diff --git a/BioChem/Compartments/Compartment.mo b/BioChem/Compartments/Compartment.mo index 96590bf..2361e28 100644 --- a/BioChem/Compartments/Compartment.mo +++ b/BioChem/Compartments/Compartment.mo @@ -2,12 +2,7 @@ within BioChem.Compartments; model Compartment "Default compartment (constant volume)" extends BioChem.Interfaces.Compartments.Compartment(V(stateSelect=StateSelect.prefer)); + extends BioChem.Icons.Compartments.Compartment; equation der(V)=0 "Compartment volume is constant"; - annotation(Documentation(info=" -

Compartment

-

-Default compartment model. -

-", 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}))); end Compartment; diff --git a/BioChem/Compartments/MainCompartment.mo b/BioChem/Compartments/MainCompartment.mo index 9eb89e2..d499369 100644 --- a/BioChem/Compartments/MainCompartment.mo +++ b/BioChem/Compartments/MainCompartment.mo @@ -2,6 +2,7 @@ within BioChem.Compartments; model MainCompartment "Main compartment (constant volume)" extends BioChem.Interfaces.Compartments.MainCompartment(V(stateSelect = StateSelect.prefer)); + extends Icons.Compartments.MainCompartment; equation der(V) = 0 "Compartment volume is constant"; annotation( @@ -11,7 +12,5 @@ equation

Main compartment model.

-", 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})}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); +", revisions = "")); end MainCompartment; diff --git a/BioChem/Compartments/package.mo b/BioChem/Compartments/package.mo index 84af0d1..3422465 100644 --- a/BioChem/Compartments/package.mo +++ b/BioChem/Compartments/package.mo @@ -1,7 +1,7 @@ within BioChem; package Compartments "Different types of compartments used in the package" - extends Icons.Library; + extends Icons.Compartments; annotation( Documentation(info = " diff --git a/BioChem/Icons/Base.mo b/BioChem/Icons/Base.mo index 5048160..8aa5170 100644 --- a/BioChem/Icons/Base.mo +++ b/BioChem/Icons/Base.mo @@ -1,6 +1,6 @@ within BioChem.Icons; -partial model Base +partial class Base annotation(Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), Documentation(info = "A base icon relevant for many components carrying the same annotations. Older annotations had the following attribute:

Diagram(coordinateSystem(extent={{-100.0,-100.0},{100.0,100.0}}, preserveAspectRatio=true, grid={10,10}))

Since this produces empty diagram, it is not clear why is it there. So it is there for now. 

This Icon will also replace Icons.IconBase, which does not seem to be used throughout the library. 


")); diff --git a/BioChem/Icons/Compartments/Compartment.mo b/BioChem/Icons/Compartments/Compartment.mo new file mode 100644 index 0000000..4bcdc68 --- /dev/null +++ b/BioChem/Icons/Compartments/Compartment.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Compartments; + +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; diff --git a/BioChem/Icons/Compartments/MainCompartment.mo b/BioChem/Icons/Compartments/MainCompartment.mo new file mode 100644 index 0000000..1bd6a49 --- /dev/null +++ b/BioChem/Icons/Compartments/MainCompartment.mo @@ -0,0 +1,14 @@ +within BioChem.Icons.Compartments; + +partial class MainCompartment "Main compartment (constant volume)" + extends BioChem.Icons.Base; + annotation( + Documentation(info = " +

MainCompartment

+ +

+Main compartment model. +

+", 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; diff --git a/BioChem/Icons/Compartments/package.mo b/BioChem/Icons/Compartments/package.mo new file mode 100644 index 0000000..ebc2388 --- /dev/null +++ b/BioChem/Icons/Compartments/package.mo @@ -0,0 +1,15 @@ +within BioChem.Icons; + +package Compartments "Different types of compartments used in the package" + extends BioChem.Icons.Library; + + annotation( + Documentation(info = " +

Compartments

+ + +\"Fig1: + ", 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; diff --git a/BioChem/Icons/Compartments/package.order b/BioChem/Icons/Compartments/package.order new file mode 100644 index 0000000..702e805 --- /dev/null +++ b/BioChem/Icons/Compartments/package.order @@ -0,0 +1,2 @@ +Compartment +MainCompartment diff --git a/BioChem/Icons/IconBase.mo b/BioChem/Icons/IconBase.mo index 60de27d..4c1b333 100644 --- a/BioChem/Icons/IconBase.mo +++ b/BioChem/Icons/IconBase.mo @@ -1,6 +1,6 @@ within BioChem.Icons; -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})), diff --git a/BioChem/Icons/Interfaces/Compartments/Compartment.mo b/BioChem/Icons/Interfaces/Compartments/Compartment.mo new file mode 100644 index 0000000..d863b21 --- /dev/null +++ b/BioChem/Icons/Interfaces/Compartments/Compartment.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Compartments; + +partial model 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; diff --git a/BioChem/Icons/Interfaces/Compartments/MainCompartment.mo b/BioChem/Icons/Interfaces/Compartments/MainCompartment.mo new file mode 100644 index 0000000..e2dfee1 --- /dev/null +++ b/BioChem/Icons/Interfaces/Compartments/MainCompartment.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Compartments; + +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; diff --git a/BioChem/Icons/Interfaces/Compartments/package.mo b/BioChem/Icons/Interfaces/Compartments/package.mo new file mode 100644 index 0000000..844d9ff --- /dev/null +++ b/BioChem/Icons/Interfaces/Compartments/package.mo @@ -0,0 +1,6 @@ +within BioChem.Icons.Interfaces; + +package Compartments "Properties for compartments" + extends BioChem.Icons.Library; + +end Compartments; diff --git a/BioChem/Icons/Interfaces/Compartments/package.order b/BioChem/Icons/Interfaces/Compartments/package.order new file mode 100644 index 0000000..702e805 --- /dev/null +++ b/BioChem/Icons/Interfaces/Compartments/package.order @@ -0,0 +1,2 @@ +Compartment +MainCompartment diff --git a/BioChem/Icons/Interfaces/Nodes/ActivatorConnector.mo b/BioChem/Icons/Interfaces/Nodes/ActivatorConnector.mo new file mode 100644 index 0000000..f7ba3cb --- /dev/null +++ b/BioChem/Icons/Interfaces/Nodes/ActivatorConnector.mo @@ -0,0 +1,5 @@ +within BioChem.Icons.Interfaces.Nodes; + +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; diff --git a/BioChem/Icons/Interfaces/Nodes/InhibitorConnector.mo b/BioChem/Icons/Interfaces/Nodes/InhibitorConnector.mo new file mode 100644 index 0000000..4ccface --- /dev/null +++ b/BioChem/Icons/Interfaces/Nodes/InhibitorConnector.mo @@ -0,0 +1,5 @@ +within BioChem.Icons.Interfaces.Nodes; + +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; diff --git a/BioChem/Icons/Interfaces/Nodes/ModifierConnector.mo b/BioChem/Icons/Interfaces/Nodes/ModifierConnector.mo new file mode 100644 index 0000000..b2c1270 --- /dev/null +++ b/BioChem/Icons/Interfaces/Nodes/ModifierConnector.mo @@ -0,0 +1,5 @@ +within BioChem.Icons.Interfaces.Nodes; + +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; diff --git a/BioChem/Icons/Interfaces/Nodes/ProductConnector.mo b/BioChem/Icons/Interfaces/Nodes/ProductConnector.mo new file mode 100644 index 0000000..4fcd464 --- /dev/null +++ b/BioChem/Icons/Interfaces/Nodes/ProductConnector.mo @@ -0,0 +1,5 @@ +within BioChem.Icons.Interfaces.Nodes; + +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; diff --git a/BioChem/Icons/Interfaces/Nodes/SubstanceConnector.mo b/BioChem/Icons/Interfaces/Nodes/SubstanceConnector.mo new file mode 100644 index 0000000..e1266ef --- /dev/null +++ b/BioChem/Icons/Interfaces/Nodes/SubstanceConnector.mo @@ -0,0 +1,5 @@ +within BioChem.Icons.Interfaces.Nodes; + +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; diff --git a/BioChem/Icons/Interfaces/Nodes/SubstrateConnector.mo b/BioChem/Icons/Interfaces/Nodes/SubstrateConnector.mo new file mode 100644 index 0000000..c1e9820 --- /dev/null +++ b/BioChem/Icons/Interfaces/Nodes/SubstrateConnector.mo @@ -0,0 +1,5 @@ +within BioChem.Icons.Interfaces.Nodes; + +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; diff --git a/BioChem/Icons/Interfaces/Nodes/package.mo b/BioChem/Icons/Interfaces/Nodes/package.mo new file mode 100644 index 0000000..1118c4f --- /dev/null +++ b/BioChem/Icons/Interfaces/Nodes/package.mo @@ -0,0 +1,5 @@ +within BioChem.Icons.Interfaces; +package Nodes "Connector interfaces used in the package" + extends BioChem.Icons.Library; + +end Nodes; diff --git a/BioChem/Icons/Interfaces/Nodes/package.order b/BioChem/Icons/Interfaces/Nodes/package.order new file mode 100644 index 0000000..81639b7 --- /dev/null +++ b/BioChem/Icons/Interfaces/Nodes/package.order @@ -0,0 +1,6 @@ +ActivatorConnector +InhibitorConnector +ModifierConnector +ProductConnector +SubstanceConnector +SubstrateConnector diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/FastEquilibrium.mo b/BioChem/Icons/Interfaces/Reactions/Basics/FastEquilibrium.mo new file mode 100644 index 0000000..81be8c4 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/FastEquilibrium.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +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; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/FourProducts.mo b/BioChem/Icons/Interfaces/Reactions/Basics/FourProducts.mo new file mode 100644 index 0000000..0855cca --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/FourProducts.mo @@ -0,0 +1,6 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +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; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/FourSubstrates.mo b/BioChem/Icons/Interfaces/Reactions/Basics/FourSubstrates.mo new file mode 100644 index 0000000..115490c --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/FourSubstrates.mo @@ -0,0 +1,6 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +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; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/FourSubstratesReversible.mo b/BioChem/Icons/Interfaces/Reactions/Basics/FourSubstratesReversible.mo new file mode 100644 index 0000000..62179d5 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/FourSubstratesReversible.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +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; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/MultipleProducts.mo b/BioChem/Icons/Interfaces/Reactions/Basics/MultipleProducts.mo new file mode 100644 index 0000000..186bd99 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/MultipleProducts.mo @@ -0,0 +1,8 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +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; + diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/MultipleSubstrates.mo b/BioChem/Icons/Interfaces/Reactions/Basics/MultipleSubstrates.mo new file mode 100644 index 0000000..56841fe --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/MultipleSubstrates.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +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; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/MultipleSubstratesReversible.mo b/BioChem/Icons/Interfaces/Reactions/Basics/MultipleSubstratesReversible.mo new file mode 100644 index 0000000..f9863a9 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/MultipleSubstratesReversible.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +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; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/OneProduct.mo b/BioChem/Icons/Interfaces/Reactions/Basics/OneProduct.mo new file mode 100644 index 0000000..c630998 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/OneProduct.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +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; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/OneSubstrate.mo b/BioChem/Icons/Interfaces/Reactions/Basics/OneSubstrate.mo new file mode 100644 index 0000000..bc2ab3f --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/OneSubstrate.mo @@ -0,0 +1,6 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +partial class OneSubstrate "SubstanceConnector for one substrate" + extends BioChem.Icons.Base; + annotation(Icon(graphics={Line(points={{-50,0},{-100,0}}, color={170,0,0}, arrowSize=25)})); +end OneSubstrate; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/OneSubstrateReversible.mo b/BioChem/Icons/Interfaces/Reactions/Basics/OneSubstrateReversible.mo new file mode 100644 index 0000000..22d1533 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/OneSubstrateReversible.mo @@ -0,0 +1,8 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +partial class OneSubstrateReversible + 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)})); +end OneSubstrateReversible; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/Reaction.mo b/BioChem/Icons/Interfaces/Reactions/Basics/Reaction.mo new file mode 100644 index 0000000..65f5a5e --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/Reaction.mo @@ -0,0 +1,6 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +partial class Reaction "Basics for a reaction edge" + annotation( + Icon(graphics = {Line(points = {{-50, 0}, {50, 0}}, color = {170, 0, 0}), Text(origin = {-4.44089e-15, 1.42109e-14}, fillColor = {77, 77, 77}, fillPattern = FillPattern.Solid, extent = {{-100, -150}, {97.9, -100}}, textString = "%name", fontName = "Arial")})); +end Reaction; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/ThreeProducts.mo b/BioChem/Icons/Interfaces/Reactions/Basics/ThreeProducts.mo new file mode 100644 index 0000000..9ea2263 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/ThreeProducts.mo @@ -0,0 +1,6 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +partial class ThreeProducts "SubstanceConnectors for three products" + annotation( + Icon(graphics = {Line(points = {{50, 0}, {100, 0}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35), Line(points = {{50, 0}, {62.5, 75}, {100, 75}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{50, 0}, {62.5, -75}, {100, -75}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier)})); +end ThreeProducts; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/ThreeSubstrates.mo b/BioChem/Icons/Interfaces/Reactions/Basics/ThreeSubstrates.mo new file mode 100644 index 0000000..3f2fdba --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/ThreeSubstrates.mo @@ -0,0 +1,6 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +partial class ThreeSubstrates "SubstanceConnectors for three substrates" + annotation( + Icon(graphics = {Line(points = {{-50, 0}, {-62.5, 75}, {-100, 75}}, color = {170, 0, 0}, smooth = Smooth.Bezier), Line(points = {{-100, 0}, {-50, 0}}, color = {170, 0, 0}), Line(points = {{-100, -75}, {-62.5, -75}, {-50, 0}}, color = {170, 0, 0}, smooth = Smooth.Bezier)})); +end ThreeSubstrates; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/ThreeSubstratesReversible.mo b/BioChem/Icons/Interfaces/Reactions/Basics/ThreeSubstratesReversible.mo new file mode 100644 index 0000000..9c4f059 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/ThreeSubstratesReversible.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +partial class ThreeSubstratesReversible + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{-50, 0}, {-60, 75}, {-100, 75}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{-100, 0}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35), Line(points = {{-100, -75}, {-60.03, -75}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35, smooth = Smooth.Bezier)})); +end ThreeSubstratesReversible; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/TwoProducts.mo b/BioChem/Icons/Interfaces/Reactions/Basics/TwoProducts.mo new file mode 100644 index 0000000..c5a02a7 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/TwoProducts.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +partial class TwoProducts "SubstanceConnectors for two products" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{50, 0}, {62.5, 50}, {102.4, 50}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{50, 0}, {62.5, -50}, {100, -50}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier)})); +end TwoProducts; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/TwoSubstrates.mo b/BioChem/Icons/Interfaces/Reactions/Basics/TwoSubstrates.mo new file mode 100644 index 0000000..e5cebce --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/TwoSubstrates.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +partial class TwoSubstrates "SubstanceConnectors for two substrates" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{-100, 50}, {-62.5, 50}, {-50, 0}}, color = {170, 0, 0}, smooth = Smooth.Bezier), Line(points = {{-100, -50}, {-62.5, -50}, {-50, 0}}, color = {170, 0, 0}, smooth = Smooth.Bezier)})); +end TwoSubstrates; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/TwoSubstratesReversible.mo b/BioChem/Icons/Interfaces/Reactions/Basics/TwoSubstratesReversible.mo new file mode 100644 index 0000000..17b8ccc --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/TwoSubstratesReversible.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Basics; + +partial class TwoSubstratesReversible + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{-100, 50}, {-62.5, 50}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{-100, -50}, {-62.5, -50}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35, smooth = Smooth.Bezier)})); +end TwoSubstratesReversible; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/package.mo b/BioChem/Icons/Interfaces/Reactions/Basics/package.mo new file mode 100644 index 0000000..1eebd4f --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/package.mo @@ -0,0 +1,6 @@ +within BioChem.Icons.Interfaces.Reactions; + +package Basics "Basic properties of reactions" + extends BioChem.Icons.Library; + +end Basics; diff --git a/BioChem/Icons/Interfaces/Reactions/Basics/package.order b/BioChem/Icons/Interfaces/Reactions/Basics/package.order new file mode 100644 index 0000000..42795fb --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Basics/package.order @@ -0,0 +1,17 @@ +OneSubstrate +OneProduct +OneSubstrateReversible +ThreeSubstratesReversible +TwoSubstratesReversible +TwoSubstrates +TwoProducts +ThreeSubstrates +ThreeProducts +Reaction +FourProducts +FourSubstrates +FourSubstratesReversible +MultipleSubstrates +MultipleProducts +MultipleSubstratesReversible +FastEquilibrium diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/Activator.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/Activator.mo new file mode 100644 index 0000000..4a54d7b --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/Activator.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class Activator "Icon for a forward activator in a reaction edge" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{0, 56.25}, {0, 6.25}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 25)})); +end Activator; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/ActivatorBackward.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/ActivatorBackward.mo new file mode 100644 index 0000000..fe392f6 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/ActivatorBackward.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class ActivatorBackward "Basics for a backward activator in a reaction edge" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{0, -56.25}, {0, -6.25}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 25)})); +end ActivatorBackward; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/ActivatorForward.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/ActivatorForward.mo new file mode 100644 index 0000000..bfecea4 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/ActivatorForward.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class ActivatorForward "Basics for a forward activator in a reaction edge" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{0, 56.25}, {0, 6.25}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 25)})); +end ActivatorForward; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/Inhibitor.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/Inhibitor.mo new file mode 100644 index 0000000..3e12cea --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/Inhibitor.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class Inhibitor + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{0, 56.25}, {0, 6.25}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 25)})); +end Inhibitor; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/InhibitorBackward.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/InhibitorBackward.mo new file mode 100644 index 0000000..e359f30 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/InhibitorBackward.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class InhibitorBackward "Basics for a backward inhibitor in a reaction edge" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{0, -56.25}, {0, -6.25}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 25)})); +end InhibitorBackward; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/InhibitorForward.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/InhibitorForward.mo new file mode 100644 index 0000000..74ec68b --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/InhibitorForward.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class InhibitorForward "Basics for a forward inhibitor in a reaction edge" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{0, 56.25}, {0, 6.25}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 25)})); +end InhibitorForward; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/Modifier.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/Modifier.mo new file mode 100644 index 0000000..f862854 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/Modifier.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class Modifier + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{0, 56.25}, {0, 6.25}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 30)})); +end Modifier; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/ModifierBackward.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/ModifierBackward.mo new file mode 100644 index 0000000..0b68364 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/ModifierBackward.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class ModifierBackward "Basics for a backward modifier in a reaction edge" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{0, -56.25}, {0, -6.715}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 25)})); +end ModifierBackward; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/ModifierForward.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/ModifierForward.mo new file mode 100644 index 0000000..1b1df2a --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/ModifierForward.mo @@ -0,0 +1,6 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class ModifierForward "Basics for a forward modifier in a reaction edge" + extends BioChem.Icons.Base; + annotation(Icon(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/Icons/Interfaces/Reactions/Modifiers/MultipleModifiers.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/MultipleModifiers.mo new file mode 100644 index 0000000..820151d --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/MultipleModifiers.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class MultipleModifiers + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Ellipse(lineColor = {255, 255, 0}, fillColor = {255, 255, 127}, fillPattern = FillPattern.Solid, lineThickness = 2, extent = {{-25.0, 65.0}, {25.0, 115.0}}), Line(origin = {0.0, 29.1679}, points = {{0.0, 29.17}, {0.0, -29.17}}, arrow = {Arrow.None, Arrow.Filled}, arrowSize = 30)})); +end MultipleModifiers; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/ThreeModifiers.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/ThreeModifiers.mo new file mode 100644 index 0000000..27689d3 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/ThreeModifiers.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class ThreeModifiers "Basics for three modifiers in a reaction edge" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{0, 56.25}, {0, 6.25}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 25)})); +end ThreeModifiers; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/TwoModifiers.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/TwoModifiers.mo new file mode 100644 index 0000000..e13faa8 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/TwoModifiers.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Reactions.Modifiers; + +partial class TwoModifiers "Basics for two modifiers in a reaction edge" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Line(points = {{0, 56.25}, {0, 6.25}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 25)})); +end TwoModifiers; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/package.mo b/BioChem/Icons/Interfaces/Reactions/Modifiers/package.mo new file mode 100644 index 0000000..871d2e2 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/package.mo @@ -0,0 +1,5 @@ +within BioChem.Icons.Interfaces.Reactions; + +package Modifiers + extends BioChem.Icons.Library; +end Modifiers; diff --git a/BioChem/Icons/Interfaces/Reactions/Modifiers/package.order b/BioChem/Icons/Interfaces/Reactions/Modifiers/package.order new file mode 100644 index 0000000..e35cac9 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/Modifiers/package.order @@ -0,0 +1,12 @@ +ModifierForward +ModifierBackward +InhibitorForward +InhibitorBackward +ActivatorForward +ActivatorBackward +TwoModifiers +Modifier +Activator +Inhibitor +ThreeModifiers +MultipleModifiers diff --git a/BioChem/Icons/Interfaces/Reactions/package.mo b/BioChem/Icons/Interfaces/Reactions/package.mo new file mode 100644 index 0000000..a17c228 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/package.mo @@ -0,0 +1,6 @@ +within BioChem.Icons.Interfaces; + +partial package Reactions + extends BioChem.Icons.Library; + +end Reactions; diff --git a/BioChem/Icons/Interfaces/Reactions/package.order b/BioChem/Icons/Interfaces/Reactions/package.order new file mode 100644 index 0000000..caeb7a4 --- /dev/null +++ b/BioChem/Icons/Interfaces/Reactions/package.order @@ -0,0 +1,2 @@ +Modifiers +Basics diff --git a/BioChem/Icons/Interfaces/Substances/InputSubstance.mo b/BioChem/Icons/Interfaces/Substances/InputSubstance.mo new file mode 100644 index 0000000..19319b6 --- /dev/null +++ b/BioChem/Icons/Interfaces/Substances/InputSubstance.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Interfaces.Substances; + +partial class InputSubstance "Basics for a substance" + extends Icons.Base; + annotation( + Icon(graphics = {Ellipse(fillColor = {123, 152, 255}, extent = {{-50, -50}, {50, 50}})})); +end InputSubstance; diff --git a/BioChem/Icons/Interfaces/Substances/Substance.mo b/BioChem/Icons/Interfaces/Substances/Substance.mo new file mode 100644 index 0000000..1d418ab --- /dev/null +++ b/BioChem/Icons/Interfaces/Substances/Substance.mo @@ -0,0 +1,8 @@ +within BioChem.Icons.Interfaces.Substances; + +partial class Substance + extends Icons.Base; + annotation( + Icon(graphics = {Ellipse(fillColor = {123, 152, 255}, extent = {{-50, -50}, {50, 50}})}), + Documentation(info = "The circle in the middle implies that the substance employing this icon will be connected to arbitrary reaction nodes through only one connector, graphically embedded in the center of the substance icon.")); +end Substance; diff --git a/BioChem/Icons/Interfaces/Substances/package.mo b/BioChem/Icons/Interfaces/Substances/package.mo new file mode 100644 index 0000000..33776cf --- /dev/null +++ b/BioChem/Icons/Interfaces/Substances/package.mo @@ -0,0 +1,5 @@ +within BioChem.Icons.Interfaces; + +package Substances + extends BioChem.Icons.Library; +end Substances; diff --git a/BioChem/Icons/Interfaces/Substances/package.order b/BioChem/Icons/Interfaces/Substances/package.order new file mode 100644 index 0000000..860249e --- /dev/null +++ b/BioChem/Icons/Interfaces/Substances/package.order @@ -0,0 +1,2 @@ +Substance +InputSubstance diff --git a/BioChem/Icons/Interfaces/package.mo b/BioChem/Icons/Interfaces/package.mo new file mode 100644 index 0000000..ca53799 --- /dev/null +++ b/BioChem/Icons/Interfaces/package.mo @@ -0,0 +1,10 @@ +within BioChem.Icons; + +partial package Interfaces + extends Modelica.Icons.InterfacesPackage; + extends Modelica.Icons.UnderConstruction; + + + annotation( + Documentation(info = "Icons employed within the package BioChem.Interfaces. The package is under construction and could be completed in future versions.")); +end Interfaces; diff --git a/BioChem/Icons/Interfaces/package.order b/BioChem/Icons/Interfaces/package.order new file mode 100644 index 0000000..a7b47ef --- /dev/null +++ b/BioChem/Icons/Interfaces/package.order @@ -0,0 +1,4 @@ +Substances +Nodes +Compartments +Reactions diff --git a/BioChem/Icons/Substances/AmbientSubstance.mo b/BioChem/Icons/Substances/AmbientSubstance.mo new file mode 100644 index 0000000..97fea06 --- /dev/null +++ b/BioChem/Icons/Substances/AmbientSubstance.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Substances; + +partial class AmbientSubstance "Substance used as a reservoir in reactions" + extends Icons.Base; + annotation( + Icon(graphics = {Text(origin = {1.77636e-15, 50}, fillPattern = FillPattern.Solid, extent = {{-100, -150}, {100, -100}}, textString = "%name", fontName = "Arial"), Line(points = {{-50, -50}, {50, 50}}, thickness = 10)})); +end AmbientSubstance; diff --git a/BioChem/Icons/Substances/BoundarySubstance.mo b/BioChem/Icons/Substances/BoundarySubstance.mo new file mode 100644 index 0000000..91e7c1b --- /dev/null +++ b/BioChem/Icons/Substances/BoundarySubstance.mo @@ -0,0 +1,8 @@ +within BioChem.Icons.Substances; + +partial class BoundarySubstance "Icon for a substance with a concentration not determined by reactions, but by events" + extends Icons.Base; + annotation( + Icon(graphics = {Text(origin = {-1.42109e-14, 50}, fillPattern = FillPattern.Solid, extent = {{-100, -150}, {100, -100}}, textString = "%name", fontName = "Arial"), Ellipse(lineColor = {170, 0, 0}, fillColor = {255, 0, 0}, fillPattern = FillPattern.Sphere, extent = {{-50, -50}, {50, 50}})}), + Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); +end BoundarySubstance; diff --git a/BioChem/Icons/Substances/PackageIcon/package.mo b/BioChem/Icons/Substances/PackageIcon/package.mo deleted file mode 100644 index 36fa768..0000000 --- a/BioChem/Icons/Substances/PackageIcon/package.mo +++ /dev/null @@ -1,9 +0,0 @@ -within BioChem.Icons.Substances; - -partial package PackageIcon "An icon for a package of substances" - 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})), - Documentation(info = "
This Icon replaces Biocehm.Icon.Package in Biocehm version 1.0.3 and thus it is not backword compatible
")); -end PackageIcon; diff --git a/BioChem/Icons/Substances/SignalSubstance.mo b/BioChem/Icons/Substances/SignalSubstance.mo new file mode 100644 index 0000000..23c27f0 --- /dev/null +++ b/BioChem/Icons/Substances/SignalSubstance.mo @@ -0,0 +1,15 @@ +within BioChem.Icons.Substances; + +partial class SignalSubstance "Substance with a concentration not determined by reactions, but by external equations (translated into SBML assignments)" + extends BioChem.Interfaces.Substances.InputSubstance; + annotation( + Documentation(info = " +

+Substance with a concentration not determined by reactions, instead the substance consentration is regulated by external equations. +

+Corresponds to SBML species changed by any SBML rules. +

+"), + Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {7.10543e-15, 50}, fillPattern = FillPattern.Solid, extent = {{-100, -150}, {100, -100}}, textString = "%name", fontName = "Arial"), Ellipse(lineColor = {0, 0, 127}, fillColor = {85, 170, 255}, fillPattern = FillPattern.Sphere, extent = {{-50, -50}, {50, 50}})}), + Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); +end SignalSubstance; diff --git a/BioChem/Icons/Substances/Substance.mo b/BioChem/Icons/Substances/Substance.mo new file mode 100644 index 0000000..afb79f4 --- /dev/null +++ b/BioChem/Icons/Substances/Substance.mo @@ -0,0 +1,7 @@ +within BioChem.Icons.Substances; + +partial class Substance "Icon for Substance with variable concentration" + extends BioChem.Icons.Base; + annotation( + Icon(graphics = {Text(origin = {7.10543e-15, 50}, fillPattern = FillPattern.Solid, extent = {{-100, -150}, {100, -100}}, textString = "%name", fontName = "Arial"), Ellipse(lineColor = {0, 85, 0}, fillColor = {0, 170, 0}, fillPattern = FillPattern.Sphere, extent = {{-50, -50}, {50, 50}})})); +end Substance; diff --git a/BioChem/Icons/Substances/package.mo b/BioChem/Icons/Substances/package.mo index a7556dd..0e4a538 100644 --- a/BioChem/Icons/Substances/package.mo +++ b/BioChem/Icons/Substances/package.mo @@ -1,8 +1,13 @@ within BioChem.Icons; partial package Substances - extends BioChem.Icons; + extends BioChem.Icons.Library; + + + annotation( - Documentation(info = "Within this package, the PackageIcon component replaces Biocehm.Icon.Package from Biocehm version 1.0.3 and thus it is not backword compatible.")); + 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})), + Documentation(info = "
")); end Substances; diff --git a/BioChem/Icons/Substances/package.order b/BioChem/Icons/Substances/package.order index 740fa03..ec40563 100644 --- a/BioChem/Icons/Substances/package.order +++ b/BioChem/Icons/Substances/package.order @@ -1 +1,4 @@ -PackageIcon +Substance +BoundarySubstance +AmbientSubstance +SignalSubstance diff --git a/BioChem/Icons/Units/PackageIcon/package.mo b/BioChem/Icons/Units/PackageIcon/package.mo deleted file mode 100644 index 0367bdc..0000000 --- a/BioChem/Icons/Units/PackageIcon/package.mo +++ /dev/null @@ -1,8 +0,0 @@ -within BioChem.Icons.Units; - -partial package PackageIcon "Icon for the Units Package" - extends Icons.Library; - extends Icons.Base; - annotation( - Icon(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")})); -end PackageIcon; diff --git a/BioChem/Icons/Units/PackageIcon/package.order b/BioChem/Icons/Units/PackageIcon/package.order deleted file mode 100644 index e69de29..0000000 diff --git a/BioChem/Icons/Units/TypeBase.mo b/BioChem/Icons/Units/TypeBase.mo deleted file mode 100644 index a99f589..0000000 --- a/BioChem/Icons/Units/TypeBase.mo +++ /dev/null @@ -1,5 +0,0 @@ -within BioChem.Icons.Units; - -type TypeBase - extends Icons.Base; -end TypeBase; diff --git a/BioChem/Icons/Units/package.mo b/BioChem/Icons/Units/package.mo index fb1f4f6..3246405 100644 --- a/BioChem/Icons/Units/package.mo +++ b/BioChem/Icons/Units/package.mo @@ -1,5 +1,8 @@ within BioChem.Icons; partial package Units "Icon for the Units Package" - + extends Icons.Library; + extends Icons.Base; + annotation( + Icon(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")})); end Units; diff --git a/BioChem/Icons/Units/package.order b/BioChem/Icons/Units/package.order index 119ffe7..d9a5378 100644 --- a/BioChem/Icons/Units/package.order +++ b/BioChem/Icons/Units/package.order @@ -1,3 +1,2 @@ TypeIntegerBase TypeRealBase -PackageIcon diff --git a/BioChem/Icons/package.order b/BioChem/Icons/package.order index 63c8535..bcb0c7d 100644 --- a/BioChem/Icons/package.order +++ b/BioChem/Icons/package.order @@ -4,3 +4,5 @@ Example Substances Units Base +Interfaces +Compartments diff --git a/BioChem/Interfaces/Compartments/Compartment.mo b/BioChem/Interfaces/Compartments/Compartment.mo index 480d998..96aa418 100644 --- a/BioChem/Interfaces/Compartments/Compartment.mo +++ b/BioChem/Interfaces/Compartments/Compartment.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Compartments; partial model Compartment + extends BioChem.Icons.Interfaces.Compartments.Compartment; inner BioChem.Units.Volume V(start = 1, stateSelect = StateSelect.prefer) "Compartment volume"; annotation( Documentation(info = " @@ -8,7 +9,5 @@ partial model Compartment A partial model describing the basics of a default compartment.

"), - defaultComponentName = "compartment", - 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, 0, 127}, fillColor = {0, 170, 255}, fillPattern = FillPattern.Solid, lineThickness = 10, extent = {{-110, -110}, {110, 110}}, radius = 20)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); + defaultComponentName = "compartment"); end Compartment; diff --git a/BioChem/Interfaces/Compartments/MainCompartment.mo b/BioChem/Interfaces/Compartments/MainCompartment.mo index abb3a46..7feafc2 100644 --- a/BioChem/Interfaces/Compartments/MainCompartment.mo +++ b/BioChem/Interfaces/Compartments/MainCompartment.mo @@ -2,12 +2,11 @@ within BioChem.Interfaces.Compartments; partial model MainCompartment extends BioChem.Interfaces.Compartments.Compartment; + extends BioChem.Icons.Interfaces.Compartments.MainCompartment; annotation( Documentation(info = "

Main compartment model.

-"), - 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"), Text(fillPattern = FillPattern.Solid, extent = {{-82.12, -80}, {80, 80}}, textString = "main", fontName = "Arial", textStyle = {TextStyle.Bold})}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); +")); end MainCompartment; diff --git a/BioChem/Interfaces/Nodes/ActivatorConnector.mo b/BioChem/Interfaces/Nodes/ActivatorConnector.mo index 5bad501..385c073 100644 --- a/BioChem/Interfaces/Nodes/ActivatorConnector.mo +++ b/BioChem/Interfaces/Nodes/ActivatorConnector.mo @@ -1,8 +1,8 @@ within BioChem.Interfaces.Nodes; connector ActivatorConnector "Connector between activators and reactions" + extends BioChem.Icons.Interfaces.Nodes.ActivatorConnector; BioChem.Units.Concentration c; flow BioChem.Units.MolarFlowRate r; input BioChem.Units.Volume V; - 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; diff --git a/BioChem/Interfaces/Nodes/InhibitorConnector.mo b/BioChem/Interfaces/Nodes/InhibitorConnector.mo index b955c16..3c50b62 100644 --- a/BioChem/Interfaces/Nodes/InhibitorConnector.mo +++ b/BioChem/Interfaces/Nodes/InhibitorConnector.mo @@ -1,8 +1,8 @@ within BioChem.Interfaces.Nodes; connector InhibitorConnector "Connector between inhibitors and reactions" + extends BioChem.Icons.Interfaces.Nodes.InhibitorConnector; BioChem.Units.Concentration c; flow BioChem.Units.MolarFlowRate r; input BioChem.Units.Volume V; - 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; diff --git a/BioChem/Interfaces/Nodes/ModifierConnector.mo b/BioChem/Interfaces/Nodes/ModifierConnector.mo index 49670fd..930f572 100644 --- a/BioChem/Interfaces/Nodes/ModifierConnector.mo +++ b/BioChem/Interfaces/Nodes/ModifierConnector.mo @@ -1,8 +1,8 @@ within BioChem.Interfaces.Nodes; connector ModifierConnector "Connector between general modifieres and reactions" + extends BioChem.Icons.Interfaces.Nodes.ModifierConnector; BioChem.Units.Concentration c; flow BioChem.Units.MolarFlowRate r; input BioChem.Units.Volume V; - 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; diff --git a/BioChem/Interfaces/Nodes/ProductConnector.mo b/BioChem/Interfaces/Nodes/ProductConnector.mo index fa314fe..6c14611 100644 --- a/BioChem/Interfaces/Nodes/ProductConnector.mo +++ b/BioChem/Interfaces/Nodes/ProductConnector.mo @@ -1,8 +1,8 @@ within BioChem.Interfaces.Nodes; connector ProductConnector "Connector between substances and reactions (product side of reaction)" + extends BioChem.Icons.Interfaces.Nodes.ProductConnector; BioChem.Units.Concentration c; flow BioChem.Units.MolarFlowRate r; input BioChem.Units.Volume V; - 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; diff --git a/BioChem/Interfaces/Nodes/SubstanceConnector.mo b/BioChem/Interfaces/Nodes/SubstanceConnector.mo index 42c68d6..cb3ca9a 100644 --- a/BioChem/Interfaces/Nodes/SubstanceConnector.mo +++ b/BioChem/Interfaces/Nodes/SubstanceConnector.mo @@ -1,8 +1,8 @@ within BioChem.Interfaces.Nodes; connector SubstanceConnector "Connector between substances and reactions" + extends BioChem.Icons.Interfaces.Nodes.SubstanceConnector; BioChem.Units.Concentration c; flow BioChem.Units.MolarFlowRate r; output BioChem.Units.Volume V; - 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; diff --git a/BioChem/Interfaces/Nodes/SubstrateConnector.mo b/BioChem/Interfaces/Nodes/SubstrateConnector.mo index 32325cf..2479c5a 100644 --- a/BioChem/Interfaces/Nodes/SubstrateConnector.mo +++ b/BioChem/Interfaces/Nodes/SubstrateConnector.mo @@ -1,8 +1,8 @@ within BioChem.Interfaces.Nodes; connector SubstrateConnector "Connector between substances and reactions (substrate side of reaction)" + extends BioChem.Icons.Interfaces.Nodes.SubstrateConnector; BioChem.Units.Concentration c; flow BioChem.Units.MolarFlowRate r; input BioChem.Units.Volume V; - 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; diff --git a/BioChem/Interfaces/Nodes/package.mo b/BioChem/Interfaces/Nodes/package.mo index f46f5e1..2177865 100644 --- a/BioChem/Interfaces/Nodes/package.mo +++ b/BioChem/Interfaces/Nodes/package.mo @@ -1,6 +1,6 @@ within BioChem.Interfaces; package Nodes "Connector interfaces used in the package" - extends Icons.Library; + extends BioChem.Icons.Library; annotation(Documentation(info="

Nodes

diff --git a/BioChem/Interfaces/Reactions/Basics/FastEquilibrium.mo b/BioChem/Interfaces/Reactions/Basics/FastEquilibrium.mo index 69282c3..5aa8c5b 100644 --- a/BioChem/Interfaces/Reactions/Basics/FastEquilibrium.mo +++ b/BioChem/Interfaces/Reactions/Basics/FastEquilibrium.mo @@ -1,7 +1,5 @@ within BioChem.Interfaces.Reactions.Basics; partial model FastEquilibrium "Basics for a reaction edge" - annotation( - Icon(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}), 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")}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); + extends BioChem.Icons.Interfaces.Reactions.Basics.FastEquilibrium; end FastEquilibrium; diff --git a/BioChem/Interfaces/Reactions/Basics/FourProducts.mo b/BioChem/Interfaces/Reactions/Basics/FourProducts.mo index c7dd8d5..27295ff 100644 --- a/BioChem/Interfaces/Reactions/Basics/FourProducts.mo +++ b/BioChem/Interfaces/Reactions/Basics/FourProducts.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions.Basics; partial model FourProducts + extends BioChem.Icons.Interfaces.Reactions.Basics.FourProducts; BioChem.Interfaces.Nodes.ProductConnector p4 annotation( Placement(transformation(origin = {100, -40}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {112.5, -87.5}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.ProductConnector p2 annotation( @@ -9,7 +10,4 @@ partial model FourProducts Placement(transformation(origin = {100, 40}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {112.5, 37.5}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.ProductConnector p1 annotation( Placement(transformation(origin = {100, 40}, 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 = {{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)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end FourProducts; diff --git a/BioChem/Interfaces/Reactions/Basics/FourSubstrates.mo b/BioChem/Interfaces/Reactions/Basics/FourSubstrates.mo index 46a4823..21c3007 100644 --- a/BioChem/Interfaces/Reactions/Basics/FourSubstrates.mo +++ b/BioChem/Interfaces/Reactions/Basics/FourSubstrates.mo @@ -1,10 +1,9 @@ within BioChem.Interfaces.Reactions.Basics; partial model FourSubstrates - 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}))); + extends BioChem.Icons.Interfaces.Reactions.Basics.FourSubstrates; BioChem.Interfaces.Nodes.SubstrateConnector s4 annotation(Placement(transformation(origin={-90,-87.5}, extent={{-10,-10},{10,10}}), iconTransformation(origin={-112.5,-87.5}, extent={{-12.5,-12.5},{12.5,12.5}}))); 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/FourSubstratesReversible.mo b/BioChem/Interfaces/Reactions/Basics/FourSubstratesReversible.mo index 2aed3bd..c2f191f 100644 --- a/BioChem/Interfaces/Reactions/Basics/FourSubstratesReversible.mo +++ b/BioChem/Interfaces/Reactions/Basics/FourSubstratesReversible.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions.Basics; partial model FourSubstratesReversible + extends BioChem.Icons.Interfaces.Reactions.Basics.FourSubstratesReversible; BioChem.Interfaces.Nodes.SubstrateConnector s4 annotation( Placement(transformation(origin = {-90, -87.5}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, -87.5}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.SubstrateConnector s2 annotation( @@ -9,7 +10,4 @@ partial model FourSubstratesReversible 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}, 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)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end FourSubstratesReversible; diff --git a/BioChem/Interfaces/Reactions/Basics/MultipleProducts.mo b/BioChem/Interfaces/Reactions/Basics/MultipleProducts.mo index 1139afd..0e14029 100644 --- a/BioChem/Interfaces/Reactions/Basics/MultipleProducts.mo +++ b/BioChem/Interfaces/Reactions/Basics/MultipleProducts.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Basics; partial model MultipleProducts "SubstanceConnector for arbitrary number of products" + extends BioChem.Icons.Interfaces.Reactions.Basics.MultipleProducts; parameter Integer dimP = 5 "number of products"; BioChem.Interfaces.Nodes.ProductConnector p[dimP] annotation( Placement(transformation(origin = {80.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {112.5, 0.0}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}), 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; diff --git a/BioChem/Interfaces/Reactions/Basics/MultipleSubstrates.mo b/BioChem/Interfaces/Reactions/Basics/MultipleSubstrates.mo index 3e87a00..ec8fa5e 100644 --- a/BioChem/Interfaces/Reactions/Basics/MultipleSubstrates.mo +++ b/BioChem/Interfaces/Reactions/Basics/MultipleSubstrates.mo @@ -1,10 +1,8 @@ within BioChem.Interfaces.Reactions.Basics; partial model MultipleSubstrates "SubstanceConnector for arbitrary number of substrates" + extends BioChem.Icons.Interfaces.Reactions.Basics.MultipleSubstrates; parameter Integer dimS = 5 "number of substrates"; BioChem.Interfaces.Nodes.SubstrateConnector s[dimS] 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( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), 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; diff --git a/BioChem/Interfaces/Reactions/Basics/MultipleSubstratesReversible.mo b/BioChem/Interfaces/Reactions/Basics/MultipleSubstratesReversible.mo index 5953f45..cc25827 100644 --- a/BioChem/Interfaces/Reactions/Basics/MultipleSubstratesReversible.mo +++ b/BioChem/Interfaces/Reactions/Basics/MultipleSubstratesReversible.mo @@ -1,10 +1,8 @@ within BioChem.Interfaces.Reactions.Basics; partial model MultipleSubstratesReversible "SubstanceConnector for arbitrary number of substrates" + extends BioChem.Icons.Interfaces.Reactions.Basics.MultipleSubstratesReversible; parameter Integer dimS = 5 "number of substrates"; BioChem.Interfaces.Nodes.SubstrateConnector s[dimS] 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 = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}), 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}})}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end MultipleSubstratesReversible; diff --git a/BioChem/Interfaces/Reactions/Basics/OneSubstrate.mo b/BioChem/Interfaces/Reactions/Basics/OneSubstrate.mo index 49e74ff..1f1c9a4 100644 --- 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" + extends BioChem.Icons.Interfaces.Reactions.Basics.OneSubstrate; 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/Basics/OneSubstrateReversible.mo b/BioChem/Interfaces/Reactions/Basics/OneSubstrateReversible.mo index de7a4ec..bc2763e 100644 --- a/BioChem/Interfaces/Reactions/Basics/OneSubstrateReversible.mo +++ b/BioChem/Interfaces/Reactions/Basics/OneSubstrateReversible.mo @@ -1,9 +1,7 @@ within BioChem.Interfaces.Reactions.Basics; partial model OneSubstrateReversible + extends BioChem.Icons.Interfaces.Reactions.Basics.OneSubstrateReversible; 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 = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Line(points = {{-50.0, 0.0}, {-100.0, 0.0}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 50)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end OneSubstrateReversible; diff --git a/BioChem/Interfaces/Reactions/Basics/Reaction.mo b/BioChem/Interfaces/Reactions/Basics/Reaction.mo index a4227cf..094878b 100644 --- a/BioChem/Interfaces/Reactions/Basics/Reaction.mo +++ b/BioChem/Interfaces/Reactions/Basics/Reaction.mo @@ -1,9 +1,7 @@ within BioChem.Interfaces.Reactions.Basics; partial model Reaction "Basics for a reaction edge" + extends BioChem.Icons.Interfaces.Reactions.Basics.Reaction; BioChem.Units.ReactionRate rr "Rate of the reaction" annotation( __MathCore_reactionrate = true); - annotation( - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Line(points = {{-50, 0}, {50, 0}}, color = {170, 0, 0}), Text(origin = {-4.44089e-15, 1.42109e-14}, fillColor = {77, 77, 77}, fillPattern = FillPattern.Solid, extent = {{-100, -150}, {97.9, -100}}, textString = "%name", fontName = "Arial")}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end Reaction; diff --git a/BioChem/Interfaces/Reactions/Basics/ThreeProducts.mo b/BioChem/Interfaces/Reactions/Basics/ThreeProducts.mo index 3733de0..86d70f6 100644 --- a/BioChem/Interfaces/Reactions/Basics/ThreeProducts.mo +++ b/BioChem/Interfaces/Reactions/Basics/ThreeProducts.mo @@ -1,13 +1,11 @@ within BioChem.Interfaces.Reactions.Basics; partial model ThreeProducts "SubstanceConnectors for three products" + extends BioChem.Icons.Interfaces.Reactions.Basics.ThreeProducts; BioChem.Interfaces.Nodes.ProductConnector p1 annotation( Placement(transformation(origin = {100, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {112.5, 75}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.ProductConnector p3 annotation( Placement(transformation(origin = {100, -80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {112.5, -75}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.ProductConnector p2 annotation( Placement(transformation(origin = {100, 0}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {112.5, -2.9976e-15}, 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}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35), Line(points = {{50, 0}, {62.5, 75}, {100, 75}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{50, 0}, {62.5, -75}, {100, -75}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end ThreeProducts; diff --git a/BioChem/Interfaces/Reactions/Basics/ThreeSubstrates.mo b/BioChem/Interfaces/Reactions/Basics/ThreeSubstrates.mo index 75831b4..322ce17 100644 --- a/BioChem/Interfaces/Reactions/Basics/ThreeSubstrates.mo +++ b/BioChem/Interfaces/Reactions/Basics/ThreeSubstrates.mo @@ -1,13 +1,11 @@ within BioChem.Interfaces.Reactions.Basics; partial model ThreeSubstrates "SubstanceConnectors for three substrates" + extends BioChem.Icons.Interfaces.Reactions.Basics.ThreeSubstrates; BioChem.Interfaces.Nodes.SubstrateConnector s1 annotation( Placement(transformation(origin = {-100, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, 75}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.SubstrateConnector s3 annotation( Placement(transformation(origin = {-100, -80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, -75}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.SubstrateConnector s2 annotation( Placement(transformation(origin = {-100, 0}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, 4.44089e-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}, {-62.5, 75}, {-100, 75}}, color = {170, 0, 0}, smooth = Smooth.Bezier), Line(points = {{-100, 0}, {-50, 0}}, color = {170, 0, 0}), Line(points = {{-100, -75}, {-62.5, -75}, {-50, 0}}, color = {170, 0, 0}, smooth = Smooth.Bezier)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end ThreeSubstrates; diff --git a/BioChem/Interfaces/Reactions/Basics/ThreeSubstratesReversible.mo b/BioChem/Interfaces/Reactions/Basics/ThreeSubstratesReversible.mo index fcbb653..f3ca40f 100644 --- a/BioChem/Interfaces/Reactions/Basics/ThreeSubstratesReversible.mo +++ b/BioChem/Interfaces/Reactions/Basics/ThreeSubstratesReversible.mo @@ -1,13 +1,11 @@ within BioChem.Interfaces.Reactions.Basics; partial model ThreeSubstratesReversible + extends BioChem.Icons.Interfaces.Reactions.Basics.ThreeSubstratesReversible; BioChem.Interfaces.Nodes.SubstrateConnector s1 annotation( Placement(transformation(origin = {-100, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, 75}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.SubstrateConnector s2 annotation( Placement(transformation(origin = {-100, 0}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, 8.88178e-15}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.SubstrateConnector s3 annotation( Placement(transformation(origin = {-100, -80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, -75}, 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}, {-60, 75}, {-100, 75}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{-100, 0}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35), Line(points = {{-100, -75}, {-60.03, -75}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35, smooth = Smooth.Bezier)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end ThreeSubstratesReversible; diff --git a/BioChem/Interfaces/Reactions/Basics/TwoProducts.mo b/BioChem/Interfaces/Reactions/Basics/TwoProducts.mo index 9e3fc32..81b8d44 100644 --- a/BioChem/Interfaces/Reactions/Basics/TwoProducts.mo +++ b/BioChem/Interfaces/Reactions/Basics/TwoProducts.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Basics; partial model TwoProducts "SubstanceConnectors for two products" + extends BioChem.Icons.Interfaces.Reactions.Basics.TwoProducts; BioChem.Interfaces.Nodes.ProductConnector p2 annotation( Placement(transformation(origin = {100, -40}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {112.5, -50}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.ProductConnector p1 annotation( Placement(transformation(origin = {100, 40}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {112.5, 50}, 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}, {62.5, 50}, {102.4, 50}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{50, 0}, {62.5, -50}, {100, -50}}, color = {170, 0, 0}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 35, smooth = Smooth.Bezier)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end TwoProducts; diff --git a/BioChem/Interfaces/Reactions/Basics/TwoSubstrates.mo b/BioChem/Interfaces/Reactions/Basics/TwoSubstrates.mo index 2ee17e3..0889e88 100644 --- a/BioChem/Interfaces/Reactions/Basics/TwoSubstrates.mo +++ b/BioChem/Interfaces/Reactions/Basics/TwoSubstrates.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Basics; partial model TwoSubstrates "SubstanceConnectors for two substrates" + extends BioChem.Icons.Interfaces.Reactions.Basics.TwoSubstrates; BioChem.Interfaces.Nodes.SubstrateConnector s1 annotation( Placement(transformation(origin = {-100, 40}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, 50}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.SubstrateConnector s2 annotation( Placement(transformation(origin = {-100, -40}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, -50}, 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, 50}, {-62.5, 50}, {-50, 0}}, color = {170, 0, 0}, smooth = Smooth.Bezier), Line(points = {{-100, -50}, {-62.5, -50}, {-50, 0}}, color = {170, 0, 0}, smooth = Smooth.Bezier)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end TwoSubstrates; diff --git a/BioChem/Interfaces/Reactions/Basics/TwoSubstratesReversible.mo b/BioChem/Interfaces/Reactions/Basics/TwoSubstratesReversible.mo index a90c1cb..33cab0e 100644 --- a/BioChem/Interfaces/Reactions/Basics/TwoSubstratesReversible.mo +++ b/BioChem/Interfaces/Reactions/Basics/TwoSubstratesReversible.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Basics; partial model TwoSubstratesReversible + extends BioChem.Icons.Interfaces.Reactions.Basics.TwoSubstratesReversible; BioChem.Interfaces.Nodes.SubstrateConnector s1 annotation( Placement(transformation(origin = {-100, 40}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, 50}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); BioChem.Interfaces.Nodes.SubstrateConnector s2 annotation( Placement(transformation(origin = {-100, -40}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-112.5, -50}, 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, 50}, {-62.5, 50}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35, smooth = Smooth.Bezier), Line(points = {{-100, -50}, {-62.5, -50}, {-50, 0}}, color = {170, 0, 0}, arrow = {Arrow.Open, Arrow.None}, arrowSize = 35, smooth = Smooth.Bezier)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end TwoSubstratesReversible; diff --git a/BioChem/Interfaces/Reactions/Basics/package.mo b/BioChem/Interfaces/Reactions/Basics/package.mo index e804aff..5d4e940 100644 --- a/BioChem/Interfaces/Reactions/Basics/package.mo +++ b/BioChem/Interfaces/Reactions/Basics/package.mo @@ -1,10 +1,6 @@ within BioChem.Interfaces.Reactions; package Basics "Basic properties of reactions" - extends Icons.Library; + extends BioChem.Icons.Library; - annotation( - Documentation(info = "", revisions = ""), - 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 Basics; diff --git a/BioChem/Interfaces/Reactions/Bbi.mo b/BioChem/Interfaces/Reactions/Bbi.mo index baaddb3..0716424 100644 --- a/BioChem/Interfaces/Reactions/Bbi.mo +++ b/BioChem/Interfaces/Reactions/Bbi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Bbi "Bi-Bi irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.TwoSubstrates; extends BioChem.Interfaces.Reactions.Basics.TwoProducts; @@ -13,7 +14,4 @@ equation s2.r = nS2 * rr; p1.r = -nP1 * rr; p2.r = -nP2 * 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 Bbi; diff --git a/BioChem/Interfaces/Reactions/Bbr.mo b/BioChem/Interfaces/Reactions/Bbr.mo index a5c6a24..b2da754 100644 --- a/BioChem/Interfaces/Reactions/Bbr.mo +++ b/BioChem/Interfaces/Reactions/Bbr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Bbr "Bi-Bi reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.TwoProducts; @@ -13,7 +14,4 @@ equation s2.r = nS2 * rr; p1.r = -nP1 * rr; p2.r = -nP2 * 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 Bbr; diff --git a/BioChem/Interfaces/Reactions/Bmi.mo b/BioChem/Interfaces/Reactions/Bmi.mo index 84a24c1..9b8ccac 100644 --- a/BioChem/Interfaces/Reactions/Bmi.mo +++ b/BioChem/Interfaces/Reactions/Bmi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Bmi "Bi-Multi irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.TwoSubstrates; extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; @@ -11,7 +12,4 @@ equation s1.r = nS1 * rr; s2.r = nS2 * rr; p.r = -nP * 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 Bmi; diff --git a/BioChem/Interfaces/Reactions/Bmr.mo b/BioChem/Interfaces/Reactions/Bmr.mo index 9acb390..3034abc 100644 --- a/BioChem/Interfaces/Reactions/Bmr.mo +++ b/BioChem/Interfaces/Reactions/Bmr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Bmr "Bi-Multi reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; @@ -11,7 +12,4 @@ equation s1.r = nS1 * rr; s2.r = nS2 * rr; p.r = -nP * 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 Bmr; diff --git a/BioChem/Interfaces/Reactions/Bqi.mo b/BioChem/Interfaces/Reactions/Bqi.mo index 2d875b3..6b1c8a1 100644 --- a/BioChem/Interfaces/Reactions/Bqi.mo +++ b/BioChem/Interfaces/Reactions/Bqi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Bqi "Bi-Quad irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.TwoSubstrates; extends BioChem.Interfaces.Reactions.Basics.FourProducts; @@ -17,7 +18,4 @@ equation p2.r = -nP2 * rr; p3.r = -nP3 * rr; p4.r = -nP4 * 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 Bqi; diff --git a/BioChem/Interfaces/Reactions/Bqr.mo b/BioChem/Interfaces/Reactions/Bqr.mo index 495757f..97601a4 100644 --- a/BioChem/Interfaces/Reactions/Bqr.mo +++ b/BioChem/Interfaces/Reactions/Bqr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Bqr "Bi-Quad reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.FourProducts; @@ -17,7 +18,4 @@ equation p2.r = -nP2 * rr; p3.r = -nP3 * rr; p4.r = -nP4 * 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 Bqr; diff --git a/BioChem/Interfaces/Reactions/Bti.mo b/BioChem/Interfaces/Reactions/Bti.mo index 0f29725..8d92430 100644 --- a/BioChem/Interfaces/Reactions/Bti.mo +++ b/BioChem/Interfaces/Reactions/Bti.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Bti "Bi-Tri irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.TwoSubstrates; extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; @@ -15,7 +16,4 @@ equation p1.r = -nP1 * rr; p2.r = -nP2 * rr; p3.r = -nP3 * 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 Bti; diff --git a/BioChem/Interfaces/Reactions/Btr.mo b/BioChem/Interfaces/Reactions/Btr.mo index 9686a1c..9e7775b 100644 --- a/BioChem/Interfaces/Reactions/Btr.mo +++ b/BioChem/Interfaces/Reactions/Btr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Btr "Bi-Tri reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; @@ -15,7 +16,4 @@ equation p1.r = -nP1 * rr; p2.r = -nP2 * rr; p3.r = -nP3 * 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 Btr; diff --git a/BioChem/Interfaces/Reactions/Bui.mo b/BioChem/Interfaces/Reactions/Bui.mo index 2803851..cf75cc2 100644 --- a/BioChem/Interfaces/Reactions/Bui.mo +++ b/BioChem/Interfaces/Reactions/Bui.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Bui "Bi-Uni irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.TwoSubstrates; extends BioChem.Interfaces.Reactions.Basics.OneProduct; @@ -11,7 +12,4 @@ equation s1.r = nS1 * rr; s2.r = nS2 * 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 Bui; diff --git a/BioChem/Interfaces/Reactions/Bur.mo b/BioChem/Interfaces/Reactions/Bur.mo index 382a8cf..0aaf79c 100644 --- a/BioChem/Interfaces/Reactions/Bur.mo +++ b/BioChem/Interfaces/Reactions/Bur.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Bur "Bi-Uni reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.OneProduct; @@ -11,7 +12,4 @@ equation s1.r = nS1 * rr; s2.r = nS2 * 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 Bur; diff --git a/BioChem/Interfaces/Reactions/Mbi.mo b/BioChem/Interfaces/Reactions/Mbi.mo index 412bf9e..bf1bd22 100644 --- a/BioChem/Interfaces/Reactions/Mbi.mo +++ b/BioChem/Interfaces/Reactions/Mbi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Mbi "Multi-Bi irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.MultipleSubstrates; extends BioChem.Interfaces.Reactions.Basics.TwoProducts; @@ -11,7 +12,4 @@ equation s.r = nS * rr; p1.r = -nP1 * rr; p2.r = -nP2 * 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 Mbi; diff --git a/BioChem/Interfaces/Reactions/Mbr.mo b/BioChem/Interfaces/Reactions/Mbr.mo index a373359..9cf5925 100644 --- a/BioChem/Interfaces/Reactions/Mbr.mo +++ b/BioChem/Interfaces/Reactions/Mbr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Mbr "Multi-Bi reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.MultipleSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.TwoProducts; @@ -11,7 +12,4 @@ equation s.r = nS * rr; p1.r = -nP1 * rr; p2.r = -nP2 * 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 Mbr; diff --git a/BioChem/Interfaces/Reactions/Mmi.mo b/BioChem/Interfaces/Reactions/Mmi.mo index bd70f1f..0590f20 100644 --- a/BioChem/Interfaces/Reactions/Mmi.mo +++ b/BioChem/Interfaces/Reactions/Mmi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Mmi "Multi-Multi irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.MultipleSubstrates; extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; @@ -9,7 +10,4 @@ partial model Mmi "Multi-Multi irreversible reaction" equation s.r = nS * rr; p.r = -nP * 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 Mmi; diff --git a/BioChem/Interfaces/Reactions/Mmr.mo b/BioChem/Interfaces/Reactions/Mmr.mo index 50e943b..529726d 100644 --- a/BioChem/Interfaces/Reactions/Mmr.mo +++ b/BioChem/Interfaces/Reactions/Mmr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Mmr "Multi-Multi reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.MultipleSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; @@ -9,7 +10,4 @@ partial model Mmr "Multi-Multi reversible reaction" equation s.r = nS * rr; p.r = -nP * 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 Mmr; diff --git a/BioChem/Interfaces/Reactions/Modifiers/Activator.mo b/BioChem/Interfaces/Reactions/Modifiers/Activator.mo index 3b793f9..b8da2e6 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/Activator.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/Activator.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model Activator "Basics for a forward activator in a reaction edge" + extends BioChem.Icons.Interfaces.Reactions.Modifiers.Activator; BioChem.Interfaces.Nodes.ActivatorConnector a1 annotation( Placement(transformation(origin = {0, 90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-1.28786e-14, 90}, extent = {{-20, -20}, {20, 20}}))); equation a1.r = 0; - annotation( - 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)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end Activator; diff --git a/BioChem/Interfaces/Reactions/Modifiers/ActivatorBackward.mo b/BioChem/Interfaces/Reactions/Modifiers/ActivatorBackward.mo index b717b65..bb34e5c 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/ActivatorBackward.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/ActivatorBackward.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model ActivatorBackward "Basics for a backward activator in a reaction edge" + extends BioChem.Icons.Interfaces.Reactions.Modifiers.ActivatorBackward; BioChem.Interfaces.Nodes.ActivatorConnector aB1 annotation( Placement(transformation(origin = {-6.66134e-16, -90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {1.77636e-15, -90}, extent = {{-20, -20}, {20, 20}}))); equation aB1.r = 0; - annotation( - 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)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end ActivatorBackward; diff --git a/BioChem/Interfaces/Reactions/Modifiers/ActivatorForward.mo b/BioChem/Interfaces/Reactions/Modifiers/ActivatorForward.mo index c38ed49..b210fcb 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/ActivatorForward.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/ActivatorForward.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model ActivatorForward "Basics for a forward activator in a reaction edge" + extends BioChem.Icons.Interfaces.Reactions.Modifiers.ActivatorBackward; BioChem.Interfaces.Nodes.ActivatorConnector aF1 annotation( Placement(transformation(origin = {-4.21885e-15, 90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-8.88178e-16, 90}, extent = {{-20, -20}, {20, 20}}))); equation aF1.r = 0; - annotation( - 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)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end ActivatorForward; diff --git a/BioChem/Interfaces/Reactions/Modifiers/Inhibitor.mo b/BioChem/Interfaces/Reactions/Modifiers/Inhibitor.mo index 171efe9..912bec7 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/Inhibitor.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/Inhibitor.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model Inhibitor + extends BioChem.Icons.Interfaces.Reactions.Modifiers.Inhibitor; BioChem.Interfaces.Nodes.InhibitorConnector i1 annotation( Placement(transformation(origin = {0, 90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-9.99201e-15, 90}, extent = {{-20, -20}, {20, 20}}))); equation i1.r = 0; - annotation( - 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)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end Inhibitor; diff --git a/BioChem/Interfaces/Reactions/Modifiers/InhibitorBackward.mo b/BioChem/Interfaces/Reactions/Modifiers/InhibitorBackward.mo index 6c76951..653655e 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/InhibitorBackward.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/InhibitorBackward.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model InhibitorBackward "Basics for a backward inhibitor in a reaction edge" + extends BioChem.Icons.Interfaces.Reactions.Modifiers.InhibitorBackward; BioChem.Interfaces.Nodes.InhibitorConnector iB1 annotation( Placement(transformation(origin = {-5.55112e-16, -90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-4.88498e-15, -90}, extent = {{-20, -20}, {20, 20}}))); equation iB1.r = 0; - annotation( - 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)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end InhibitorBackward; diff --git a/BioChem/Interfaces/Reactions/Modifiers/InhibitorForward.mo b/BioChem/Interfaces/Reactions/Modifiers/InhibitorForward.mo index cd1dd82..46fb0c9 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/InhibitorForward.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/InhibitorForward.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model InhibitorForward "Basics for a forward inhibitor in a reaction edge" + extends BioChem.Icons.Interfaces.Reactions.Modifiers.InhibitorForward; BioChem.Interfaces.Nodes.InhibitorConnector iF1 annotation( Placement(transformation(origin = {-2.66454e-15, 90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {1.06581e-14, 90}, extent = {{-20, -20}, {20, 20}}))); equation iF1.r = 0; - annotation( - 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)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end InhibitorForward; diff --git a/BioChem/Interfaces/Reactions/Modifiers/Modifier.mo b/BioChem/Interfaces/Reactions/Modifiers/Modifier.mo index 2527656..0b4977a 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/Modifier.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/Modifier.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model Modifier + extends BioChem.Icons.Interfaces.Reactions.Modifiers.Modifier; BioChem.Interfaces.Nodes.ModifierConnector m1 annotation( Placement(transformation(origin = {5.55111e-16, 90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-3.10862e-15, 90}, extent = {{-20, -20}, {20, 20}}))); equation m1.r = 0; - annotation( - 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 = 30)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end Modifier; diff --git a/BioChem/Interfaces/Reactions/Modifiers/ModifierBackward.mo b/BioChem/Interfaces/Reactions/Modifiers/ModifierBackward.mo index a432819..6e0f29a 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/ModifierBackward.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/ModifierBackward.mo @@ -1,11 +1,9 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model ModifierBackward "Basics for a backward modifier in a reaction edge" + extends BioChem.Icons.Interfaces.Reactions.Modifiers.ModifierBackward; BioChem.Interfaces.Nodes.ModifierConnector mB1 annotation( Placement(transformation(origin = {0, -90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-6.66134e-15, -90}, extent = {{-20, -20}, {20, 20}}))); equation mB1.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, -6.715}}, color = {0, 0, 255}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 25)})); end ModifierBackward; diff --git a/BioChem/Interfaces/Reactions/Modifiers/ModifierForward.mo b/BioChem/Interfaces/Reactions/Modifiers/ModifierForward.mo index d26e993..ed31165 100644 --- 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" + extends BioChem.Icons.Interfaces.Reactions.Modifiers.ModifierForward; 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/Modifiers/MultipleModifiers.mo b/BioChem/Interfaces/Reactions/Modifiers/MultipleModifiers.mo index 0c03a99..2bf42f0 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/MultipleModifiers.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/MultipleModifiers.mo @@ -1,12 +1,10 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model MultipleModifiers + extends BioChem.Icons.Interfaces.Reactions.Modifiers.MultipleModifiers; parameter Integer dimM "number of modifiers"; BioChem.Interfaces.Nodes.ModifierConnector m[dimM] annotation( Placement(transformation(origin = {-2.9976e-15, 90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-8.88178e-16, 90}, extent = {{-18.75, -18.75}, {18.75, 18.75}}))); equation m.r = fill(0, dimM); - annotation( - Icon(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Ellipse(lineColor = {255, 255, 0}, fillColor = {255, 255, 127}, fillPattern = FillPattern.Solid, lineThickness = 2, extent = {{-25.0, 65.0}, {25.0, 115.0}}), Line(origin = {0.0, 29.1679}, points = {{0.0, 29.17}, {0.0, -29.17}}, arrow = {Arrow.None, Arrow.Filled}, arrowSize = 30)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end MultipleModifiers; diff --git a/BioChem/Interfaces/Reactions/Modifiers/ThreeModifiers.mo b/BioChem/Interfaces/Reactions/Modifiers/ThreeModifiers.mo index 6bc584b..a9bb271 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/ThreeModifiers.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/ThreeModifiers.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model ThreeModifiers "Basics for three modifiers in a reaction edge" + extends BioChem.Icons.Interfaces.Reactions.Modifiers.ThreeModifiers; BioChem.Interfaces.Nodes.ModifierConnector m1 annotation( Placement(transformation(origin = {-50, 90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-50, 90}, extent = {{-20, -20}, {20, 20}}))); BioChem.Interfaces.Nodes.ModifierConnector m2 annotation( @@ -11,7 +12,4 @@ equation 0 = m1.r; 0 = m2.r; 0 = m3.r; - annotation( - 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)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end ThreeModifiers; diff --git a/BioChem/Interfaces/Reactions/Modifiers/TwoModifiers.mo b/BioChem/Interfaces/Reactions/Modifiers/TwoModifiers.mo index 35a2c38..b9c51e6 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/TwoModifiers.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/TwoModifiers.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions.Modifiers; partial model TwoModifiers "Basics for two modifiers in a reaction edge" + extends BioChem.Icons.Interfaces.Reactions.Modifiers.TwoModifiers; BioChem.Interfaces.Nodes.ModifierConnector m2 annotation( Placement(transformation(origin = {50, 90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {50, 90}, extent = {{-20, -20}, {20, 20}}))); BioChem.Interfaces.Nodes.ModifierConnector m1 annotation( @@ -8,7 +9,4 @@ partial model TwoModifiers "Basics for two modifiers in a reaction edge" equation 0 = m1.r; 0 = m2.r; - annotation( - 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)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end TwoModifiers; diff --git a/BioChem/Interfaces/Reactions/Modifiers/package.mo b/BioChem/Interfaces/Reactions/Modifiers/package.mo index 48ba82e..2874433 100644 --- a/BioChem/Interfaces/Reactions/Modifiers/package.mo +++ b/BioChem/Interfaces/Reactions/Modifiers/package.mo @@ -1,10 +1,6 @@ within BioChem.Interfaces.Reactions; package Modifiers "Partial models of modifiers to reactions" - extends Icons.Library; + extends BioChem.Icons.Library; - annotation( - Documentation(info = "", revisions = ""), - 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 Modifiers; diff --git a/BioChem/Interfaces/Reactions/Mqi.mo b/BioChem/Interfaces/Reactions/Mqi.mo index 10a29a2..1397c46 100644 --- a/BioChem/Interfaces/Reactions/Mqi.mo +++ b/BioChem/Interfaces/Reactions/Mqi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Mqi "Multi-Quad irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.MultipleSubstrates; extends BioChem.Interfaces.Reactions.Basics.FourProducts; @@ -15,7 +16,4 @@ equation p2.r = -nP2 * rr; p3.r = -nP3 * rr; p4.r = -nP4 * 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 Mqi; diff --git a/BioChem/Interfaces/Reactions/Mqr.mo b/BioChem/Interfaces/Reactions/Mqr.mo index f06fbdb..3e7e5fc 100644 --- a/BioChem/Interfaces/Reactions/Mqr.mo +++ b/BioChem/Interfaces/Reactions/Mqr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Mqr "Multi-Quad reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.MultipleSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.FourProducts; @@ -15,7 +16,4 @@ equation p2.r = -nP2 * rr; p3.r = -nP3 * rr; p4.r = -nP4 * 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 Mqr; diff --git a/BioChem/Interfaces/Reactions/Mti.mo b/BioChem/Interfaces/Reactions/Mti.mo index 56db3fc..cce7f0a 100644 --- a/BioChem/Interfaces/Reactions/Mti.mo +++ b/BioChem/Interfaces/Reactions/Mti.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Mti "Multi-Tri irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.MultipleSubstrates; extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; @@ -13,7 +14,4 @@ equation p1.r = -nP1 * rr; p2.r = -nP2 * rr; p3.r = -nP3 * 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 Mti; diff --git a/BioChem/Interfaces/Reactions/Mtr.mo b/BioChem/Interfaces/Reactions/Mtr.mo index a0397d7..d948e39 100644 --- a/BioChem/Interfaces/Reactions/Mtr.mo +++ b/BioChem/Interfaces/Reactions/Mtr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Mtr "Multi-Tri reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.MultipleSubstrates; extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; @@ -13,7 +14,4 @@ equation p1.r = -nP1 * rr; p2.r = -nP2 * rr; p3.r = -nP3 * 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 Mtr; diff --git a/BioChem/Interfaces/Reactions/Mui.mo b/BioChem/Interfaces/Reactions/Mui.mo index 15e5808..29a5d15 100644 --- a/BioChem/Interfaces/Reactions/Mui.mo +++ b/BioChem/Interfaces/Reactions/Mui.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Mui "Multi-Uni irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.MultipleSubstrates; extends BioChem.Interfaces.Reactions.Basics.OneProduct; @@ -9,7 +10,4 @@ partial model Mui "Multi-Uni irreversible reaction" equation s.r = nS * 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 Mui; diff --git a/BioChem/Interfaces/Reactions/Mur.mo b/BioChem/Interfaces/Reactions/Mur.mo index b092d52..3d4433a 100644 --- a/BioChem/Interfaces/Reactions/Mur.mo +++ b/BioChem/Interfaces/Reactions/Mur.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Mur "Multi-Uni reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.MultipleSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.OneProduct; @@ -9,7 +10,4 @@ partial model Mur "Multi-Uni reversible reaction" equation s.r = nS * 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 Mur; diff --git a/BioChem/Interfaces/Reactions/Qbi.mo b/BioChem/Interfaces/Reactions/Qbi.mo index 7afd623..a1b6990 100644 --- a/BioChem/Interfaces/Reactions/Qbi.mo +++ b/BioChem/Interfaces/Reactions/Qbi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Qbi "Quad-Bi irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.FourSubstrates; extends BioChem.Interfaces.Reactions.Basics.TwoProducts; @@ -17,7 +18,4 @@ equation s4.r = nS4 * rr; p1.r = -nP1 * rr; p2.r = -nP2 * 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 Qbi; diff --git a/BioChem/Interfaces/Reactions/Qbr.mo b/BioChem/Interfaces/Reactions/Qbr.mo index f665f4e..723bf1a 100644 --- a/BioChem/Interfaces/Reactions/Qbr.mo +++ b/BioChem/Interfaces/Reactions/Qbr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Qbr "Quad-Bi reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.FourSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.TwoProducts; @@ -17,7 +18,4 @@ equation s4.r = nS4 * rr; p1.r = -nP1 * rr; p2.r = -nP2 * 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 Qbr; diff --git a/BioChem/Interfaces/Reactions/Qmi.mo b/BioChem/Interfaces/Reactions/Qmi.mo index 68327d2..2aed744 100644 --- a/BioChem/Interfaces/Reactions/Qmi.mo +++ b/BioChem/Interfaces/Reactions/Qmi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Qmi "Quad-Multi irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.FourSubstrates; extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; @@ -15,7 +16,4 @@ equation s3.r = nS3 * rr; s4.r = nS4 * rr; p.r = -nP * 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 Qmi; diff --git a/BioChem/Interfaces/Reactions/Qmr.mo b/BioChem/Interfaces/Reactions/Qmr.mo index c134c5d..be8608b 100644 --- a/BioChem/Interfaces/Reactions/Qmr.mo +++ b/BioChem/Interfaces/Reactions/Qmr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Qmr "Quad-Multi reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.FourSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; @@ -15,7 +16,4 @@ equation s3.r = nS3 * rr; s4.r = nS4 * rr; p.r = -nP * 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 Qmr; diff --git a/BioChem/Interfaces/Reactions/Qqi.mo b/BioChem/Interfaces/Reactions/Qqi.mo index 6e19e56..25cba1f 100644 --- a/BioChem/Interfaces/Reactions/Qqi.mo +++ b/BioChem/Interfaces/Reactions/Qqi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Qqi "Quad-Quad irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.FourSubstrates; extends BioChem.Interfaces.Reactions.Basics.FourProducts; @@ -21,7 +22,4 @@ equation p2.r = -nP2 * rr; p3.r = -nP3 * rr; p4.r = -nP4 * 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 Qqi; diff --git a/BioChem/Interfaces/Reactions/Qqr.mo b/BioChem/Interfaces/Reactions/Qqr.mo index eedc864..ac05678 100644 --- a/BioChem/Interfaces/Reactions/Qqr.mo +++ b/BioChem/Interfaces/Reactions/Qqr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Qqr "Quad-Quad reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.FourSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.FourProducts; @@ -21,7 +22,4 @@ equation p2.r = -nP2 * rr; p3.r = -nP3 * rr; p4.r = -nP4 * 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 Qqr; diff --git a/BioChem/Interfaces/Reactions/Qti.mo b/BioChem/Interfaces/Reactions/Qti.mo index 01f23ab..295930f 100644 --- a/BioChem/Interfaces/Reactions/Qti.mo +++ b/BioChem/Interfaces/Reactions/Qti.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Qti "Quad-Tri irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.FourSubstrates; extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; @@ -19,7 +20,4 @@ equation p1.r = -nP1 * rr; p2.r = -nP2 * rr; p3.r = -nP3 * 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 Qti; diff --git a/BioChem/Interfaces/Reactions/Qtr.mo b/BioChem/Interfaces/Reactions/Qtr.mo index 7f61e91..1fe3c74 100644 --- a/BioChem/Interfaces/Reactions/Qtr.mo +++ b/BioChem/Interfaces/Reactions/Qtr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Qtr "Quad-Tri reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.FourSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; @@ -19,7 +20,4 @@ equation p1.r = -nP1 * rr; p2.r = -nP2 * rr; p3.r = -nP3 * rr; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end Qtr; diff --git a/BioChem/Interfaces/Reactions/Qui.mo b/BioChem/Interfaces/Reactions/Qui.mo index 07c522f..a599604 100644 --- a/BioChem/Interfaces/Reactions/Qui.mo +++ b/BioChem/Interfaces/Reactions/Qui.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Qui "Quad-Uni irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.FourSubstrates; extends BioChem.Interfaces.Reactions.Basics.OneProduct; @@ -15,7 +16,4 @@ equation s3.r = nS3 * rr; s4.r = nS4 * rr; p1.r = -nP1 * rr; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end Qui; diff --git a/BioChem/Interfaces/Reactions/Qur.mo b/BioChem/Interfaces/Reactions/Qur.mo index 30fc6f3..12a07e6 100644 --- a/BioChem/Interfaces/Reactions/Qur.mo +++ b/BioChem/Interfaces/Reactions/Qur.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Qur "Quad-Uni reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.FourSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.OneProduct; @@ -15,7 +16,4 @@ equation s3.r = nS3 * rr; s4.r = nS4 * 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 Qur; diff --git a/BioChem/Interfaces/Reactions/Tbi.mo b/BioChem/Interfaces/Reactions/Tbi.mo index 9727700..ed38ec6 100644 --- a/BioChem/Interfaces/Reactions/Tbi.mo +++ b/BioChem/Interfaces/Reactions/Tbi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Tbi "Tri-Bi irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.ThreeSubstrates; extends BioChem.Interfaces.Reactions.Basics.TwoProducts; @@ -15,7 +16,4 @@ equation s3.r = nS3 * rr; p1.r = -nP1 * rr; p2.r = -nP2 * 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 Tbi; diff --git a/BioChem/Interfaces/Reactions/Tbr.mo b/BioChem/Interfaces/Reactions/Tbr.mo index 5258fea..654c361 100644 --- a/BioChem/Interfaces/Reactions/Tbr.mo +++ b/BioChem/Interfaces/Reactions/Tbr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Tbr "Tri-Bi reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.ThreeSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.TwoProducts; @@ -15,7 +16,4 @@ equation s3.r = nS3 * rr; p1.r = -nP1 * rr; p2.r = -nP2 * 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 Tbr; diff --git a/BioChem/Interfaces/Reactions/Tmi.mo b/BioChem/Interfaces/Reactions/Tmi.mo index d31f5c1..d1a588d 100644 --- a/BioChem/Interfaces/Reactions/Tmi.mo +++ b/BioChem/Interfaces/Reactions/Tmi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Tmi "Tri-Multi irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.ThreeSubstrates; extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; @@ -13,7 +14,4 @@ equation s2.r = nS2 * rr; s3.r = nS3 * rr; p.r = -nP * 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 Tmi; diff --git a/BioChem/Interfaces/Reactions/Tmr.mo b/BioChem/Interfaces/Reactions/Tmr.mo index 025470a..b286931 100644 --- a/BioChem/Interfaces/Reactions/Tmr.mo +++ b/BioChem/Interfaces/Reactions/Tmr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Tmr "Tri-Multi reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.ThreeSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; @@ -13,7 +14,4 @@ equation s2.r = nS2 * rr; s3.r = nS3 * rr; p.r = -nP * 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 Tmr; diff --git a/BioChem/Interfaces/Reactions/Tqi.mo b/BioChem/Interfaces/Reactions/Tqi.mo index f2c7dd8..3d46193 100644 --- a/BioChem/Interfaces/Reactions/Tqi.mo +++ b/BioChem/Interfaces/Reactions/Tqi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Tqi "Tri-Quad irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.ThreeSubstrates; extends BioChem.Interfaces.Reactions.Basics.FourProducts; @@ -19,7 +20,4 @@ equation p2.r = -nP2 * rr; p3.r = -nP3 * rr; p4.r = -nP4 * 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 Tqi; diff --git a/BioChem/Interfaces/Reactions/Tqr.mo b/BioChem/Interfaces/Reactions/Tqr.mo index 176537f..2117acf 100644 --- a/BioChem/Interfaces/Reactions/Tqr.mo +++ b/BioChem/Interfaces/Reactions/Tqr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Tqr "Tri-Quad reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.ThreeSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.FourProducts; @@ -19,7 +20,4 @@ equation p2.r = -nP2 * rr; p3.r = -nP3 * rr; p4.r = -nP4 * 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 Tqr; diff --git a/BioChem/Interfaces/Reactions/Tti.mo b/BioChem/Interfaces/Reactions/Tti.mo index c1a3faa..8b4eabd 100644 --- a/BioChem/Interfaces/Reactions/Tti.mo +++ b/BioChem/Interfaces/Reactions/Tti.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Tti "Tri-Tri irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.ThreeSubstrates; extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; @@ -17,7 +18,4 @@ equation p1.r = -nP1 * rr; p2.r = -nP2 * rr; p3.r = -nP3 * 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 Tti; diff --git a/BioChem/Interfaces/Reactions/Ttr.mo b/BioChem/Interfaces/Reactions/Ttr.mo index 4695dc8..24e8702 100644 --- a/BioChem/Interfaces/Reactions/Ttr.mo +++ b/BioChem/Interfaces/Reactions/Ttr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Ttr "Tri-Tri reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.ThreeSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; @@ -17,7 +18,4 @@ equation p1.r = -nP1 * rr; p2.r = -nP2 * rr; p3.r = -nP3 * 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 Ttr; diff --git a/BioChem/Interfaces/Reactions/Tui.mo b/BioChem/Interfaces/Reactions/Tui.mo index 20de2d6..34c5d67 100644 --- a/BioChem/Interfaces/Reactions/Tui.mo +++ b/BioChem/Interfaces/Reactions/Tui.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Tui "Tri-Uni irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.ThreeSubstrates; extends BioChem.Interfaces.Reactions.Basics.OneProduct; @@ -13,7 +14,4 @@ equation s2.r = nS2 * rr; s3.r = nS3 * 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 Tui; diff --git a/BioChem/Interfaces/Reactions/Tur.mo b/BioChem/Interfaces/Reactions/Tur.mo index 8acc0b9..a0e5e3d 100644 --- a/BioChem/Interfaces/Reactions/Tur.mo +++ b/BioChem/Interfaces/Reactions/Tur.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Tur "Tri-Uni reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.ThreeSubstratesReversible; extends BioChem.Interfaces.Reactions.Basics.OneProduct; @@ -13,7 +14,4 @@ equation s2.r = nS2 * rr; s3.r = nS3 * 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 Tur; diff --git a/BioChem/Interfaces/Reactions/Ubi.mo b/BioChem/Interfaces/Reactions/Ubi.mo index 5c5bb32..ff4da47 100644 --- a/BioChem/Interfaces/Reactions/Ubi.mo +++ b/BioChem/Interfaces/Reactions/Ubi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Ubi "Uni-Bi irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.OneSubstrate; extends BioChem.Interfaces.Reactions.Basics.TwoProducts; @@ -11,7 +12,4 @@ equation s1.r = nS1 * rr; p1.r = -nP1 * rr; p2.r = -nP2 * 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 Ubi; diff --git a/BioChem/Interfaces/Reactions/Ubr.mo b/BioChem/Interfaces/Reactions/Ubr.mo index bbb85c8..9c8fb56 100644 --- a/BioChem/Interfaces/Reactions/Ubr.mo +++ b/BioChem/Interfaces/Reactions/Ubr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Ubr "Uni-Bi reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; extends BioChem.Interfaces.Reactions.Basics.TwoProducts; @@ -11,7 +12,4 @@ equation s1.r = nS1 * rr; p1.r = -nP1 * rr; p2.r = -nP2 * 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 Ubr; diff --git a/BioChem/Interfaces/Reactions/Umi.mo b/BioChem/Interfaces/Reactions/Umi.mo index d03254a..1fdba6d 100644 --- a/BioChem/Interfaces/Reactions/Umi.mo +++ b/BioChem/Interfaces/Reactions/Umi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Umi "Uni-Multi irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.OneSubstrate; extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; @@ -9,7 +10,4 @@ partial model Umi "Uni-Multi irreversible reaction" equation s1.r = nS1 * rr; p.r = -nP * 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 Umi; diff --git a/BioChem/Interfaces/Reactions/Umr.mo b/BioChem/Interfaces/Reactions/Umr.mo index db58642..2cbb026 100644 --- a/BioChem/Interfaces/Reactions/Umr.mo +++ b/BioChem/Interfaces/Reactions/Umr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Umr "Uni-Multi reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; @@ -9,7 +10,4 @@ partial model Umr "Uni-Multi reversible reaction" equation s1.r = nS1 * rr; p.r = -nP * 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 Umr; diff --git a/BioChem/Interfaces/Reactions/Uqi.mo b/BioChem/Interfaces/Reactions/Uqi.mo index 34bdf17..1a60787 100644 --- a/BioChem/Interfaces/Reactions/Uqi.mo +++ b/BioChem/Interfaces/Reactions/Uqi.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Uqi "Uni-Quad irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.OneSubstrate; extends BioChem.Interfaces.Reactions.Basics.FourProducts; @@ -15,7 +16,4 @@ equation p2.r = -nP2 * rr; p3.r = -nP3 * rr; p4.r = -nP4 * 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 Uqi; diff --git a/BioChem/Interfaces/Reactions/Uqr.mo b/BioChem/Interfaces/Reactions/Uqr.mo index e36e62d..ac90f4e 100644 --- a/BioChem/Interfaces/Reactions/Uqr.mo +++ b/BioChem/Interfaces/Reactions/Uqr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Uqr + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; extends BioChem.Interfaces.Reactions.Basics.FourProducts; @@ -15,7 +16,4 @@ equation p2.r = -nP2 * rr; p3.r = -nP3 * rr; p4.r = -nP4 * 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 Uqr; diff --git a/BioChem/Interfaces/Reactions/Uti.mo b/BioChem/Interfaces/Reactions/Uti.mo index e041fca..1ab94a1 100644 --- a/BioChem/Interfaces/Reactions/Uti.mo +++ b/BioChem/Interfaces/Reactions/Uti.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Uti "Uni-Tri irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.OneSubstrate; extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; @@ -13,7 +14,4 @@ equation p1.r = -nP1 * rr; p2.r = -nP2 * rr; p3.r = -nP3 * 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 Uti; diff --git a/BioChem/Interfaces/Reactions/Utr.mo b/BioChem/Interfaces/Reactions/Utr.mo index b1a58d7..76d8683 100644 --- a/BioChem/Interfaces/Reactions/Utr.mo +++ b/BioChem/Interfaces/Reactions/Utr.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Utr "Uni-Tri reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; @@ -13,7 +14,4 @@ equation p1.r = -nP1 * rr; p2.r = -nP2 * rr; p3.r = -nP3 * 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 Utr; diff --git a/BioChem/Interfaces/Reactions/Uui.mo b/BioChem/Interfaces/Reactions/Uui.mo index 03be889..75a9b97 100644 --- a/BioChem/Interfaces/Reactions/Uui.mo +++ b/BioChem/Interfaces/Reactions/Uui.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Uui "Uni-Uni irreversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.OneSubstrate; extends BioChem.Interfaces.Reactions.Basics.OneProduct; @@ -9,5 +10,4 @@ partial model Uui "Uni-Uni irreversible reaction" 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 index 510fb5f..1d28a76 100644 --- a/BioChem/Interfaces/Reactions/Uur.mo +++ b/BioChem/Interfaces/Reactions/Uur.mo @@ -1,6 +1,7 @@ within BioChem.Interfaces.Reactions; partial model Uur "Uni-Uni reversible reaction" + extends BioChem.Icons.Base; extends BioChem.Interfaces.Reactions.Basics.Reaction; extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; extends BioChem.Interfaces.Reactions.Basics.OneProduct; @@ -9,5 +10,4 @@ partial model Uur "Uni-Uni reversible reaction" 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/Reactions/package.mo b/BioChem/Interfaces/Reactions/package.mo index bd6cae1..6a03398 100644 --- a/BioChem/Interfaces/Reactions/package.mo +++ b/BioChem/Interfaces/Reactions/package.mo @@ -1,7 +1,7 @@ within BioChem.Interfaces; package Reactions "Partial models, extended by models in the subpackage Reactions" - extends Icons.Library; + extends BioChem.Icons.Library; annotation( Documentation(info = " @@ -17,7 +17,5 @@ All reactions need at least one substrate and at least one product. This package \"Fig1:Reactions\"
Figure 1: Some of the reactions
- ", revisions = ""), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); + ", revisions = "")); end Reactions; diff --git a/BioChem/Interfaces/Substances/InputSubstance.mo b/BioChem/Interfaces/Substances/InputSubstance.mo index 30ada95..5e64bf3 100644 --- a/BioChem/Interfaces/Substances/InputSubstance.mo +++ b/BioChem/Interfaces/Substances/InputSubstance.mo @@ -1,7 +1,7 @@ within BioChem.Interfaces.Substances; partial model InputSubstance "Basics for a substance" - + extends BioChem.Icons.Interfaces.Substances.InputSubstance; input BioChem.Units.Concentration c "Current concentration of substance (mM)"; BioChem.Units.MolarFlowRate rNet "Net flow rate of substance into the node"; BioChem.Units.AmountOfSubstance n "Number of moles of substance in pool (mol)"; @@ -20,5 +20,5 @@ The base class for all substances.

Corresponds to SBML species changed by SBML rules and with the boundaryCondition attribute set to true and the constant attribute set to false.

-"), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Ellipse(fillColor={123,152,255}, extent={{-50,-50},{50,50}})}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); +")); end InputSubstance; diff --git a/BioChem/Interfaces/Substances/Substance.mo b/BioChem/Interfaces/Substances/Substance.mo index c1cee65..e0bcab1 100644 --- a/BioChem/Interfaces/Substances/Substance.mo +++ b/BioChem/Interfaces/Substances/Substance.mo @@ -1,6 +1,8 @@ within BioChem.Interfaces.Substances; partial model Substance + extends BioChem.Icons.Interfaces.Substances.Substance; + BioChem.Units.Concentration c( stateSelect=StateSelect.prefer) "Current concentration of substance (mM)"; BioChem.Units.MolarFlowRate rNet "Net flow rate of substance into the node"; BioChem.Units.AmountOfSubstance n( stateSelect=StateSelect.prefer) "Number of moles of substance in pool (mol)"; @@ -21,7 +23,6 @@ The base class for all substances.

Corresponds to SBML species changed by SBML rules and with the boundaryCondition attribute set to true and the constant attribute set to false.

-"), - Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Ellipse(fillColor={123,152,255}, extent={{-50,-50},{50,50}})}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); +")); end Substance; diff --git a/BioChem/Interfaces/Substances/package.mo b/BioChem/Interfaces/Substances/package.mo index 4912662..5a65cc7 100644 --- a/BioChem/Interfaces/Substances/package.mo +++ b/BioChem/Interfaces/Substances/package.mo @@ -1,8 +1,8 @@ within BioChem.Interfaces; package Substances - extends Icons.Library; + extends BioChem.Icons.Interfaces.Substances; - 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})), Documentation(info=" + annotation(Documentation(info="

Substances

This package contains partial models of different kinds of nodes needed to represent substances in biological and biochemical systems. The basic attributes corresponding to the properties that are studied during simulations, i.e., the amount and the concentration of the substance, are declared in these partial models. ", revisions="")); diff --git a/BioChem/Interfaces/package.mo b/BioChem/Interfaces/package.mo index 82fc1e4..a6a7711 100644 --- 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 Modelica.Icons.InterfacesPackage; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Documentation(info = " + extends BioChem.Icons.Interfaces; + annotation(Documentation(info = "

Interfaces

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.
diff --git a/BioChem/Reactions/Activation/package.mo b/BioChem/Reactions/Activation/package.mo index a5e7765..18ae14f 100644 --- a/BioChem/Reactions/Activation/package.mo +++ b/BioChem/Reactions/Activation/package.mo @@ -16,7 +16,7 @@ package Activation "Activation kinetics reactions"

Reversible mixed activation kinetics.

- "), 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 Umar; model Umai "Irreversible mixed activation kinetics" @@ -32,7 +32,7 @@ package Activation "Activation kinetics reactions"

Irreversible mixed activation kinetics.

- "), 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 Umai; model Uctr "Reversible catalytic activation" @@ -49,7 +49,7 @@ package Activation "Activation kinetics reactions"

Reversible catalytic activation.

- "), 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 Uctr; model Ucti "Irreversible catalytic activation" @@ -64,7 +64,7 @@ package Activation "Activation kinetics reactions"

Irreversible catalytic activation.

- "), 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 Ucti; model Uar "Reversible specific activation kinetics" @@ -81,7 +81,7 @@ package Activation "Activation kinetics reactions"

Reversible specific activation kinetics.

- "), 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 Uar; model Uaii "Irreversible specific activation kinetics" @@ -96,7 +96,7 @@ package Activation "Activation kinetics reactions"

Irreversible specific activation kinetics.

- "), 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 Uaii; model Uai "Irreversible substrate activation" @@ -110,7 +110,7 @@ package Activation "Activation kinetics reactions"

Irreversible substrate activation.

- "), 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 Uai; annotation(Documentation(info=" @@ -122,5 +122,5 @@ This package contains models for irreversible and reversible activation reaction

- ", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); + ", revisions="")); end Activation; diff --git a/BioChem/Reactions/BiSubstrate/package.mo b/BioChem/Reactions/BiSubstrate/package.mo index 6ed12fc..1b1af70 100644 --- a/BioChem/Reactions/BiSubstrate/package.mo +++ b/BioChem/Reactions/BiSubstrate/package.mo @@ -27,7 +27,7 @@ package BiSubstrate "Bi-substrate reactions"

Ping pong bi-bi kinetics.

- "), 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 Ppbr; model Ordubr "Ordered uni-bi kinetics" @@ -50,7 +50,7 @@ package BiSubstrate "Bi-substrate reactions"

Ordered uni-bi kinetics.

- "), 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 Ordubr; model Ordbur "Ordered bi-uni kinetics" @@ -73,7 +73,7 @@ package BiSubstrate "Bi-substrate reactions"

Ordered bi-uni kinetics.

- "), 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 Ordbur; model Ordbbr "Ordered bi-bi kinetics" @@ -105,7 +105,7 @@ package BiSubstrate "Bi-substrate reactions"

Ordered bi-bi kinetics.

- "), 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 Ordbbr; annotation(Documentation(info=" @@ -117,5 +117,5 @@ package BiSubstrate "Bi-substrate reactions"
- ", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); + ", revisions="")); end BiSubstrate; diff --git a/BioChem/Reactions/FastEquilibrium/package.mo b/BioChem/Reactions/FastEquilibrium/package.mo index f783be9..c136e91 100644 --- a/BioChem/Reactions/FastEquilibrium/package.mo +++ b/BioChem/Reactions/FastEquilibrium/package.mo @@ -11,7 +11,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr equation p1.c=s1.c*kP1/kS1; s1.r + p1.r=0; - 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 Uuf; model Utf "Uni-Tri fast (instant) equilibrium reaction" @@ -27,7 +26,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr p2.c=s1.c*kP2/kS1; p3.c=s1.c*kP3/kS1; s1.r + p1.r + p2.r + p3.r=0; - 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 Utf; model Ubf "Uni-Bi fast (instant) equilibrium reaction" @@ -41,7 +39,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr p1.c=s1.c*kP1/kS1; p2.c=s1.c*kP2/kS1; s1.r + p1.r + p2.r=0; - 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 Ubf; model Ttf "Tri-Tri fast (instant) equilibrium reaction" @@ -61,7 +58,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr s2.c=s1.c*kS2/kS1; s3.c=s1.c*kS3/kS1; s1.r + s2.r + s3.r + p1.r + p2.r + p3.r=0; - 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 Ttf; model Btf "Bi-Tri fast (instant) equilibrium reaction" @@ -79,7 +75,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr p3.c=s1.c*kP3/kS1; s2.c=s1.c*kS2/kS1; s1.r + s2.r + p1.r + p2.r + p3.r=0; - 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 Btf; model Bbf "Bi-Bi fast (instant) equilibrium reaction" @@ -95,7 +90,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr p2.c=s1.c*kP2/kS1; s2.c=s1.c*kS2/kS1; s1.r + s2.r + p1.r + p2.r=0; - 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 Bbf; model Qqf "Quad-Quad fast (instant) equilibrium reaction" @@ -119,7 +113,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr s3.c=s1.c*kS3/kS1; s4.c=s1.c*kS4/kS1; s1.r + s2.r + s3.r + s4.r + p1.r + p2.r + p3.r + p4.r=0; - 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 Qqf; model Uqf @@ -137,7 +130,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr p3.c=s1.c*kP3/kS1; p4.c=s1.c*kP4/kS1; s1.r + p1.r + p2.r + p3.r + p4.c=0; - 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 Uqf; model Bqf "Bi-Quad fast (instant) equilibrium reaction" @@ -157,7 +149,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr p4.c=s1.c*kP4/kS1; s2.c=s1.c*kS2/kS1; s1.r + s2.r + p1.r + p2.r + p3.r + p4.r=0; - 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 Bqf; model Tqf "Tri-Quad fast (instant) equilibrium reaction" @@ -179,7 +170,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr s2.c=s1.c*kS2/kS1; s3.c=s1.c*kS3/kS1; s1.r + s2.r + s3.r + p1.r + p2.r + p3.r + p4.r=0; - 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 Tqf; model Mmf "Multi-Multi fast (instant) equilibrium reaction" @@ -196,7 +186,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr s[i].c=s[1].c*kS[i]/kS[1]; end for; sum(s.r) + sum(p.r)=0; - 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 Mmf; model Umf "Uni-Multi fast (instant) equilibrium reaction" @@ -210,7 +199,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr p[i].c=s1.c*kP[i]/kS1; end for; s1.r + sum(p.r)=0; - 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 Umf; model Bmf "Bi-Multi fast (instant) equilibrium reaction" @@ -226,7 +214,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr end for; s2.c=s1.c*kS2/kS1; s1.r + s2.r + sum(p.r)=0; - 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 Bmf; model Qmf "Quad-Multi fast (instant) equilibrium reaction" @@ -246,7 +233,6 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr s3.c=s1.c*kS3/kS1; s4.c=s1.c*kS4/kS1; s1.r + s2.r + s3.r + s4.r + sum(p.r)=0; - 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 Qmf; model Tmf "Tri-Multi fast (instant) equilibrium reaction" @@ -264,10 +250,9 @@ package FastEquilibrium "Base classes for reactions with fast (instant) equilibr s2.c=s1.c*kS2/kS1; s3.c=s1.c*kS3/kS1; s1.r + s2.r + s3.r + sum(p.r)=0; - 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 Tmf; - annotation(Diagram(coordinateSystem(extent={{-100.0,-100.0},{100.0,100.0}}, preserveAspectRatio=true, grid={10,10})), Documentation(info=" + annotation(Documentation(info="

FastEquilibrium

The reaction in the FastEquilibrium package is used to model reactions that are very fast, and could be seen as an instant balance. These models are approximated to very fast reactions, if translated to SBML.
diff --git a/BioChem/Reactions/Hill/package.mo b/BioChem/Reactions/Hill/package.mo index 9cdbc91..3c29864 100644 --- a/BioChem/Reactions/Hill/package.mo +++ b/BioChem/Reactions/Hill/package.mo @@ -1,6 +1,6 @@ within BioChem.Reactions; package Hill "Hill reactions kinetics" - extends Icons.Library; + extends BioChem.Icons.Library; model Hillr "Reversible Hill kinetics" extends BioChem.Interfaces.Reactions.Uur; parameter Real h=1 "Hill Coefficient"; @@ -14,7 +14,7 @@ package Hill "Hill reactions kinetics"

Reversible Hill kinetics.

- "), 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 Hillr; model Hillmr "Reversible Hill kinetics with one modifier" @@ -38,7 +38,7 @@ package Hill "Hill reactions kinetics"

Reversible Hill kinetics with one modifier.

- "), 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 Hillmr; model Hillmmr "Reversible Hill kinetics with two modifiers" @@ -65,7 +65,7 @@ package Hill "Hill reactions kinetics"

Reversible Hill kinetics with two modifiers.

- "), 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 Hillmmr; model Hilli "Irreversible Hill kinetics" @@ -79,7 +79,7 @@ package Hill "Hill reactions kinetics"

Irreversible Hill kinetics.

- "), 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 Hilli; annotation(Documentation(info=" @@ -91,5 +91,5 @@ package Hill "Hill reactions kinetics"

- ", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); + ", revisions="")); end Hill; diff --git a/BioChem/Reactions/Inhibition/package.mo b/BioChem/Reactions/Inhibition/package.mo index 41880fc..dfbc1c4 100644 --- a/BioChem/Reactions/Inhibition/package.mo +++ b/BioChem/Reactions/Inhibition/package.mo @@ -16,7 +16,7 @@ package Inhibition "Inhibition kinetics reactions"

Uncompetitive inhibition (reversible).

- "), 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 Uucr; model Uuci "Irreversible uncompetitive inhibition" @@ -31,7 +31,7 @@ package Inhibition "Inhibition kinetics reactions"

Irreversible uncompetitive inhibition.

- "), 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 Uuci; model Usir "Reversible substrate inhibition kinetics" @@ -47,7 +47,7 @@ package Inhibition "Inhibition kinetics reactions"

Reversible substrate inhibition kinetics.

- "), 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 Usir; model Usii "Irreversible substrate inhibition kinetics" @@ -61,7 +61,7 @@ package Inhibition "Inhibition kinetics reactions"

Irreversible substrate inhibition kinetics.

- "), 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 Usii; model Unir "Noncompetitive inhibition (reversible)" @@ -78,7 +78,7 @@ package Inhibition "Inhibition kinetics reactions"

Noncompetitive inhibition (reversible).

- "), 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 Unir; model Unii "Irreversible non-competitive inhibition kinetics" @@ -93,7 +93,7 @@ package Inhibition "Inhibition kinetics reactions"

Irreversible non-competitive inhibition kinetics.

- "), 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 Unii; model Umr "Reversible mixed inhibition kinetics" @@ -111,7 +111,7 @@ package Inhibition "Inhibition kinetics reactions"

Reversible mixed inhibition kinetics.

- "), 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 Umr; model Umi "Irreversible mixed inhibition kinetics" @@ -127,7 +127,7 @@ package Inhibition "Inhibition kinetics reactions"

Irreversible mixed inhibition kinetics.

- "), 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 Umi; model Ucir "Competitive inhibition (reversible)" @@ -144,7 +144,7 @@ package Inhibition "Inhibition kinetics reactions"

Competitive inhibition (reversible).

- "), 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 Ucir; model Ucii "Irreversible competitive inhibition kinetics" @@ -159,7 +159,7 @@ package Inhibition "Inhibition kinetics reactions"

Irreversible competitive inhibition kinetics.

- "), 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 Ucii; model Ualii "Irreversible allosteric inhibition" @@ -176,7 +176,7 @@ package Inhibition "Inhibition kinetics reactions"

Irreversible allosteric inhibition.

- "), 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 Ualii; annotation(Documentation(info=" @@ -191,5 +191,5 @@ In this package, different types of irreversible and reversible inhibition react - ", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); + ", revisions="")); end Inhibition; diff --git a/BioChem/Reactions/MassAction/Irreversible/BiBi/package.mo b/BioChem/Reactions/MassAction/Irreversible/BiBi/package.mo index 456b8f5..93b905e 100644 --- a/BioChem/Reactions/MassAction/Irreversible/BiBi/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/BiBi/package.mo @@ -1,7 +1,7 @@ within BioChem.Reactions.MassAction.Irreversible; package BiBi "A+B -> C+D reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Bbifi "Bi-bi irrerversible forward inhibition reaction" extends BioChem.Interfaces.Reactions.Bbi; @@ -9,10 +9,6 @@ package BiBi "A+B -> C+D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Bbifi; model Bbifafi "Bi-bi irrerversible forward activation, forward inhibition reaction" @@ -22,10 +18,6 @@ package BiBi "A+B -> C+D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Bbifafi; model Bbifa "Bi-bi irrerversible forward activation reaction" @@ -34,10 +26,6 @@ package BiBi "A+B -> C+D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Bbifa; model Bbi "Bi-bi irrerversible reaction" @@ -45,15 +33,9 @@ package BiBi "A+B -> C+D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Bbi; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with two reactants and two products.

-"), - 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 BiBi; diff --git a/BioChem/Reactions/MassAction/Irreversible/BiTri/package.mo b/BioChem/Reactions/MassAction/Irreversible/BiTri/package.mo index 4d41823..60935da 100644 --- a/BioChem/Reactions/MassAction/Irreversible/BiTri/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/BiTri/package.mo @@ -1,7 +1,7 @@ within BioChem.Reactions.MassAction.Irreversible; package BiTri "A+B -> C+D+E reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Btifi "Bi-tri irrerversible forward inhibition reaction" extends BioChem.Interfaces.Reactions.Bti; @@ -9,10 +9,6 @@ package BiTri "A+B -> C+D+E reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Btifi; model Btifafi "Bi-tri irrerversible forward activation, forward inhibition reaction" @@ -22,10 +18,6 @@ package BiTri "A+B -> C+D+E reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Btifafi; model Btifa "Bi-tri irrerversible forward activation reaction" @@ -34,10 +26,6 @@ package BiTri "A+B -> C+D+E reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Btifa; model Bti "Bi-tri irrerversible reaction" @@ -45,15 +33,9 @@ package BiTri "A+B -> C+D+E reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Bti; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with two reactants and three products.

-"), - 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 BiTri; diff --git a/BioChem/Reactions/MassAction/Irreversible/BiUni/package.mo b/BioChem/Reactions/MassAction/Irreversible/BiUni/package.mo index 8c4c52b..15e7d0a 100644 --- a/BioChem/Reactions/MassAction/Irreversible/BiUni/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/BiUni/package.mo @@ -1,7 +1,7 @@ within BioChem.Reactions.MassAction.Irreversible; package BiUni "A+B -> C reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Buifi "Bi-uni irrerversible forward inhibition reaction" extends BioChem.Interfaces.Reactions.Bui; @@ -9,10 +9,6 @@ package BiUni "A+B -> C reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Buifi; model Buifafi "Bi-uni irrerversible forward activation, forward inhibition reaction" @@ -22,10 +18,6 @@ package BiUni "A+B -> C reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Buifafi; model Buifa "Bi-uni irrerversible forward activation reaction" @@ -34,10 +26,6 @@ package BiUni "A+B -> C reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Buifa; model Bui "Bi-uni irrerversible reaction" @@ -45,15 +33,9 @@ package BiUni "A+B -> C reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - annotation( - Documentation, - 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 Bui; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with two reactants and one product.

-"), - 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 BiUni; diff --git a/BioChem/Reactions/MassAction/Irreversible/TriBi/package.mo b/BioChem/Reactions/MassAction/Irreversible/TriBi/package.mo index 9fd550c..f68d40b 100644 --- a/BioChem/Reactions/MassAction/Irreversible/TriBi/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/TriBi/package.mo @@ -1,7 +1,7 @@ within BioChem.Reactions.MassAction.Irreversible; package TriBi "A+B+C -> D+E reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Tbifi "Tri-bi irrerversible forward inhibition reaction" extends BioChem.Interfaces.Reactions.Tbi; @@ -9,10 +9,6 @@ package TriBi "A+B+C -> D+E reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Tbifi; model Tbifafi "Tri-bi irrerversible forward activation, forward inhibition reaction" @@ -22,10 +18,6 @@ package TriBi "A+B+C -> D+E reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Tbifafi; model Tbifa "Tri-bi irrerversible forward activation reaction" @@ -34,10 +26,6 @@ package TriBi "A+B+C -> D+E reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Tbifa; model Tbi "Tri-bi irrerversible reaction" @@ -45,15 +33,9 @@ package TriBi "A+B+C -> D+E reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Tbi; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with three reactants and two products

-"), - 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 TriBi; diff --git a/BioChem/Reactions/MassAction/Irreversible/TriTri/package.mo b/BioChem/Reactions/MassAction/Irreversible/TriTri/package.mo index 06f03f3..572e902 100644 --- a/BioChem/Reactions/MassAction/Irreversible/TriTri/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/TriTri/package.mo @@ -9,10 +9,6 @@ package TriTri "A+B+C -> D+E+F reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Ttifi; model Ttifafi "Tri-tri irrerversible forward activation, forward inhibition reaction" @@ -22,10 +18,6 @@ package TriTri "A+B+C -> D+E+F reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Ttifafi; model Ttifa "Tri-tri irrerversible forward activation reaction" @@ -34,10 +26,6 @@ package TriTri "A+B+C -> D+E+F reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Ttifa; model Tti "Tri-tri irrerversible reaction" @@ -45,15 +33,9 @@ package TriTri "A+B+C -> D+E+F reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Tti; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with three reactants and three products.

-"), - 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 TriTri; diff --git a/BioChem/Reactions/MassAction/Irreversible/TriUni/package.mo b/BioChem/Reactions/MassAction/Irreversible/TriUni/package.mo index 9098a74..f5b398b 100644 --- a/BioChem/Reactions/MassAction/Irreversible/TriUni/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/TriUni/package.mo @@ -1,7 +1,7 @@ within BioChem.Reactions.MassAction.Irreversible; package TriUni "A+B+C -> D reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Tuifi "Tri-uni irrerversible forward inhibition reaction" extends BioChem.Interfaces.Reactions.Tui; @@ -9,10 +9,6 @@ package TriUni "A+B+C -> D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Tuifi; model Tuifafi "Tri-uni irrerversible forward activation, forward inhibition reaction" @@ -22,10 +18,6 @@ package TriUni "A+B+C -> D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Tuifafi; model Tuifa "Tri-uni irrerversible forward activation reaction" @@ -34,10 +26,6 @@ package TriUni "A+B+C -> D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Tuifa; model Tui "Tri-uni irrerversible reaction" @@ -45,15 +33,9 @@ package TriUni "A+B+C -> D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - annotation( - Documentation, - 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 Tui; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with three reactants and one product.

-"), - 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 TriUni; diff --git a/BioChem/Reactions/MassAction/Irreversible/UniBi/package.mo b/BioChem/Reactions/MassAction/Irreversible/UniBi/package.mo index c86cb20..1339983 100644 --- a/BioChem/Reactions/MassAction/Irreversible/UniBi/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/UniBi/package.mo @@ -1,7 +1,7 @@ within BioChem.Reactions.MassAction.Irreversible; package UniBi "A -> B+C reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Ubifi "Uni-bi irrerversible forward inhibition reaction" extends BioChem.Interfaces.Reactions.Ubi; @@ -9,10 +9,6 @@ package UniBi "A -> B+C reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V; - annotation( - Documentation, - 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 Ubifi; model Ubifafi "Uni-bi irrerversible forward activation, forward inhibition reaction" @@ -22,10 +18,6 @@ package UniBi "A -> B+C reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V; - annotation( - Documentation, - 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 Ubifafi; model Ubifa "Uni-bi irrerversible forward activation reaction" @@ -41,9 +33,7 @@ package UniBi "A -> B+C reactions"
  • Main Author 2006: Erik Ulfhielm
  • Main Author 2004-2005: Emma Larsdotter Nilsson
    • -"), - 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 Ubifa; model Ubi "Uni-bi irrerversible reaction" @@ -58,9 +48,7 @@ package UniBi "A -> B+C reactions"
  • Main Author 2006: Erik Ulfhielm
  • Main Author 2004-2005: Emma Larsdotter Nilsson
    • -"), - 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 Ubi; annotation( Documentation(info = " diff --git a/BioChem/Reactions/MassAction/Irreversible/UniTri/package.mo b/BioChem/Reactions/MassAction/Irreversible/UniTri/package.mo index 1b15c1d..b780b03 100644 --- a/BioChem/Reactions/MassAction/Irreversible/UniTri/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/UniTri/package.mo @@ -1,7 +1,7 @@ within BioChem.Reactions.MassAction.Irreversible; package UniTri "A -> B+C+D reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Utifi "Uni-tri irrerversible forward inhibition reaction" extends BioChem.Interfaces.Reactions.Uti; @@ -9,10 +9,6 @@ package UniTri "A -> B+C+D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V; - annotation( - Documentation, - 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 Utifi; model Utifafi "Uni-tri irrerversible forward activation, forward inhibition reaction" @@ -22,10 +18,6 @@ package UniTri "A -> B+C+D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V; - annotation( - Documentation, - 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 Utifafi; model Utifa "Uni-tri irrerversible forward activation reaction" @@ -34,10 +26,6 @@ package UniTri "A -> B+C+D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V; - annotation( - Documentation, - 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 Utifa; model Uti "Uni-tri irrerversible reaction" @@ -45,15 +33,9 @@ package UniTri "A -> B+C+D reactions" parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V; - annotation( - Documentation, - 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 Uti; annotation( Documentation(info = "

    This package contains models for stoichiometric reactions with one reactant and three products.

    -"), - 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 UniTri; diff --git a/BioChem/Reactions/MassAction/Irreversible/UniUni/package.mo b/BioChem/Reactions/MassAction/Irreversible/UniUni/package.mo index 5a1f5cf..7a62243 100644 --- a/BioChem/Reactions/MassAction/Irreversible/UniUni/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/UniUni/package.mo @@ -1,14 +1,13 @@ within BioChem.Reactions.MassAction.Irreversible; package UniUni "A -> B reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Uuifi "Uni-uni irrerversible forward inhibition reaction" extends BioChem.Interfaces.Reactions.Uui; extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; equation rr=k1/iF1.c*s1.c^nS1*s1.V; - annotation(Documentation(), 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 Uuifi; model Uuifafi "Uni-uni irrerversible forward activation, forward inhibition reaction" @@ -18,7 +17,6 @@ package UniUni "A -> B reactions" parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; equation rr=k1*aF1.c/iF1.c*s1.c^nS1*s1.V; - annotation(Documentation(), 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 Uuifafi; model Uuifa "Uni-uni irrerversible forward activation reaction" @@ -27,7 +25,6 @@ package UniUni "A -> B reactions" parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; equation rr=k1*aF1.c*s1.c^nS1*s1.V; - annotation(Documentation(), 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 Uuifa; model Uui "Uni-uni irrerversible reaction" @@ -35,10 +32,9 @@ package UniUni "A -> B reactions" parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; equation rr=k1*s1.c^nS1*s1.V; - annotation(Documentation(), 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; annotation(Documentation(info="

    This package contains models for stoichiometric reactions with one reactant and one product.

    -"), 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 UniUni; diff --git a/BioChem/Reactions/MassAction/Irreversible/package.mo b/BioChem/Reactions/MassAction/Irreversible/package.mo index 16907db..cce1a64 100644 --- a/BioChem/Reactions/MassAction/Irreversible/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/package.mo @@ -1,27 +1,10 @@ within BioChem.Reactions.MassAction; package Irreversible "Irreversible reactions" - extends Icons.Library; - - - - - - - - - - - - - - - + extends BioChem.Icons.Library; annotation( Documentation(info = "

    This package contains models for irreversible reactions with one to three reactants and products.

    - "), - 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 Irreversible; diff --git a/BioChem/Reactions/MassAction/Reversible/package.mo b/BioChem/Reactions/MassAction/Reversible/package.mo index 1254f02..d5feaf2 100644 --- a/BioChem/Reactions/MassAction/Reversible/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/package.mo @@ -1,10 +1,10 @@ within BioChem.Reactions.MassAction; package Reversible "Reversible reactions" - extends Icons.Library; + extends BioChem.Icons.Library; package UniUni "A <-> B reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Uurfibi "Uni-uni reversible forward inhibition, backward inhibition reaction" extends BioChem.Interfaces.Reactions.Uur; @@ -14,10 +14,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfibi; model Uurfibabi "Uni-uni reversible forward inhibition, backward activation, backward inhibition reaction" @@ -29,10 +25,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfibabi; model Uurfiba "Uni-uni reversible forward inhibition, backward activation reaction" @@ -43,10 +35,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfiba; model Uurfi "Uni-uni reversible forward inhibition reaction" @@ -56,10 +44,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfi; model Uurfafibi "Uni-uni reversible forward activation, forward inhibition, backward inhibition reaction" @@ -71,10 +55,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfafibi; model Uurfafibabi "Uni-uni reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" @@ -87,10 +67,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfafibabi; model Uurfafiba "Uni-uni reversible forward activation, forward inhibition, backward activation reaction" @@ -102,10 +78,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfafiba; model Uurfafi "Uni-uni reversible forward activation, forward inhibition reaction" @@ -116,10 +88,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfafi; model Uurfabi "Uni-uni reversible forward activation, backward inhibition reaction" @@ -130,10 +98,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfabi; model Uurfababi "Uni-uni reversible forward activation, backward activation, backward inhibition reaction" @@ -145,10 +109,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfababi; model Uurfaba "Uni-uni reversible forward activation, backward activation reaction" @@ -159,10 +119,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfaba; model Uurfa "Uni-uni reversible forward activation reaction" @@ -172,10 +128,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurfa; model Uurbi "Uni-uni reversible backward inhibition reaction" @@ -185,10 +137,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurbi; model Uurbabi "Uni-uni reversible backward activation, backward inhibition reaction" @@ -199,10 +147,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurbabi; model Uurba "Uni-uni reversible backward activation reaction" @@ -212,10 +156,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Uurba; model Uur "Uni-uni reversible reaction" @@ -224,21 +164,15 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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; annotation( Documentation(info = "

    This package contains models for stoichiometric reactions with one reactant and one product.

    - "), - 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 UniUni; package UniTri "A <-> B+C+D reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Utrfibi "Uni-tri reversible forward inhibition, backward inhibition reaction" extends BioChem.Interfaces.Reactions.Utr; @@ -248,10 +182,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfibi; model Utrfibabi "Uni-tri reversible forward inhibition, backward activation, backward inhibition reaction" @@ -263,10 +193,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfibabi; model Utrfiba "Uni-tri reversible forward inhibition, backward activation reaction" @@ -277,10 +203,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfiba; model Utrfi "Uni-tri reversible forward inhibition reaction" @@ -290,10 +212,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfi; model Utrfafibi "Uni-tri reversible forward activation, forward inhibition, backward inhibition reaction" @@ -305,10 +223,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfafibi; model Utrfafibabi "Uni-tri reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" @@ -321,10 +235,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfafibabi; model Utrfafiba "Uni-tri reversible forward activation, forward inhibition, backward activation reaction" @@ -336,10 +246,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfafiba; model Utrfafi "Uni-tri reversible forward activation, forward inhibition reaction" @@ -350,10 +256,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfafi; model Utrfabi "Uni-tri reversible forward activation, backward inhibition reaction" @@ -364,10 +266,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfabi; model Utrfababi "Uni-tri reversible forward activation, backward activation, backward inhibition reaction" @@ -379,10 +277,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfababi; model Utrfaba "Uni-tri reversible forward activation, backward activation reaction" @@ -393,10 +287,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfaba; model Utrfa "Uni-tri reversible forward activation reaction" @@ -406,10 +296,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrfa; model Utrbi "Uni-tri reversible backward inhibition reaction" @@ -419,10 +305,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrbi; model Utrbabi "Uni-tri reversible backward activation, backward inhibition reaction" @@ -433,10 +315,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrbabi; model Utrba "Uni-tri reversible backward activation reaction" @@ -446,10 +324,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utrba; model Utr "Uni-tri reversible reaction" @@ -458,17 +332,11 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - 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 Utr; annotation( Documentation(info = "

    This package contains models for stoichiometric reactions with one reactant and three products.

    - "), - 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 UniTri; package UniBi "A <-> B+C reactions" @@ -482,10 +350,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfibi; model Ubrfibabi "Uni-bi reversible forward inhibition, backward activation, backward inhibition reaction" @@ -497,10 +361,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfibabi; model Ubrfiba "Uni-bi reversible forward inhibition, backward activation reaction" @@ -511,10 +371,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfiba; model Ubrfi "Uni-bi reversible forward inhibition reaction" @@ -524,10 +380,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfi; model Ubrfafibi "Uni-bi reversible forward activation, forward inhibition, backward inhibition reaction" @@ -539,10 +391,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfafibi; model Ubrfafibabi "Uni-bi reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" @@ -555,10 +403,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfafibabi; model Ubrfafiba "Uni-bi reversible forward activation, forward inhibition, backward activation reaction" @@ -570,10 +414,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfafiba; model Ubrfafi "Uni-bi reversible forward activation, forward inhibition reaction" @@ -584,10 +424,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfafi; model Ubrfabi "Uni-bi reversible forward activation, backward inhibition reaction" @@ -598,10 +434,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfabi; model Ubrfababi "Uni-bi reversible forward activation, backward activation, backward inhibition reaction" @@ -613,10 +445,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfababi; model Ubrfaba "Uni-bi reversible forward activation, backward activation reaction" @@ -627,10 +455,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfaba; model Ubrfa "Uni-bi reversible forward activation reaction" @@ -640,10 +464,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrfa; model Ubrbi "Uni-bi reversible backward inhibition reaction" @@ -653,10 +473,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrbi; model Ubrbabi "Uni-bi reversible backward activation, backward inhibition reaction" @@ -667,10 +483,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrbabi; model Ubrba "Uni-bi reversible backward activation reaction" @@ -680,10 +492,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubrba; model Ubr "Uni-bi reversible reaction" @@ -692,17 +500,11 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Ubr; annotation( Documentation(info = "

    This package contains models for stoichiometric reactions with one reactant and two products.

    - "), - 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 UniBi; package BiUni "A+B <-> C reactions" @@ -716,10 +518,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfibi; model Burfibabi "Bi-uni reversible forward inhibition, backward activation, backward inhibition reaction" @@ -731,10 +529,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfibabi; model Burfiba "Bi-uni reversible forward inhibition, backward activation reaction" @@ -745,10 +539,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfiba; model Burfi "Bi-uni reversible forward inhibition reaction" @@ -758,10 +548,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfi; model Burfafibi "Bi-uni reversible forward activation, forward inhibition, backward inhibition reaction" @@ -773,10 +559,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfafibi; model Burfafibabi "Bi-uni reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" @@ -789,10 +571,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfafibabi; model Burfafiba "Bi-uni reversible forward activation, forward inhibition, backward activation reaction" @@ -804,10 +582,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfafiba; model Burfafi "Bi-uni reversible forward activation, forward inhibition reaction" @@ -818,10 +592,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfafi; model Burfabi "Bi-uni reversible forward activation, backward inhibition reaction" @@ -832,10 +602,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfabi; model Burfababi "Bi-uni reversible forward activation, backward activation, backward inhibition reaction" @@ -847,10 +613,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfababi; model Burfaba "Bi-uni reversible forward activation, backward activation reaction" @@ -861,10 +623,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfaba; model Burfa "Bi-uni reversible forward activation reaction" @@ -874,10 +632,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burfa; model Burbi "Bi-uni reversible backward inhibition reaction" @@ -887,10 +641,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burbi; model Burbabi "Bi-uni reversible backward activation, backward inhibition reaction" @@ -901,10 +651,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burbabi; model Burba "Bi-uni reversible backward activation reaction" @@ -914,10 +660,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Burba; model Bur "Bi-uni reversible reaction" @@ -926,21 +668,15 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - 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 Bur; annotation( Documentation(info = "

    This package contains models for stoichiometric reactions with two reactants and one product.

    - "), - 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 BiUni; package BiBi "A+B <-> C+D reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Bbrfibi "Bi-bi reversible forward inhibition, backward inhibition reaction" extends BioChem.Interfaces.Reactions.Bbr; @@ -950,10 +686,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfibi; model Bbrfibabi "Bi-bi reversible forward inhibition, backward activation, backward inhibition reaction" @@ -965,10 +697,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfibabi; model Bbrfiba "Bi-bi reversible forward inhibition, backward activation reaction" @@ -979,10 +707,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfiba; model Bbrfi "Bi-bi reversible forward inhibition reaction" @@ -992,10 +716,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfi; model Bbrfafibi "Bi-bi reversible forward activation, forward inhibition, backward inhibition reaction" @@ -1007,10 +727,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfafibi; model Bbrfafibabi "Bi-bi reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" @@ -1023,10 +739,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfafibabi; model Bbrfafiba "Bi-bi reversible forward activation, forward inhibition, backward activation reaction" @@ -1038,10 +750,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfafiba; model Bbrfafi "Bi-bi reversible forward activation, forward inhibition reaction" @@ -1052,10 +760,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfafi; model Bbrfabi "Bi-bi reversible forward activation, backward inhibition reaction" @@ -1066,10 +770,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfabi; model Bbrfababi "Bi-bi reversible forward activation, backward activation, backward inhibition reaction" @@ -1081,10 +781,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfababi; model Bbrfaba "Bi-bi reversible forward activation, backward activation reaction" @@ -1095,10 +791,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfaba; model Bbrfa "Bi-bi reversible forward activation reaction" @@ -1108,10 +800,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrfa; model Bbrbi "Bi-bi reversible backward inhibition reaction" @@ -1121,10 +809,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrbi; model Bbrbabi "Bi-bi reversible backward activation, backward inhibition reaction" @@ -1135,10 +819,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrbabi; model Bbrba "Bi-bi reversible backward activation reaction" @@ -1148,10 +828,6 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbrba; model Bbr "Bi-bi reversible reaction" @@ -1160,28 +836,16 @@ package Reversible "Reversible reactions" parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; equation rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - 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 Bbr; annotation( Documentation(info = "

    This package contains models for stoichiometric reactions with two reactants and two products.

    - "), - 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 BiBi; - - - - annotation( Documentation(info = "

    This package contains models for reversible reactions with one to three reactants and products.

    - "), - 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 Reversible; diff --git a/BioChem/Reactions/MassAction/package.mo b/BioChem/Reactions/MassAction/package.mo index 686ab7a..fac9a86 100644 --- a/BioChem/Reactions/MassAction/package.mo +++ b/BioChem/Reactions/MassAction/package.mo @@ -1,6 +1,6 @@ within BioChem.Reactions; package MassAction "Mass-action kinetics reactions" - extends Icons.Library; + extends BioChem.Icons.Library; annotation(Documentation(info="

    MassAction

    @@ -17,5 +17,5 @@ and then adding an equation for the relation between the reaction rate and the p

    - ", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); + ", revisions="")); end MassAction; diff --git a/BioChem/Reactions/MichaelisMenten/package.mo b/BioChem/Reactions/MichaelisMenten/package.mo index 8a1cd23..4dbdede 100644 --- a/BioChem/Reactions/MichaelisMenten/package.mo +++ b/BioChem/Reactions/MichaelisMenten/package.mo @@ -1,6 +1,6 @@ within BioChem.Reactions; package MichaelisMenten "Michaelis-Menten kinetics reactions" - extends Icons.Library; + extends BioChem.Icons.Library; model Uur "Uni-uni reversible simple Michaelis-Menten" extends BioChem.Interfaces.Reactions.Uur; parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; @@ -13,7 +13,7 @@ package MichaelisMenten "Michaelis-Menten kinetics reactions"

    Uni-uni reversible simple Michaelis-Menten.

    - "), 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; model Uui "Uni-uni irreversible simple Michaelis-Menten" @@ -26,7 +26,7 @@ package MichaelisMenten "Michaelis-Menten kinetics reactions"

    Uni-uni irreversible simple Michaelis-Menten.

    - "), 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; model Uuhr "Uni-Uni reversible simple Michaelis-Menten with Haldane adjustment" @@ -41,7 +41,7 @@ package MichaelisMenten "Michaelis-Menten kinetics reactions"

    Uni-Uni reversible simple Michaelis-Menten with Haldane adjustment.

    - "), 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 Uuhr; model Isouur "Iso uni-uni" @@ -57,7 +57,7 @@ package MichaelisMenten "Michaelis-Menten kinetics reactions"

    Iso uni-uni.

    - "), 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 Isouur; annotation(Documentation(info=" @@ -72,5 +72,5 @@ Michaelis-Menten kinetics describes the kinetics of many enzymes. It is named af
    - ", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); + ", revisions="")); end MichaelisMenten; diff --git a/BioChem/Reactions/package.mo b/BioChem/Reactions/package.mo index b4f0625..7dfae48 100644 --- a/BioChem/Reactions/package.mo +++ b/BioChem/Reactions/package.mo @@ -1,7 +1,7 @@ within BioChem; package Reactions "Reaction edges" - extends Icons.Library; + extends BioChem.Icons.Library; diff --git a/BioChem/Substances/AmbientSubstance.mo b/BioChem/Substances/AmbientSubstance.mo index 799d12f..e4252f1 100644 --- a/BioChem/Substances/AmbientSubstance.mo +++ b/BioChem/Substances/AmbientSubstance.mo @@ -1,6 +1,7 @@ within BioChem.Substances; -model AmbientSubstance "Substance used as a reservoir in reactions" +model AmbientSubstance "Icon for a substance used as a reservoir in reactions" + extends BioChem.Icons.Substances.AmbientSubstance; extends BioChem.Interfaces.Substances.Substance; equation der(n) = 0; @@ -11,7 +12,6 @@ Substance used as a reservoir in reactions.

    Corresponds to the empty list of reactants or the empty list of products in an SBML reaction.

    -"), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {1.77636e-15, 50}, fillPattern = FillPattern.Solid, extent = {{-100, -150}, {100, -100}}, textString = "%name", fontName = "Arial"), Line(points = {{-50, -50}, {50, 50}}, thickness = 10)}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); +")); + end AmbientSubstance; diff --git a/BioChem/Substances/BoundarySubstance.mo b/BioChem/Substances/BoundarySubstance.mo index 13dcbd2..7af6bca 100644 --- a/BioChem/Substances/BoundarySubstance.mo +++ b/BioChem/Substances/BoundarySubstance.mo @@ -1,6 +1,7 @@ within BioChem.Substances; model BoundarySubstance "Substance with a concentration not determined by reactions, but by events" + extends BioChem.Icons.Substances.BoundarySubstance; extends BioChem.Interfaces.Substances.InputSubstance(n.stateSelect = StateSelect.prefer, c.stateSelect = StateSelect.prefer); equation der(n) = 0; @@ -12,7 +13,5 @@ The concentration of the substance can only be changed by events.

    Corresponds to SBML species not changed by any SBML rules and with either or both of the boundaryCondition and fixed attributes set to true

    -"), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {-1.42109e-14, 50}, fillPattern = FillPattern.Solid, extent = {{-100, -150}, {100, -100}}, textString = "%name", fontName = "Arial"), Ellipse(lineColor = {170, 0, 0}, fillColor = {255, 0, 0}, fillPattern = FillPattern.Sphere, extent = {{-50, -50}, {50, 50}})}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); +")); end BoundarySubstance; diff --git a/BioChem/Substances/SignalSubstance.mo b/BioChem/Substances/SignalSubstance.mo index 25a7289..be056ee 100644 --- a/BioChem/Substances/SignalSubstance.mo +++ b/BioChem/Substances/SignalSubstance.mo @@ -1,6 +1,7 @@ within BioChem.Substances; -model SignalSubstance "Substance with a concentration not determined by reactions, but by external equations (translated into SBML assignments)" +model SignalSubstance "Icon for a substance with a concentration not determined by reactions, but by external equations (translated into SBML assignments)" + extends BioChem.Icons.Substances.SignalSubstance; extends BioChem.Interfaces.Substances.InputSubstance; annotation( Documentation(info = " @@ -9,7 +10,5 @@ Substance with a concentration not determined by reactions, instead the substanc

    Corresponds to SBML species changed by any SBML rules.

    -"), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {7.10543e-15, 50}, fillPattern = FillPattern.Solid, extent = {{-100, -150}, {100, -100}}, textString = "%name", fontName = "Arial"), Ellipse(lineColor = {0, 0, 127}, fillColor = {85, 170, 255}, fillPattern = FillPattern.Sphere, extent = {{-50, -50}, {50, 50}})}), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); +")); end SignalSubstance; diff --git a/BioChem/Substances/Substance.mo b/BioChem/Substances/Substance.mo index 13d967a..414dbcc 100644 --- a/BioChem/Substances/Substance.mo +++ b/BioChem/Substances/Substance.mo @@ -1,6 +1,7 @@ within BioChem.Substances; model Substance "Substance with variable concentration" + extends BioChem.Icons.Substances.Substance; extends BioChem.Interfaces.Substances.Substance; equation der(n)=rNet; @@ -8,5 +9,5 @@ equation

    A substance with variable concentration.

    -"), Icon(coordinateSystem(extent={{-100,-100},{100,100}}, preserveAspectRatio=true, grid={10,10}), graphics={Text(origin={7.10543e-15,50}, fillPattern=FillPattern.Solid, extent={{-100,-150},{100,-100}}, textString="%name", fontName="Arial"),Ellipse(lineColor={0,85,0}, fillColor={0,170,0}, fillPattern=FillPattern.Sphere, extent={{-50,-50},{50,50}})}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); +")); end Substance; diff --git a/BioChem/Substances/package.mo b/BioChem/Substances/package.mo index 55341ae..544e660 100644 --- a/BioChem/Substances/package.mo +++ b/BioChem/Substances/package.mo @@ -1,7 +1,7 @@ within BioChem; package Substances "Reaction nodes" - extends BioChem.Icons.Substances.PackageIcon; + extends BioChem.Icons.Substances; annotation( Documentation(info = " @@ -25,43 +25,11 @@ The is a substance used as a reservoir in reactions. This corresponds to the empty list of reactants or the empty list of products in an SBML reaction. When the concentration is not determined by reactions, the -SignalSubstance - model is used. Then the substance concentration is regulated by external equations, and it corresponds to SBML species changed by any SBML rules. -

    - -\"Fig1: -", revisions = ""), - 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}))); - -/* - annotation( - Documentation(info = " -

    Substances

    -

    - This package contains different types of nodes needed for representing a substance in a biochemical pathway. - Substances are connected to reactions through connectors placed - on the rim of the circle representing the substance.
    -The substance models are specified by extending the partial models of substance nodes in -Substances - and adding additional attributes and equations. -The -Substances - - model is used when the concentration in a substance node is allowed to change without restrictions during a simulation, while - -BoundarySubstances - is used when the concentration can only be changed using events. This correspond to species with the fixed or boundary attribute set in SBML.
    -The -AmbientSubstance - is a substance used as a reservoir in reactions. This corresponds to the empty list of reactants or the empty list of products in an SBML reaction. -When the concentration is not determined by reactions, the - SignalSubstance model is used. Then the substance concentration is regulated by external equations, and it corresponds to SBML species changed by any SBML rules.

    \"Fig1: ", revisions = "")); -*/ + end Substances; diff --git a/BioChem/Units/package.mo b/BioChem/Units/package.mo index 23b8d44..90fba10 100644 --- a/BioChem/Units/package.mo +++ b/BioChem/Units/package.mo @@ -1,42 +1,33 @@ within BioChem; package Units "Units used in BioChem" - extends BioChem.Icons.Units.PackageIcon; - type VolumetricReactionRate = - Icons.Units.TypeRealBase(final quantity="Volumetric reaction rate",final unit = "mol/(s.l)") - "Volumetric reaction rate [mol/(l.s)}" ; - type VolumeChangeConstant = Icons.Units.TypeRealBase(quantity = "Volume change constant", unit = "l/s") "Volume change constant [1/s]" ; - type Volume "Volume [l]" - extends Modelica.Units.NonSI.Volume_litre; - annotation(Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Volume; - type StoichiometricCoefficient = Icons.Units.TypeRealBase(quantity = "Stoichiometric coefficient", unit = "1") "Stoichiometric coefficient"; - type ReactionRate = Icons.Units.TypeRealBase(quantity = "Reaction rate", unit = "mol/s") "Reaction rate [mos/s]"; - type ReactionCoefficient = Icons.Units.TypeRealBase(quantity = "Reaction coefficient", unit = "1") "Reaction coefficient" ; - type Pressure - extends Modelica.Units.SI.Pressure; - annotation(Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Pressure; - type MolarFlowRate = Icons.Units.TypeRealBase(quantity = "Molar flow rate", unit = "mol/s") "Molar flow rate [mol/s]" ; - type IonicCharge = Icons.Units.TypeIntegerBase(quantity = "Ionic charge", unit = "1") "Ionic charge"; - type DilutionRate = Icons.Units.TypeRealBase(quantity = "Dilution rate", unit = "/s") "Dilution rate [?]" ; - type Concentration = Icons.Units.TypeRealBase(quantity = "Concentration", unit = "mol/l", min = 0) "Concentration [mol/l]" ; + extends BioChem.Icons.Units; + type AmountOfSubstance = Icons.Units.TypeRealBase(quantity = "AmountOfSubstance", unit = "mol", min = 0) "Amount of substance [mol]" ; type Celcius extends Modelica.Units.NonSI.Temperature_degC ; annotation(Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end Celcius; - type AmountOfSubstance = Icons.Units.TypeRealBase(quantity = "AmountOfSubstance", unit = "mol", min = 0) "Amount of substance [mol]" ; + type Concentration = Icons.Units.TypeRealBase(quantity = "Concentration", unit = "mol/l", min = 0) "Concentration [mol/l]" ; + type DilutionRate = Icons.Units.TypeRealBase(quantity = "Dilution rate", unit = "/s") "Dilution rate [?]" ; type EquilibriumCoefficient = Icons.Units.TypeRealBase(quantity = "Equilibrium coefficient", unit = "1") ""; - annotation( - Documentation(info = " -

    Units

    -

    - This pace contains definitions of units that are common in biochemical models. -

    - ", revisions = ""), - 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}))); + type IonicCharge = Icons.Units.TypeIntegerBase(quantity = "Ionic charge", unit = "1") "Ionic charge"; + type MolarFlowRate = Icons.Units.TypeRealBase(quantity = "Molar flow rate", unit = "mol/s") "Molar flow rate [mol/s]" ; + type Pressure + extends Modelica.Units.SI.Pressure; + annotation(Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); + end Pressure; + type ReactionCoefficient = Icons.Units.TypeRealBase(quantity = "Reaction coefficient", unit = "1") "Reaction coefficient" ; + type ReactionRate = Icons.Units.TypeRealBase(quantity = "Reaction rate", unit = "mol/s") "Reaction rate [mos/s]"; + type StoichiometricCoefficient = Icons.Units.TypeRealBase(quantity = "Stoichiometric coefficient", unit = "1") "Stoichiometric coefficient"; + type Volume "Volume [l]" + extends Modelica.Units.NonSI.Volume_litre; + annotation(Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); + end Volume; + type VolumeChangeConstant = Icons.Units.TypeRealBase(quantity = "Volume change constant", unit = "l/s") "Volume change constant [1/s]" ; + type VolumetricReactionRate = + Icons.Units.TypeRealBase(final quantity="Volumetric reaction rate",final unit = "mol/(s.l)") + "Volumetric reaction rate [mol/(l.s)}" ; annotation( Documentation(info = "

    Units

    diff --git a/BioChem/Units/package.order b/BioChem/Units/package.order index b395494..5c6ef6c 100644 --- a/BioChem/Units/package.order +++ b/BioChem/Units/package.order @@ -1,14 +1,14 @@ -VolumetricReactionRate -VolumeChangeConstant -Volume -StoichiometricCoefficient -ReactionRate -ReactionCoefficient -Pressure -MolarFlowRate -IonicCharge -DilutionRate -Concentration -Celcius AmountOfSubstance +Celcius +Concentration +DilutionRate EquilibriumCoefficient +IonicCharge +MolarFlowRate +Pressure +ReactionCoefficient +ReactionRate +StoichiometricCoefficient +Volume +VolumeChangeConstant +VolumetricReactionRate