join " "
-			#"#{oldhtml}<br><br>#{el_info}"
+			"<a href=\"javascript:window.ctx.changeAllDrawMethods('points');\">Canvas</a><br><br>#{el_info}"
 		$("#ctx-info").html htmlInfo
 
 	avgCenterOfAllElements: =>
 		avgs = [0.0, 0.0, 0.0]
 		total_atoms = 0
 		for el in @elements
 			elAvg = el.avgCenter()
-			avgs[0] += elAvg[0]
-			avgs[1] += elAvg[1]
-			avgs[2] += elAvg[2]
+			ela = el.atoms.length
+			avgs[0] += elAvg[0]*ela
+			avgs[1] += elAvg[1]*ela
+			avgs[2] += elAvg[2]*ela
 			total_atoms += el.atoms.length
 		(a/total_atoms for a in avgs)
 
-
-

Element.coffee

@@ -9,7 +9,7 @@ class Element
 			@cc = @parent.cc
 
 		@info = {}
-	
+
 	writeContextInfo: =>
 		if @.constructor.name != "Residue"
 			# THIS WILL BREAK IE COMPAT.
@@ -31,6 +31,7 @@ class Element
 
 	propogateInfo: (info) ->
 		@info = info
+		@info.drawColor = if @info.drawColor? then @info.drawColor else randomRGB()
 		#if not @info.drawColor?
 		#	@info.drawColor = randomRGB()
 		for c in @children
@@ -57,22 +58,33 @@ class Element
 			@.drawPoints()
 
 	drawPaths: => 
+		isBonded = (a1, a2) ->
+			if a1.parent.typeName() != a2.parent.typeName()
+				false
+			else if atomAtomDistance(a1, a2) < 3 and a1.parent.isProtein()
+				true
+			else if atomAtomDistance(a1, a2) < 10 and a1.parent.isDNA()
+				true
+			else
+				false
+
 		x = @cc.context
-		@info.drawColor = if @info.drawColor? then @info.drawColor else randomRGB()
 
 		for i in [2..@atoms.length-1]
-			x.beginPath()
-			a2 = @atoms[i]
-			a1 = @atoms[i-1]
-			if atomAtomDistance(a1, a2) < 10
-				x.moveTo(a1.x, a1.y)
-				x.lineTo(a2.x, a2.y)
-			x.strokeStyle = arrayToRGB (c + a1.z for c in @info.drawColor)
-			#x.lineJoin = "round"
-			#x.lineCap = "round"
-			x.lineWidth = (3*a1.z + 200)/200
-			x.closePath()
-			x.stroke()
+			for j in [i+1..i+5] when j < @atoms.length-1
+				x.beginPath()
+				a2 = @atoms[i]
+				a1 = @atoms[j]
+				if isBonded a1, a2 
+					x.moveTo(a1.x, a1.y)
+					x.lineTo(a2.x, a2.y)
+				x.strokeStyle = arrayToRGB (c + a1.z for c in @info.drawColor)
+				#x.lineJoin = "round"
+				#x.lineCap = "round"
+				lw = (3*a1.z + 200)/200
+				x.lineWidth = if lw > 0 then lw else lw
+				x.closePath()
+				x.stroke()
 
 	drawPoints: =>
 		@atoms.sort sortByZ
@@ -99,3 +111,10 @@ class Element
 			avgs[2] += a.z
 		(a/@atoms.length for a in avgs)
 
+	translateTo: (center) =>
+		for a in @atoms
+			a.x -= center[0]
+			a.y -= center[1]
+			a.z -= center[2]
+
+