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within BioChem.Icons; | ||
|
||
partial class Base | ||
annotation(Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), | ||
Documentation(info = "<html><head></head><body><font size=\"5\">A base icon relevant for many components carrying the same annotations. Older annotations had the following attribute:</font><div><br></div><div> | ||
<pre style=\"margin-top: 0px; margin-bottom: 0px;\"><!--StartFragment--><span style=\" font-family:'Courier New'; font-size:12pt; color:#0000ff;\">Diagram</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">(</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#0000ff;\">coordinateSystem</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">(extent={{-</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">100.0</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">,-</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">100.0</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">},{</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">100.0</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">,</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">100.0</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">}}, preserveAspectRatio=</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b0000;\">true</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">, grid={</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">10</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">,</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">10</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">}))</span><!--EndFragment--></pre><pre style=\"margin-top: 0px; margin-bottom: 0px;\"><span style=\"font-family: 'Courier New'; font-size: 12pt;\"><br></span></pre><p><span style=\"font-size: 12pt;\"><font face=\"Arial\">Since this produces empty diagram, it is not clear why is it there. So it is there for now. </font></span></p><p><span style=\"font-size: 12pt;\"><font face=\"Arial\">This Icon will also replace Icons.IconBase, which does not seem to be used throughout the library. </font></span></p><pre style=\"margin-top: 0px; margin-bottom: 0px;\"><br></pre></div></body></html>")); | ||
end Base; |
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within BioChem.Icons.Compartments; | ||
|
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partial class Compartment "Default compartment (constant volume)" | ||
extends BioChem.Icons.Base; | ||
annotation( | ||
Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillColor = {0, 85, 0}, fillPattern = FillPattern.Solid, extent = {{-100, -170}, {100, -120}}, textString = "%name", fontName = "Arial"), Rectangle(lineColor = {0, 85, 0}, fillColor = {199, 199, 149}, fillPattern = FillPattern.Solid, lineThickness = 10, extent = {{-110, -110}, {110, 110}}, radius = 20)})); | ||
end Compartment; |
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within BioChem.Icons.Compartments; | ||
|
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partial class MainCompartment "Main compartment (constant volume)" | ||
extends BioChem.Icons.Base; | ||
annotation( | ||
Documentation(info = "<html> | ||
<h1>MainCompartment</h1> | ||
<p> | ||
Main compartment model. | ||
</p> | ||
</html>", revisions = ""), | ||
Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillColor = {0, 85, 0}, fillPattern = FillPattern.Solid, extent = {{-100, -170}, {100, -120}}, textString = "%name", fontName = "Arial"), Rectangle(lineColor = {0, 85, 0}, fillColor = {199, 199, 149}, fillPattern = FillPattern.Solid, lineThickness = 10, extent = {{-110, -110}, {110, 110}}, radius = 20), Text(fillPattern = FillPattern.Solid, extent = {{-82.12, -80}, {80, 80}}, textString = "main", fontName = "Arial", textStyle = {TextStyle.Bold})})); | ||
end MainCompartment; |
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within BioChem.Icons; | ||
|
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package Compartments "Different types of compartments used in the package" | ||
extends BioChem.Icons.Library; | ||
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annotation( | ||
Documentation(info = "<html> | ||
<h1>Compartments</h1> | ||
<a name=\"fig1\"></a> | ||
<img src=\"modelica://BioChem/Resources/Images/Compartment.png\" alt=\"Fig1: Compartments\"> | ||
</html>", revisions = ""), | ||
Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Rectangle(origin = {5, -7.55952}, lineColor = {0, 85, 0}, fillColor = {199, 199, 149}, fillPattern = FillPattern.Solid, lineThickness = 10, extent = {{-70, -70}, {40, 30}}, radius = 20)}), | ||
Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); | ||
end Compartments; |
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Compartment | ||
MainCompartment |
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within BioChem.Icons; | ||
|
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model IconBase | ||
partial class IconBase | ||
extends Modelica.Icons.ObsoleteModel; | ||
annotation( | ||
Diagram(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10})), | ||
Icon(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {0.0, -127.1933}, fillPattern = FillPattern.Solid, extent = {{-100.0, -27.1933}, {100.0, 27.1933}}, textString = "%name", fontName = "Arial")})); | ||
Icon(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {0.0, -127.1933}, fillPattern = FillPattern.Solid, extent = {{-100.0, -27.1933}, {100.0, 27.1933}}, textString = "%name", fontName = "Arial")}), | ||
Documentation(info = "<html><head></head><body><font size=\"5\">This Icon does not seem to be used throughout the library and is going to be replace by Icons.Base in future versions. The Diagram annotation does not seem to play any rule as it produces only an empty diagram.</font></body></html>")); | ||
end IconBase; |
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within BioChem.Icons.Interfaces.Compartments; | ||
|
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partial class Compartment | ||
extends BioChem.Icons.Base; | ||
annotation( | ||
Icon(graphics = {Text(fillColor = {0, 85, 0}, fillPattern = FillPattern.Solid, extent = {{-100, -170}, {100, -120}}, textString = "%name", fontName = "Arial"), Rectangle(lineColor = {0, 0, 127}, fillColor = {0, 170, 255}, fillPattern = FillPattern.Solid, lineThickness = 10, extent = {{-110, -110}, {110, 110}}, radius = 20)})); | ||
end Compartment; |
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within BioChem.Icons.Interfaces.Compartments; | ||
|
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partial class MainCompartment | ||
extends BioChem.Icons.Interfaces.Compartments.Compartment; | ||
annotation( | ||
Icon(graphics = {Text(fillColor = {0, 85, 0}, fillPattern = FillPattern.Solid, extent = {{-100, -170}, {100, -120}}, textString = "%name", fontName = "Arial"), Text(fillPattern = FillPattern.Solid, extent = {{-82.12, -80}, {80, 80}}, textString = "main", fontName = "Arial", textStyle = {TextStyle.Bold})})); | ||
end MainCompartment; |
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within BioChem.Icons.Interfaces; | ||
|
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package Compartments "Properties for compartments" | ||
extends BioChem.Icons.Library; | ||
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end Compartments; |
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Compartment | ||
MainCompartment |
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within BioChem.Icons.Interfaces.Nodes; | ||
|
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partial class ActivatorConnector "Icon for a connector between activators and reactions" | ||
annotation(Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(lineColor={0,85,0}, fillColor={255,255,255}, extent={{-20,-20},{20,20}}),Line(points={{-20,20},{20,-20}}, color={0,85,0}),Line(points={{-20,-20},{20,20}}, color={0,85,0})}), Icon(coordinateSystem(extent={{-100,-100},{100,100}}, preserveAspectRatio=true, grid={10,10}), graphics={Ellipse(fillColor={0,128,0}, fillPattern=FillPattern.Solid, extent={{-100,-100},{100,100}}),Polygon(fillColor={255,255,255}, pattern=LinePattern.None, fillPattern=FillPattern.Solid, points={{-10,80},{-10,10},{-80,10},{-80,-10},{-10,-10},{-10,-80},{10,-80},{10,-10},{80,-10},{80,10},{10,10},{10,80}})})); | ||
end ActivatorConnector; |
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within BioChem.Icons.Interfaces.Nodes; | ||
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partial class InhibitorConnector "Icon for a connector between inhibitors and reactions" | ||
annotation(Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(lineColor={0,85,0}, fillColor={255,255,255}, extent={{-20,-20},{20,20}}),Line(points={{-20,20},{20,-20}}, color={0,85,0}),Line(points={{-20,-20},{20,20}}, color={0,85,0})}), Icon(coordinateSystem(extent={{-100,-100},{100,100}}, preserveAspectRatio=true, grid={10,10}), graphics={Ellipse(fillColor={170,0,0}, fillPattern=FillPattern.Solid, extent={{-100,-100},{100,100}}),Polygon(fillColor={255,255,255}, pattern=LinePattern.None, fillPattern=FillPattern.Solid, points={{-80,10},{-80,-10},{80,-10},{80,10}})})); | ||
end InhibitorConnector; |
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within BioChem.Icons.Interfaces.Nodes; | ||
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partial class ModifierConnector "Icon for a connector between general modifieres and reactions" | ||
annotation(Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(lineColor={0,85,0}, fillColor={255,255,255}, extent={{-20,-20},{20,20}}),Line(points={{-20,20},{20,-20}}, color={0,85,0}),Line(points={{-20,-20},{20,20}}, color={0,85,0})}), Icon(coordinateSystem(extent={{-100,-100},{100,100}}, preserveAspectRatio=true, grid={10,10}), graphics={Ellipse(fillColor={255,255,0}, fillPattern=FillPattern.Solid, extent={{-100,-100},{100,100}})})); | ||
end ModifierConnector; |
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within BioChem.Icons.Interfaces.Nodes; | ||
|
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partial class ProductConnector "Icon for a connector between substances and reactions (product side of reaction)" | ||
annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Ellipse(lineColor={0,85,127}, fillColor={255,255,255}, fillPattern=FillPattern.Solid, extent={{-100,-100},{100,100}})}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(lineColor={0,85,0}, fillColor={255,255,255}, extent={{-20,-20},{20,20}}),Line(points={{-20,20},{20,-20}}, color={0,85,0}),Line(points={{-20,-20},{20,20}}, color={0,85,0})})); | ||
end ProductConnector; |
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within BioChem.Icons.Interfaces.Nodes; | ||
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partial class SubstanceConnector "Icon for a connector between substances and reactions" | ||
annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Ellipse(lineColor={0,85,0}, fillColor={0,85,127}, extent={{-100,-100},{100,100}})}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(lineColor={0,85,0}, fillColor={255,255,255}, extent={{-20,-20},{20,20}}),Line(points={{-20,20},{20,-20}}, color={0,85,0}),Line(points={{-20,-20},{20,20}}, color={0,85,0})})); | ||
end SubstanceConnector; |
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within BioChem.Icons.Interfaces.Nodes; | ||
|
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partial class SubstrateConnector "Icon for a connector between substances and reactions (substrate side of reaction)" | ||
annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Ellipse(lineColor={0,85,127}, fillColor={0,85,127}, fillPattern=FillPattern.Solid, extent={{-100,-100},{100,100}})}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(lineColor={0,85,0}, fillColor={255,255,255}, extent={{-20,-20},{20,20}}),Line(points={{-20,20},{20,-20}}, color={0,85,0}),Line(points={{-20,-20},{20,20}}, color={0,85,0})})); | ||
end SubstrateConnector; |
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within BioChem.Icons.Interfaces; | ||
package Nodes "Connector interfaces used in the package" | ||
extends BioChem.Icons.Library; | ||
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end Nodes; |
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ActivatorConnector | ||
InhibitorConnector | ||
ModifierConnector | ||
ProductConnector | ||
SubstanceConnector | ||
SubstrateConnector |
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within BioChem.Icons.Interfaces.Reactions.Basics; | ||
|
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partial class FastEquilibrium "Basics for a reaction edge" | ||
extends BioChem.Icons.Base; | ||
annotation( | ||
Icon(graphics = {Line(points = {{-50.0, 0.0}, {50.0, 0.0}}, color = {0, 0, 255}, pattern = LinePattern.DashDotDot, thickness = 2), Text(origin = {-0.0, 0.0}, fillColor = {77, 77, 77}, fillPattern = FillPattern.Solid, extent = {{-100.0, -150.0}, {97.9, -100.0}}, textString = "%name", fontName = "Arial")})); | ||
end FastEquilibrium; |
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within BioChem.Icons.Interfaces.Reactions.Basics; | ||
|
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partial class FourProducts | ||
annotation( | ||
Icon(graphics = {Line(points = {{50, 0}, {62.5, 87.5}, {100, 87.5}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{50, 0}, {62.5, -87.5}, {100, -87.5}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{50, 0}, {62.5, 37.5}, {100, 37.5}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{50, 0}, {62.5, -37.5}, {100, -37.5}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier)})); | ||
end FourProducts; |
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within BioChem.Icons.Interfaces.Reactions.Basics; | ||
|
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partial class FourSubstrates | ||
extends BioChem.Icons.Base; | ||
annotation(Icon(graphics={Line(points={{-100,87.5},{-62.5,87.5},{-50,0}}, color={170,0,0}, smooth=Smooth.Bezier),Line(points={{-100,-87.5},{-62.5,-87.5},{-50,0}}, color={170,0,0}, smooth=Smooth.Bezier),Line(points={{-100,-37.5},{-62.5,-37.5},{-50,0}}, color={170,0,0}, smooth=Smooth.Bezier),Line(points={{-100,37.5},{-62.5,37.5},{-50,0}}, color={170,0,0}, smooth=Smooth.Bezier)})); | ||
end FourSubstrates; |
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BioChem/Icons/Interfaces/Reactions/Basics/FourSubstratesReversible.mo
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within BioChem.Icons.Interfaces.Reactions.Basics; | ||
|
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partial class FourSubstratesReversible | ||
extends BioChem.Icons.Base; | ||
annotation( | ||
Icon(graphics = {Line(points = {{-100, 87.5}, {-62.5, 87.5}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{-100, -87.5}, {-62.5, -87.5}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{-100, -37.5}, {-62.5, -37.5}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{-100, 37.5}, {-62.5, 37.5}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35, smooth = Smooth.Bezier)})); | ||
end FourSubstratesReversible; |
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BioChem/Icons/Interfaces/Reactions/Basics/MultipleProducts.mo
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within BioChem.Icons.Interfaces.Reactions.Basics; | ||
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partial class MultipleProducts "SubstanceConnector for arbitrary number of products" | ||
extends BioChem.Icons.Base; | ||
annotation( | ||
Icon(graphics = {Line(points = {{48.33, 0.0}, {98.33, 0.0}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 50), Ellipse(origin = {112.5, -0.0}, lineColor = {170, 0, 0}, fillColor = {170, 0, 0}, extent = {{-20.0, -20.0}, {20.0, 20.0}})})); | ||
end MultipleProducts; | ||
|
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BioChem/Icons/Interfaces/Reactions/Basics/MultipleSubstrates.mo
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within BioChem.Icons.Interfaces.Reactions.Basics; | ||
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partial class MultipleSubstrates "SubstanceConnector for arbitrary number of substrates" | ||
extends BioChem.Icons.Base; | ||
annotation( | ||
Icon(graphics = {Line(points = {{-100, 0}, {-50, 0}}, color = {170, 0, 0}), Ellipse(lineColor = {170, 0, 0}, fillColor = {170, 0, 0}, extent = {{-131.2, -18.75}, {-93.75, 18.75}})})); | ||
end MultipleSubstrates; |
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BioChem/Icons/Interfaces/Reactions/Basics/MultipleSubstratesReversible.mo
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within BioChem.Icons.Interfaces.Reactions.Basics; | ||
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partial class MultipleSubstratesReversible "SubstanceConnector for arbitrary number of substrates" | ||
extends BioChem.Icons.Base; | ||
annotation( | ||
Icon(graphics = {Line(points = {{-50.0, 0.0}, {-100.0, 0.0}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 50), Ellipse(origin = {-112.5, 0.0}, fillColor = {255, 255, 255}, extent = {{-20.0, -20.0}, {20.0, 20.0}})})); | ||
end MultipleSubstratesReversible; |
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within BioChem.Icons.Interfaces.Reactions.Basics; | ||
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||
partial class OneProduct "SubstanceConnector for one product" | ||
extends BioChem.Icons.Base; | ||
annotation( | ||
Icon(graphics = {Line(points = {{50, 0}, {100, 0}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 50)})); | ||
end OneProduct; |
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