release 1.1.1 (#37)

* new release version 1.1.1 * minor improvements (#36) * Delete BioChem/Icons/Substances/PackageIcon directory * Delete BioChem/Icons/Substances/Package directory * removing unnecessary extend statement * Introducing a basic ChemicalPort without being expressed in terms of Cell volume. * new release version 1.1.1 * remove unnecessary documentation * removing unnecessary annotations * unnecessary annotations
OpenModelica · May 8, 2021 · e1e3458 · e1e3458
1 parent 1bf14bd
commit e1e3458
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diff --git a/BioChem/Icons/Base.mo b/BioChem/Icons/Base.mo
@@ -4,6 +4,4 @@ partial class Base
   annotation(Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), 
     Documentation(info = "<html><head></head><body><font size=\"5\">A base icon relevant for many components carrying the same annotations. Older annotations had the following attribute:</font><div><br></div><div>
 <pre style=\"margin-top: 0px; margin-bottom: 0px;\"><!--StartFragment--><span style=\" font-family:'Courier New'; font-size:12pt; color:#0000ff;\">Diagram</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">(</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#0000ff;\">coordinateSystem</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">(extent={{-</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">100.0</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">,-</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">100.0</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">},{</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">100.0</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">,</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">100.0</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">}}, preserveAspectRatio=</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b0000;\">true</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">, grid={</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">10</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">,</span><span style=\" font-family:'Courier New'; font-size:12pt; color:#8b008b;\">10</span><span style=\"font-family: 'Courier New'; font-size: 12pt;\">}))</span><!--EndFragment--></pre><pre style=\"margin-top: 0px; margin-bottom: 0px;\"><span style=\"font-family: 'Courier New'; font-size: 12pt;\"><br></span></pre><p><span style=\"font-size: 12pt;\"><font face=\"Arial\">Since this produces empty diagram, it is not clear why is it there. So it is there for now.&nbsp;</font></span></p><p><span style=\"font-size: 12pt;\"><font face=\"Arial\">This Icon will also replace Icons.IconBase, which does not seem to be used throughout the library.&nbsp;</font></span></p><pre style=\"margin-top: 0px; margin-bottom: 0px;\"><br></pre></div></body></html>"));
-
-
 end Base;
diff --git a/BioChem/Icons/Substances/AmbientSubstance.mo b/BioChem/Icons/Substances/AmbientSubstance.mo
@@ -1,7 +1,7 @@
 within BioChem.Icons.Substances;
 
 partial class AmbientSubstance "Substance used as a reservoir in reactions"
- extends Icons.Base;
+ extends BioChem.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
@@ -1,8 +1,7 @@
 within BioChem.Icons.Substances;
 
 partial class BoundarySubstance "Icon for a substance with a concentration not determined by reactions, but by events"
-  extends Icons.Base; 
+  extends BioChem.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})));
+    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}})}));
 end BoundarySubstance;
diff --git a/BioChem/Icons/Substances/PackageIcon/package.order b/BioChem/Icons/Substances/PackageIcon/package.order
diff --git a/BioChem/Icons/Substances/SignalSubstance.mo b/BioChem/Icons/Substances/SignalSubstance.mo
@@ -1,15 +1,7 @@
 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;
+partial class SignalSubstance "Icon for a substance with a concentration not determined by reactions, but by external equations (translated into SBML assignments)"
+  extends BioChem.Icons.Base;
   annotation(
-    Documentation(info = "<html>
-<p>
-Substance with a concentration not determined by reactions, instead the substance consentration is regulated by external equations.
-<p>
-Corresponds to SBML species changed by any SBML rules.
-</p>
-</html>"),
-    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})));
+    Icon(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}})}));
 end SignalSubstance;
diff --git a/BioChem/Icons/Units/package.mo b/BioChem/Icons/Units/package.mo
@@ -1,8 +1,7 @@
 within BioChem.Icons;
 
 partial package Units "Icon for the Units Package"
-  extends Icons.Library;
-  extends Icons.Base;
+  extends BioChem.Icons.Library;
   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/Interfaces/Nodes/ActivatorConnector.mo b/BioChem/Interfaces/Nodes/ActivatorConnector.mo
@@ -2,7 +2,6 @@ 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;
+  extends ChemicalPort;
   input BioChem.Units.Volume V;
 end ActivatorConnector;
diff --git a/BioChem/Interfaces/Nodes/ChemicalPort.mo b/BioChem/Interfaces/Nodes/ChemicalPort.mo
@@ -0,0 +1,6 @@
+within BioChem.Interfaces.Nodes;
+
+connector ChemicalPort
+  BioChem.Units.Concentration c;
+  flow BioChem.Units.MolarFlowRate r;
+end ChemicalPort;
diff --git a/BioChem/Interfaces/Nodes/InhibitorConnector.mo b/BioChem/Interfaces/Nodes/InhibitorConnector.mo
@@ -2,7 +2,6 @@ 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;
+  extends ChemicalPort;
   input BioChem.Units.Volume V;
 end InhibitorConnector;
diff --git a/BioChem/Interfaces/Nodes/ModifierConnector.mo b/BioChem/Interfaces/Nodes/ModifierConnector.mo
@@ -2,7 +2,6 @@ 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;
+  extends ChemicalPort;
   input BioChem.Units.Volume V;
 end ModifierConnector;
diff --git a/BioChem/Interfaces/Nodes/ProductConnector.mo b/BioChem/Interfaces/Nodes/ProductConnector.mo
@@ -2,7 +2,6 @@ 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;
+  extends ChemicalPort;
   input BioChem.Units.Volume V;
 end ProductConnector;
diff --git a/BioChem/Interfaces/Nodes/SubstanceConnector.mo b/BioChem/Interfaces/Nodes/SubstanceConnector.mo
@@ -2,7 +2,6 @@ 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;
+  extends ChemicalPort;
   output BioChem.Units.Volume V;
 end SubstanceConnector;
diff --git a/BioChem/Interfaces/Nodes/SubstrateConnector.mo b/BioChem/Interfaces/Nodes/SubstrateConnector.mo
@@ -2,7 +2,6 @@ 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;
+  extends ChemicalPort;
   input BioChem.Units.Volume V;
 end SubstrateConnector;
diff --git a/BioChem/Interfaces/Nodes/package.order b/BioChem/Interfaces/Nodes/package.order
@@ -1,3 +1,4 @@
+ChemicalPort
 ActivatorConnector
 InhibitorConnector
 ModifierConnector

diff --git a/BioChem/Substances/package.mo b/BioChem/Substances/package.mo
@@ -31,4 +31,4 @@ When the concentration is not determined by reactions, the
 <a name=\"fig1\"></a>
 <img src=\"modelica://BioChem/Resources/Images/Substance.png\" alt=\"Fig1: Substance\">
 </html></html>", revisions = ""));
-end Substances;
+end Substances;
diff --git a/BioChem/UsersGuide/ReleaseNotes.mo b/BioChem/UsersGuide/ReleaseNotes.mo
@@ -3,5 +3,5 @@ within BioChem.UsersGuide;
 class ReleaseNotes
   extends Modelica.Icons.ReleaseNotes;
   annotation(
-    Documentation(info = "<html><head></head><body><h2>History</h2><p>The first version of the library was created by Emma Larsdotter Nilsson at Linköping University. The current version of the library has been further developed by Erik Ulfhielm at Linköping University, and by MathCore Engineering AB.</p><ul><li>Main Author 2020-2021: Atiyah Elsheikh (Mathemodica.com) &amp; Martin Sjölund (Linköping University)</li><li>Main Author 2007-2009: MathCore Engineering AB</li><li>Main Author 2006: Erik Ulfhielm</li><li>Main Author 2004-2005: Emma Larsdotter Nilsson</li></ul><p><br></p><h2>Versions</h2><ul><li>Version 1.1.0 (2021-05-02)<ul><li>Moving, simplifying and cleaning embedded graphical annotations to own package Icons&nbsp;</li><li>A UsersGuide package&nbsp;</li><li>improved implementation of Units package &nbsp;</li></ul></li><li>Version 1.0.3 (2021-04-06)<ul><li>Conversion script to MSL 4.0.0</li></ul></li><li>Version 1.0.2 (2020-06-02)<ul><li>All major components are separated into *.mo files</li><li>MSL 3.2.3</li></ul></li><li>Version 1.0.1 (2013-04-18)<ul><li>Applied patch to latest version provided by MathCore Engineering AB.</li><li>Changed uses-annotation to MSL 3.2, encoding to ASCII+HTML entities, and started using modelica:// URLs for image sources (Martin Sjölund).</li></ul></li><li>Version 1.0 (2009-08-31)</li><li>Version 0.96 (2008-12-19)</li></ul></body></html>"));
+    Documentation(info = "<html><head></head><body><h2>History</h2><p>The first version of the library was created by Emma Larsdotter Nilsson at Linköping University. The current version of the library has been further developed by Erik Ulfhielm at Linköping University, and by MathCore Engineering AB.</p><ul><li>Main Author 2020-2021: Atiyah Elsheikh (Mathemodica.com) &amp; Martin Sjölund (Linköping University)</li><li>Main Author 2007-2009: MathCore Engineering AB</li><li>Main Author 2006: Erik Ulfhielm</li><li>Main Author 2004-2005: Emma Larsdotter Nilsson</li></ul><p><br></p><h2>Versions</h2><ul><li>Version 1.1.1 (2021-05-08)<ul><li>Removing a bug in the Icons package and minor improvements</li></ul></li><li>Version 1.1.0 (2021-05-02)<ul><li>Moving, simplifying and cleaning embedded graphical annotations to own package Icons&nbsp;</li><li>A UsersGuide package&nbsp;</li><li>improved implementation of Units package &nbsp;</li></ul></li><li>Version 1.0.3 (2021-04-06)<ul><li>Conversion script to MSL 4.0.0</li></ul></li><li>Version 1.0.2 (2020-06-02)<ul><li>All major components are separated into *.mo files</li><li>MSL 3.2.3</li></ul></li><li>Version 1.0.1 (2013-04-18)<ul><li>Applied patch to latest version provided by MathCore Engineering AB.</li><li>Changed uses-annotation to MSL 3.2, encoding to ASCII+HTML entities, and started using modelica:// URLs for image sources (Martin Sjölund).</li></ul></li><li>Version 1.0 (2009-08-31)</li><li>Version 0.96 (2008-12-19)</li></ul></body></html>"));
 end ReleaseNotes;
diff --git a/BioChem/package.mo b/BioChem/package.mo
@@ -17,7 +17,7 @@ Users Guide discusses some aspects of the <em>BioChem</em> Library, including a
 </ul>
  </body></html>"),
     uses(Modelica(version = "4.0.0")),
-    version = "1.1.0",
+    version = "1.1.1",
     Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Line(origin = {3.55271e-15, 3.76}, points = {{-50, -60}, {-50, -27.52}, {10, -27.52}}, smooth = Smooth.Bezier), Line(origin = {-1.135, 4.09474}, points = {{-48.865, 10}, {-48.865, -27.61}, {11.135, -27.61}}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 30, smooth = Smooth.Bezier), Ellipse(origin = {30.4112, -23.4648}, lineColor = {0, 85, 0}, fillColor = {0, 170, 0}, fillPattern = FillPattern.Sphere, extent = {{-20.4112, -20}, {20.4112, 20}}), Ellipse(origin = {6.28735, -0.665395}, lineColor = {161, 107, 0}, fillColor = {250, 167, 0}, fillPattern = FillPattern.Sphere, extent = {{-76.2873, -79.3346}, {-35.4736, -39.3346}}), Ellipse(origin = {4.98569, -1.03187}, lineColor = {117, 0, 0}, fillColor = {170, 0, 0}, fillPattern = FillPattern.Sphere, extent = {{-75.8122, -6.13331}, {-34.9857, 33.8667}})}),
     Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})));
 end BioChem;