OpenModelica · AtiyahElsheikh · Apr 6, 2021 · Apr 8, 2020 · Apr 10, 2020 · Apr 11, 2020
diff --git a/BioChem/Compartments/Compartment.mo b/BioChem/Compartments/Compartment.mo
@@ -1,13 +1,13 @@
 within BioChem.Compartments;
 
 model Compartment "Default compartment (constant volume)"
+  extends BioChem.Interfaces.Compartments.Compartment(V(stateSelect=StateSelect.prefer));
+equation
+  der(V)=0 "Compartment volume is constant";
   annotation(Documentation(info="<html>
 <h1>Compartment</h1>
 <p>
 Default 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)}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
-  extends BioChem.Interfaces.Compartments.Compartment(V(stateSelect=StateSelect.prefer));
-equation
-  der(V)=0 "Compartment volume is constant";
 end Compartment;
diff --git a/BioChem/Examples/package.mo b/BioChem/Examples/package.mo
@@ -1,7 +1,7 @@
 within BioChem;
 
 package Examples "Some examples of BioChem models"
-  extends Icons.Library;
+  extends Modelica.Icons.ExamplesPackage;
 
   model InsulinSignaling_Sedaghat "Metabolic insulin signaling pathway in rat adipocytes"
     extends BioChem.Compartments.Compartment;

diff --git a/BioChem/Icons/Substances/Package/package.mo b/BioChem/Icons/Substances/Package/package.mo
@@ -0,0 +1,8 @@
+within BioChem.Icons.Substances;
+
+partial package Package
+  extends BioChem.Icons.Library; 
+annotation(
+    Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Ellipse(origin = {-10, -50}, lineColor = {0, 56, 0}, fillColor = {0, 85, 0}, fillPattern = FillPattern.Sphere, extent = {{-60, -20}, {-20, 20}}), Ellipse(origin = {38, -10}, lineColor = {100, 100, 0}, fillColor = {255, 255, 0}, fillPattern = FillPattern.Sphere, extent = {{-28, -60}, {12, -20}}), Ellipse(origin = {-30.0032, -2.75056}, lineColor = {0, 0, 71}, fillColor = {0, 0, 127}, fillPattern = FillPattern.Sphere, extent = {{0.0032, -13.4697}, {40, 26.5303}})}),
+    Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})));
+end Package;
diff --git a/BioChem/Icons/Substances/Package/package.order b/BioChem/Icons/Substances/Package/package.order
diff --git a/BioChem/Icons/Substances/package.mo b/BioChem/Icons/Substances/package.mo
@@ -0,0 +1,5 @@
+within BioChem.Icons;
+
+partial package Substances
+  extends BioChem.Icons;
+end Substances;
diff --git a/BioChem/Icons/Substances/package.order b/BioChem/Icons/Substances/package.order
@@ -0,0 +1 @@
+Package
diff --git a/BioChem/Icons/UnitsPackage.mo b/BioChem/Icons/UnitsPackage.mo
@@ -0,0 +1,6 @@
+within BioChem.Icons;
+
+partial package UnitsPackage
+  extends Icons.Library;
+  annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Text(origin={0,-13.3333}, fillPattern=FillPattern.Solid, extent={{-100,-86.6667},{73.34,43.3333}}, textString="C", fontName="Arial"),Text(origin={0,-10}, fillPattern=FillPattern.Solid, extent={{6.51,6.81},{50,53.19}}, textString="o", fontName="Arial")}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
+end UnitsPackage;
diff --git a/BioChem/Icons/package.mo b/BioChem/Icons/package.mo
@@ -1,21 +1,26 @@
 within BioChem;
 
 package Icons "Icons"
-  extends Library;
+  extends Modelica.Icons.IconsPackage;
   partial package Library
-    annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(fillColor={235,235,235}, fillPattern=FillPattern.Solid, extent={{-100,-100},{80,50}}),Polygon(fillColor={210,210,210}, fillPattern=FillPattern.Solid, points={{-100,50},{-80,70},{100,70},{80,50},{-100,50}}),Polygon(fillColor={210,210,210}, fillPattern=FillPattern.Solid, points={{100,70},{100,-80},{80,-100},{80,50},{100,70}})}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
+    annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(fillColor={235,235,235}, fillPattern=FillPattern.Solid, extent={{-100,-100},{80,50}}),Polygon(fillColor={210,210,210}, fillPattern=FillPattern.Solid, points={{-100,50},{-80,70},{100,70},{80,50},{-100,50}}),Polygon(fillColor={210,210,210}, fillPattern=FillPattern.Solid, points={{100,70},{100,-80},{80,-100},{80,50},{100,70}})}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})),
+      Documentation(info = "<html><head></head><body><b>Remark </b>This package is somehow equivalent to Modelica.Icons.Package. However, the graphics is nicer and therefore I am leaving it.</body></html>"));
   end Library;
 
   model IconBase
     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")}));
   end IconBase;
 
   partial package Example "Icon for an example model"
-    annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(fillColor={255,255,255}, fillPattern=FillPattern.Solid, extent={{-100,-100},{80,50}}),Polygon(fillColor={255,255,255}, fillPattern=FillPattern.Solid, points={{-100,50},{-80,70},{100,70},{80,50},{-100,50}}),Polygon(fillColor={255,255,255}, fillPattern=FillPattern.Solid, points={{100,70},{100,-80},{80,-100},{80,50},{100,70}}),Text(fillColor={0,0,255}, fillPattern=FillPattern.Solid, extent={{-85,-85},{65,35}}, textString="Example", fontName="Arial"),Text(fillColor={255,0,0}, extent={{-120,73},{120,132}}, textString="%name", fontName="Arial")}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
+    annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(fillColor={255,255,255}, fillPattern=FillPattern.Solid, extent={{-100,-100},{80,50}}),Polygon(fillColor={255,255,255}, fillPattern=FillPattern.Solid, points={{-100,50},{-80,70},{100,70},{80,50},{-100,50}}),Polygon(fillColor={255,255,255}, fillPattern=FillPattern.Solid, points={{100,70},{100,-80},{80,-100},{80,50},{100,70}}),Text(fillColor={0,0,255}, fillPattern=FillPattern.Solid, extent={{-85,-85},{65,35}}, textString="Example", fontName="Arial"),Text(fillColor={255,0,0}, extent={{-120,73},{120,132}}, textString="%name", fontName="Arial")}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})),
+      Documentation(info = "<html><head></head><body>The implementation of this Icon looks nicer than the implementation of Modelica.Icoms.Example.</body></html>"));
   end Example;
 
+
+
+
   annotation(Documentation(info="<html>
 <h1>Icons</h1>
 This package contains icons that are used in the library.
-</html>", revisions=""));
+</html>", revisions= "<html><head></head><body><ul><li>March 2021, little improvements and additional reuse of Modelica.Icons, by Atiyah Elsheikh (Mathemodica.com)</li></ul></body></html>"));
 end Icons;
diff --git a/BioChem/Icons/package.order b/BioChem/Icons/package.order
@@ -1,3 +1,5 @@
 Library
 IconBase
 Example
+UnitsPackage
+Substances
diff --git a/BioChem/Interfaces/Reactions/Basics/FourSubstrates.mo b/BioChem/Interfaces/Reactions/Basics/FourSubstrates.mo
@@ -6,4 +6,5 @@ partial model FourSubstrates
   BioChem.Interfaces.Nodes.SubstrateConnector s2 annotation(Placement(transformation(origin={-90,-35}, extent={{-10,-10},{10,10}}), iconTransformation(origin={-112.5,-37.5}, extent={{-12.5,-12.5},{12.5,12.5}})));
   BioChem.Interfaces.Nodes.SubstrateConnector s3 annotation(Placement(transformation(origin={-90,25}, extent={{-10,-10},{10,10}}), iconTransformation(origin={-112.5,37.5}, extent={{-12.5,-12.5},{12.5,12.5}})));
   BioChem.Interfaces.Nodes.SubstrateConnector s1 annotation(Placement(transformation(origin={-87.5,87.5}, extent={{-10,-10},{10,10}}), iconTransformation(origin={-112.5,87.5}, extent={{-12.5,-12.5},{12.5,12.5}})));
+  annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), 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)}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
 end FourSubstrates;
diff --git a/BioChem/Interfaces/Reactions/Basics/OneSubstrate.mo b/BioChem/Interfaces/Reactions/Basics/OneSubstrate.mo
@@ -1,6 +1,6 @@
 within BioChem.Interfaces.Reactions.Basics;
 
 partial model OneSubstrate "SubstanceConnector for one substrate"
-  annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Line(points={{-50,0},{-100,0}}, color={170,0,0}, arrowSize=25)}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
   BioChem.Interfaces.Nodes.SubstrateConnector s1 annotation(Placement(transformation(origin={-80,0}, extent={{-10,-10},{10,10}}), iconTransformation(origin={-112.5,-2.22045e-16}, extent={{-12.5,-12.5},{12.5,12.5}})));
+  annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Line(points={{-50,0},{-100,0}}, color={170,0,0}, arrowSize=25)}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
 end OneSubstrate;
diff --git a/BioChem/Interfaces/Reactions/Modifiers/ModifierForward.mo b/BioChem/Interfaces/Reactions/Modifiers/ModifierForward.mo
@@ -1,8 +1,8 @@
 within BioChem.Interfaces.Reactions.Modifiers;
 
 partial model ModifierForward "Basics for a forward modifier in a reaction edge"
-  annotation(Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Line(points={{0,56.25},{0,6.25}}, color={0,0,255}, arrow={Arrow.None,Arrow.Open}, arrowSize=25)}));
   BioChem.Interfaces.Nodes.ModifierConnector mF1 annotation(Placement(transformation(origin={1.11022e-16,90}, extent={{-10,-10},{10,10}}), iconTransformation(origin={-1.5099e-14,90}, extent={{-20,-20},{20,20}})));
 equation
   mF1.r=0;
+  annotation(Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Line(points={{0,56.25},{0,6.25}}, color={0,0,255}, arrow={Arrow.None,Arrow.Open}, arrowSize=25)}));
 end ModifierForward;
diff --git a/BioChem/Interfaces/Reactions/Uui.mo b/BioChem/Interfaces/Reactions/Uui.mo
@@ -6,8 +6,8 @@ partial model Uui "Uni-Uni irreversible reaction"
   extends BioChem.Interfaces.Reactions.Basics.OneProduct;
   BioChem.Units.StoichiometricCoefficient nS1=1 "Stoichiometric coefficient for the substrate";
   BioChem.Units.StoichiometricCoefficient nP1=1 "Stoichiometric coefficient for the product";
-  annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
 equation
   s1.r=nS1*rr;
   p1.r=-nP1*rr;
+  annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
 end Uui;
diff --git a/BioChem/Interfaces/Reactions/Uur.mo b/BioChem/Interfaces/Reactions/Uur.mo
@@ -6,8 +6,8 @@ partial model Uur "Uni-Uni reversible reaction"
   extends BioChem.Interfaces.Reactions.Basics.OneProduct;
   BioChem.Units.StoichiometricCoefficient nS1=1 "Stoichiometric coefficient for the substrate";
   BioChem.Units.StoichiometricCoefficient nP1=1 "Stoichiometric coefficient for the product";
-  annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
 equation
   s1.r=nS1*rr;
   p1.r=-nP1*rr;
+  annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
 end Uur;
diff --git a/BioChem/Interfaces/package.mo b/BioChem/Interfaces/package.mo
@@ -1,7 +1,7 @@
 within BioChem;
 package Interfaces "Connection points and icons used in the BioChem package"
-  extends Icons.Library;
-  annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Documentation(info="<html>
+  extends Modelica.Icons.InterfacesPackage;
+  annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Documentation(info = "<html>
 <h1>Interfaces</h1>
 This package contains partial models that can be used as building blocks for components such as different types of substances, compartments, and reactions.
 The models are designed to make it easy to create new customized components as well as to make these components possible to translate to and from SBML.<br>
@@ -13,5 +13,5 @@ The package contains the following packages: <br>
 <li>Substances - Basic substance types.</li>
 </ul>
 
- </html>", revisions=""), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
+ </html>", revisions = "<html><head></head><body><ul><li>March 2021, Making use of Modelica.Icons.ExamplesPackage, &nbsp;Atiyah Elsheikh (Mathemodica.com)</li></ul></body></html>"), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
 end Interfaces;
diff --git a/BioChem/Math/package.mo b/BioChem/Math/package.mo
@@ -24,7 +24,7 @@ package Math
   end factorial;
 
   function sec "secant trigonometric function"
-    input Modelica.SIunits.Angle alpha "input angle";
+    input Modelica.Units.SI.Angle alpha "input angle";
     output Real y "output value";
   algorithm
     y := 1 / cos(alpha);
@@ -34,7 +34,7 @@ package Math
   end sec;
 
   function cot "Cotangent trigonometric function"
-    input Modelica.SIunits.Angle alpha "input angle";
+    input Modelica.Units.SI.Angle alpha "input angle";
     output Real y "output value";
   algorithm
     y := 1 / tan(alpha);
@@ -44,7 +44,7 @@ package Math
   end cot;
 
   function csc "cosecant trigonometric function"
-    input Modelica.SIunits.Angle alpha "input angle";
+    input Modelica.Units.SI.Angle alpha "input angle";
     output Real y "output value";
   algorithm
     y := 1 / sin(alpha);
@@ -54,7 +54,7 @@ package Math
   end csc;
 
   function sech "hyperbolic secant trigonometric function"
-    input Modelica.SIunits.Angle alpha "input angle";
+    input Modelica.Units.SI.Angle alpha "input angle";
     output Real y "output value";
   algorithm
     y := 1 / cosh(alpha);
@@ -64,7 +64,7 @@ package Math
   end sech;
 
   function csch "hyperbolic cosecant trigonometric function"
-    input Modelica.SIunits.Angle alpha "input angle";
+    input Modelica.Units.SI.Angle alpha "input angle";
     output Real y "output value";
   algorithm
     y := 1 / sinh(alpha);
@@ -74,7 +74,7 @@ package Math
   end csch;
 
   function coth "hyperbolic cotangent trigonometric function"
-    input Modelica.SIunits.Angle alpha "input angle";
+    input Modelica.Units.SI.Angle alpha "input angle";
     output Real y "output value";
   algorithm
     y := 1 / tanh(alpha);