SBML2TikZ

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The graph below shows the rendering of several glyphs in the Athena Modular CAD environment. While Athena's export to the SBML Render Extension is not fully functional, species glyphs like the ones shown below are stored faithfully according to the extension's specifications.

PGF/TikZ Output
\documentclass{article}
\usepackage{tikz}
\usepackage{pgf}
\usepackage[total={622pt,445pt}, centering, a3paper, landscape]{geometry}
\pagestyle{empty}
\begin{document}
\begin{center}
\begin{tikzpicture}[xscale = 1, yscale = -1]
{
% List of colors used:
\definecolor{Color_0}{RGB}{0,0,0};
\definecolor{Color_1}{RGB}{0,128,0};
\definecolor{Color_2}{RGB}{0,0,139};
\definecolor{Color_3}{RGB}{255,0,0};
\definecolor{Color_4}{RGB}{0,191,255};
\definecolor{Color_5}{RGB}{169,169,169};
\definecolor{Color_6}{RGB}{128,128,128};
% List of gradients used:
\definecolor{color0}{RGB}{255,255,255};
\definecolor{color1}{RGB}{70,130,180};
\pgfdeclareverticalshading {LinearGradient_0} { 70pt } {color(0pt)=(color0!100); color(73.96073pt)=(color1!100)}
\definecolor{color0}{RGB}{255,255,255};
\definecolor{color1}{RGB}{135,206,235};
\pgfdeclareverticalshading {LinearGradient_1} { 70pt } {color(0pt)=(color0!100); color(73.96073pt)=(color1!100)}
\definecolor{color0}{RGB}{255,255,255};
\definecolor{color1}{RGB}{211,211,211};
\pgfdeclareverticalshading {LinearGradient_2} { 70pt } {color(0pt)=(color0!100); color(73.96073pt)=(color1!100)}
\definecolor{color0}{RGB}{255,255,255};
\definecolor{color1}{RGB}{192,192,192};
\pgfdeclareverticalshading {LinearGradient_3} { 70pt } {color(0pt)=(color0!100); color(73.96073pt)=(color1!100)}
{
   % Group for J0
   \draw[line width = 2pt, color = Color_4!100,  ] (314pt, 221pt) -- (314pt, 191.5pt);
   \draw[line width = 2pt, color = Color_4!100,  ] (314pt, 191.5pt) -- (314pt, 172pt);
   {
      \pgftransformshift{\pgfpoint{ 314pt }{ 172pt } }
      \pgftransformcm { 0 }{ -1 }{ -1 }{ 0 }{\pgfpoint{ 0pt }{ 0pt } }
      {
         % LineEnding for S0
         {
            % Polygon for S0
            \pgftransformshift{\pgfpoint{ 0pt }{ -1.5pt } }
            \draw [line width = 2pt, color = Color_4!100, fill = Color_0!100 ]
            (0pt,0pt)--(5pt,1.5pt)--(0pt,3pt)--(0pt, 0pt) -- cycle;
         }
      }
   }
}
{
   % Group for J1
   \draw[line width = 2pt, color = Color_4!100,  ] (333.51611328125pt, 129pt) -- (343.301086425781pt, 120.727233886719pt);
   \draw[line width = 2pt, color = Color_4!100,  ] (343.301086425781pt, 120.727233886719pt) -- (344pt, 120.136344909668pt);
   {
      \pgftransformshift{\pgfpoint{ 344pt }{ 120.1363pt } }
      \pgftransformcm { 0.7636553 }{ -0.6456242 }{ 0.6456242 }{ 0.7636554 }{\pgfpoint{ 0pt }{ 0pt } }
      {
         % LineEnding for EMPTY
         {
            % Polygon for EMPTY
            \pgftransformshift{\pgfpoint{ 0pt }{ -1.5pt } }
            \draw [line width = 2pt, color = Color_4!100, fill = Color_0!100 ]
            (0pt,0pt)--(5pt,1.5pt)--(0pt,3pt)--(0pt, 0pt) -- cycle;
         }
      }
   }
}
{
   % Rectangle for Promoter_0
   \pgftransformshift{\pgfpoint{ 168pt }{ 145pt } }
   \def \wholeShape {(0pt,0pt) rectangle(60pt,46pt)}
   \fill[shading = LinearGradient_0, shading angle = -135] \wholeShape;
   \draw[line width = 2pt, color = Color_0!100 ] \wholeShape;
}
{
   % Polygon for Promoter_0
   \pgftransformshift{\pgfpoint{ 168pt }{ 145pt } }
   \pgftransformcm { 3.230769 }{ 0 }{ 0 }{ 1.61 }{\pgfpoint{ 9pt }{ 6.9pt } }
   \draw [line width = 2pt, color = Color_0!100, fill = Color_1!100 ]
   (0pt,20pt)--(0pt,10pt)--(0pt, 10pt) .. controls (0pt, 3pt) and (0pt, 3pt) ..(5pt,3pt)--(5pt,3pt)--(10pt,3pt)--(10pt,3pt)--(10pt,0pt)--(10pt,0pt)--(13pt,5pt)--(13pt,5pt)--(10pt,10pt)--(10pt,10pt)--(10pt,7pt)--(10pt,7pt)--(5pt,7pt)--(5pt, 7pt) .. controls (3pt, 7pt) and (3pt, 7pt) ..(3pt,10pt)--(3pt,10pt)--(3pt,20pt);
}
{
   % Text for Promoter_0
   \draw (168pt, 211.7126pt) node[text = Color_2!100, font = \fontsize{ 8.25 } { 8.25 }\fontfamily\sfdefault\selectfont] { Promoter\_0 };
}
{
   % Rectangle for Terminator_0
   \pgftransformshift{\pgfpoint{ 169pt }{ 222pt } }
   \def \wholeShape {(0pt,0pt) rectangle(60pt,46pt)}
   \fill[shading = LinearGradient_0, shading angle = -135] \wholeShape;
   \draw[line width = 2pt, color = Color_0!100 ] \wholeShape;
}
{
   % Polygon for Terminator_0
   \pgftransformshift{\pgfpoint{ 169pt }{ 222pt } }
   \pgftransformcm { 2.25 }{ 0 }{ 0 }{ 1.725 }{\pgfpoint{ 16.5pt }{ 12.65pt } }
   \draw [line width = 2pt, color = Color_0!100, fill = Color_3!100 ]
   (0pt,3.5pt)--(3.5pt,0pt)--(8.5pt,0pt)--(12pt,3.5pt)--(12pt,8.5pt)--(8.5pt,12pt)--(3.5pt,12pt)--(0pt,8.5pt)--(0pt, 3.5pt) -- cycle;
}
{
   % Text for Terminator_0
   \draw (169pt, 288.7126pt) node[text = Color_2!100, font = \fontsize{ 8.25 } { 8.25 }\fontfamily\sfdefault\selectfont] { Terminator\_0 };
}
{
   % Rectangle for Gene_0
   \pgftransformshift{\pgfpoint{ 284pt }{ 226pt } }
   \def \wholeShape {(0pt,0pt) rectangle(60pt,46pt)}
   \fill[shading = LinearGradient_0, shading angle = -135] \wholeShape;
   \draw[line width = 2pt, color = Color_0!100 ] \wholeShape;
}
{
   % Polygon for Gene_0
   \pgftransformshift{\pgfpoint{ 284pt }{ 226pt } }
   \pgftransformcm { 1.4 }{ 0 }{ 0 }{ 3.22 }{\pgfpoint{ 9pt }{ 6.9pt } }
   \draw [line width = 2pt, color = Color_0!100, fill = Color_4!100 ]
   (0pt,8pt)--(0pt,2pt)--(20pt,2pt)--(20pt,0pt)--(30pt,5pt)--(20pt,10pt)--(20pt,8pt)--(0pt, 8pt) -- cycle;
}
{
   % Text for Gene_0
   \draw (284pt, 292.7126pt) node[text = Color_2!100, font = \fontsize{ 8.25 } { 8.25 }\fontfamily\sfdefault\selectfont] { Gene\_0 };
}
{
   % Rectangle for S0
   \pgftransformshift{\pgfpoint{ 299pt }{ 134pt } }
   \def \wholeShape {(0pt,0pt) rectangle(30pt,23pt)}
   \fill[rounded corners = 3pt, shading = LinearGradient_1, shading angle = -135 ] \wholeShape;
   \draw[line width = 1.25pt, color = Color_5!100, rounded corners = 3pt ] \wholeShape;
}
{
   % Text for S0
   \draw (329pt, 152.4126pt) node[text = Color_2!100, font = \fontsize{ 8.25 } { 8.25 }\fontfamily\sfdefault\selectfont] { S0 };
}
{
   % Curve for EMPTY
   \pgftransformshift{\pgfpoint{ 359pt }{ 89pt } }
   \draw [line width = 1.25pt, color = Color_6!100,shading = LinearGradient_2, shading angle = 45 ]
   (0pt,20pt)--(20pt,0pt);
}
{
   % Ellipses for EMPTY
   \pgftransformshift{\pgfpoint{ 359pt }{ 89pt } }
   \def \wholeShape {(10pt,10pt) ellipse(10pt and 10pt)}
   \fill[shading = LinearGradient_2, shading angle = -135] \wholeShape;
   \draw[line width = 1.25pt, color = Color_6!100 ] \wholeShape;
}
{
   % Group for EMPTY
   {
      % Curve for EMPTY
      \pgftransformshift{\pgfpoint{ 359pt }{ 89pt } }
      \draw [line width = 1.25pt, color = Color_6!100,shading = LinearGradient_2, shading angle = 45 ]
      (0pt,20pt)--(20pt,0pt);
   }
}
{
   % Rectangle for RBS_0
   \pgftransformshift{\pgfpoint{ 394pt }{ 225pt } }
   \def \wholeShape {(0pt,0pt) rectangle(60pt,46pt)}
   \fill[shading = LinearGradient_0, shading angle = -135] \wholeShape;
   \draw[line width = 2pt, color = Color_0!100 ] \wholeShape;
}
{
   % Ellipses for RBS_0
   \pgftransformshift{\pgfpoint{ 394pt }{ 225pt } }
   \def \wholeShape {(30pt,23pt) ellipse(10pt and 10pt)}
   \fill[color = Color_4!100] \wholeShape;
   \draw[line width = 2pt, color = Color_0!100 ] \wholeShape;
}
{
   % Text for RBS_0
   \draw (394pt, 291.7126pt) node[text = Color_2!100, font = \fontsize{ 8.25 } { 8.25 }\fontfamily\sfdefault\selectfont] { RBS\_0 };
}
{
   % Polygon for P_0
   \pgftransformshift{\pgfpoint{ 170pt }{ 321pt } }
   \draw [line width = 2pt, color = Color_0!100, shading = LinearGradient_3, shading angle = -135 ]
   (0pt,0pt)--(50pt,0pt)--(40.0000005960464pt,16.5pt)--(50pt,33pt)--(0pt,33pt)--(9.99999940395355pt,16.5pt)--(0pt, 0pt) -- cycle;
}
{
   % Text for P_0
   \draw (220pt, 344.4126pt) node[text = Color_0!100, font = \fontsize{ 8.25 } { 8.25 }\fontfamily\sfdefault\selectfont] { P\_0 };
}
{
   % Polygon for O_0
   \pgftransformshift{\pgfpoint{ 240pt }{ 321pt } }
   \draw [line width = 2pt, color = Color_0!100, shading = LinearGradient_3, shading angle = -135 ]
   (9.99999940395355pt,0pt)--(40.0000005960464pt,0pt)--(50pt,16.5pt)--(40.0000005960464pt,33pt)--(9.99999940395355pt,33pt)--(0pt,16.5pt)--(9.99999940395355pt, 0pt) -- cycle;
}
{
   % Text for O_0
   \draw (290pt, 344.4126pt) node[text = Color_0!100, font = \fontsize{ 8.25 } { 8.25 }\fontfamily\sfdefault\selectfont] { O\_0 };
}
{
   % Polygon for Tag_0
   \pgftransformshift{\pgfpoint{ 321pt }{ 322pt } }
   \draw [line width = 2pt, color = Color_0!100, shading = LinearGradient_3, shading angle = -135 ]
   (0pt,0pt)--(40.0000005960464pt,0pt)--(50pt,16.5pt)--(40.0000005960464pt,33pt)--(0pt,33pt)--(0pt, 0pt) -- cycle;
}
{
   % Text for Tag_0
   \draw (371pt, 345.4126pt) node[text = Color_0!100, font = \fontsize{ 8.25 } { 8.25 }\fontfamily\sfdefault\selectfont] { Tag\_0 };
}
{
   % Polygon for n_0
   \pgftransformshift{\pgfpoint{ 399pt }{ 323pt } }
   \draw [line width = 2pt, color = Color_0!100, shading = LinearGradient_3, shading angle = -135 ]
   (0pt,26.4000000953674pt)--(0pt,0pt)--(50pt,0pt)--(50pt, 26.4000000953674pt) .. controls (50pt, 33pt) and (50pt, 33pt) .. (43.4000000953674pt,33pt)--(6.59999990463257pt, 33pt) .. controls (0pt, 33pt) and (0pt, 33pt) .. (0pt, 26.4000000953674pt) -- cycle;
}
{
   % Text for n_0
   \draw (449pt, 346.4126pt) node[text = Color_0!100, font = \fontsize{ 8.25 } { 8.25 }\fontfamily\sfdefault\selectfont] { n\_0 };
}
}
\end{tikzpicture}
\end{center}
\end{document}