C visible, transparent atom labels

src/draw/draw2d.jl

@@ -28,6 +28,7 @@ Default setting parameters of the molecule drawing canvas.
                    `:alongside` for others (default)
 - `:atomcolor`(Dict{Symbol,Color}) atom symbol and bond colors for organic atoms
 - `:defaul_atom_color`(Dict{Symbol,Color}) colors for other atoms
+- `:C_visible`(Bool) if C atoms should be visible
 """
 const DRAW_SETTING = Dict(
     :display_terminal_carbon => false,
@@ -48,7 +49,8 @@ const DRAW_SETTING = Dict(
         :Br => Color(0, 192, 0),
         :I => Color(0, 128, 0)
     ),
-    :default_atom_color => Color(0, 192, 192)
+    :default_atom_color => Color(0, 192, 192),
+    :C_visible => false
 )
 
 # For 3d rendering, we use white for hydrogen
@@ -87,7 +89,7 @@ Return whether the atom is visible in the 2D drawing.
     mul_ = multiplicity(mol)
     mas_ = getproperty.(nodeattrs(mol), :mass)
     for i in 1:nodecount(mol)
-        sym_[i] === :C || continue
+        (sym_[i] === :C && ! setting[:C_visible]) || continue
         chg_[i] == 0 || continue
         mul_[i] == 1 || continue
         mas_[i] === nothing || continue
@@ -298,12 +300,13 @@ end
 
 
 function drawatomindex!(canvas::Canvas, mol::UndirectedGraph;
-                        color=Color(0, 0, 0), bgcolor=Color(240, 240, 255))
+                        color=Color(0, 0, 0), bgcolor=Color(240, 240, 255),
+                        opacity=1.0)
     isatomvisible_ = isatomvisible(mol)
     for i in nodeset(mol)
         offset = isatomvisible_[i] ? (0.0, canvas.fontsize/2.0) : (0.0, 0.0)
         pos = Point2D(canvas.coords, i) + offset
-        setatomnote!(canvas, pos, string(i), color, bgcolor)
+        setatomnote!(canvas, pos, string(i), color, bgcolor, opacity)
     end
     return
 end

src/draw/svg.jl

@@ -7,7 +7,8 @@ export
     SvgCanvas,
     tosvg,
     drawsvg,
-    initcanvas!
+    initcanvas!,
+    savesvg
 
 using Printf
 
@@ -324,15 +325,15 @@ setatomleft!(canvas::SvgCanvas, pos, sym, color, hcnt, charge) = atomsymbol!(
 )
 
 
-function setatomnote!(canvas::SvgCanvas, pos, text, color, bgcolor)
+function setatomnote!(canvas::SvgCanvas, pos, text, color, bgcolor, opacity)
     size = round(Int, canvas.fontsize * canvas.annotsizef)
     bxy = svgcoords(pos)
     txy = svgcoords(pos + (0, size))
     c = svgcolor(color)
     bc = svgcolor(bgcolor)
     elem = """<g>
-     <rect $(bxy) width="$(size)" height="$(size)" rx="$(size/2)" ry="$(size/2)" fill="$(bc)" />
-     <text $(txy) font-size="$(size)" fill="$(c)">$(text)</text>
+     <rect $(bxy) width="$(size)" height="$(size)" rx="$(size/2)" ry="$(size/2)" fill="$(bc)" opacity="$(opacity)" />
+     <text $(txy) font-size="$(size)" fill="$(c)">$(text) </text>
     </g>
     """
     push!(canvas.elements, elem)
@@ -493,3 +494,17 @@ function drawwave!(canvas::SvgCanvas, seg, ucolor, vcolor)
     push!(canvas.elements, elem)
     return
 end
+
+"""
+write svg string to file.
+"""
+function savesvg(the_svg_string::String, filename::String)
+    if ! contains(filename, ".svg")
+        filename *= ".svg"
+    end
+
+    f = open(filename, "w")
+    write(f, the_svg_string)
+    close(f)
+    return filename
+end