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6 changes: 3 additions & 3 deletions BioChem/Compartments/Compartment.mo
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
within BioChem.Compartments;

model Compartment "Default compartment (constant volume)"
extends BioChem.Interfaces.Compartments.Compartment(V(stateSelect=StateSelect.prefer));
equation
der(V)=0 "Compartment volume is constant";
annotation(Documentation(info="<html>
<h1>Compartment</h1>
<p>
Default compartment model.
</p>
</html>", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Text(fillColor={0,85,0}, fillPattern=FillPattern.Solid, extent={{-100,-170},{100,-120}}, textString="%name", fontName="Arial"),Rectangle(lineColor={0,85,0}, fillColor={199,199,149}, fillPattern=FillPattern.Solid, lineThickness=10, extent={{-110,-110},{110,110}}, radius=20)}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
extends BioChem.Interfaces.Compartments.Compartment(V(stateSelect=StateSelect.prefer));
equation
der(V)=0 "Compartment volume is constant";
end Compartment;
2 changes: 1 addition & 1 deletion BioChem/Interfaces/Reactions/Basics/FourSubstrates.mo
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
within BioChem.Interfaces.Reactions.Basics;

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})));
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;
2 changes: 1 addition & 1 deletion BioChem/Interfaces/Reactions/Basics/OneSubstrate.mo
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
within BioChem.Interfaces.Reactions.Basics;

partial model OneSubstrate "SubstanceConnector for one substrate"
annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Line(points={{-50,0},{-100,0}}, color={170,0,0}, arrowSize=25)}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
BioChem.Interfaces.Nodes.SubstrateConnector s1 annotation(Placement(transformation(origin={-80,0}, extent={{-10,-10},{10,10}}), iconTransformation(origin={-112.5,-2.22045e-16}, extent={{-12.5,-12.5},{12.5,12.5}})));
annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Line(points={{-50,0},{-100,0}}, color={170,0,0}, arrowSize=25)}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
end OneSubstrate;
2 changes: 1 addition & 1 deletion BioChem/Interfaces/Reactions/Modifiers/ModifierForward.mo
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
within BioChem.Interfaces.Reactions.Modifiers;

partial model ModifierForward "Basics for a forward modifier in a reaction edge"
annotation(Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Line(points={{0,56.25},{0,6.25}}, color={0,0,255}, arrow={Arrow.None,Arrow.Open}, arrowSize=25)}));
BioChem.Interfaces.Nodes.ModifierConnector mF1 annotation(Placement(transformation(origin={1.11022e-16,90}, extent={{-10,-10},{10,10}}), iconTransformation(origin={-1.5099e-14,90}, extent={{-20,-20},{20,20}})));
equation
mF1.r=0;
annotation(Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Line(points={{0,56.25},{0,6.25}}, color={0,0,255}, arrow={Arrow.None,Arrow.Open}, arrowSize=25)}));
end ModifierForward;
2 changes: 1 addition & 1 deletion BioChem/Interfaces/Reactions/Uui.mo
Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,8 @@ partial model Uui "Uni-Uni irreversible reaction"
extends BioChem.Interfaces.Reactions.Basics.OneProduct;
BioChem.Units.StoichiometricCoefficient nS1=1 "Stoichiometric coefficient for the substrate";
BioChem.Units.StoichiometricCoefficient nP1=1 "Stoichiometric coefficient for the product";
annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
equation
s1.r=nS1*rr;
p1.r=-nP1*rr;
annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
end Uui;
2 changes: 1 addition & 1 deletion BioChem/Interfaces/Reactions/Uur.mo
Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,8 @@ partial model Uur "Uni-Uni reversible reaction"
extends BioChem.Interfaces.Reactions.Basics.OneProduct;
BioChem.Units.StoichiometricCoefficient nS1=1 "Stoichiometric coefficient for the substrate";
BioChem.Units.StoichiometricCoefficient nP1=1 "Stoichiometric coefficient for the product";
annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
equation
s1.r=nS1*rr;
p1.r=-nP1*rr;
annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
end Uur;
78 changes: 39 additions & 39 deletions BioChem/Reactions/Activation/package.mo
Original file line number Diff line number Diff line change
@@ -1,22 +1,7 @@
within BioChem.Reactions;
package Activation "Activation kinetics reactions"
extends Icons.Library;
annotation(Documentation(info="<html>
<h1>Activation</h1>
<p>
This package contains models for irreversible and reversible activation reaction kinetics.
</p>

<br>
<img src=\"modelica://BioChem/Resources/Images/Activation.png\" >
<br>
</html>", 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})));
model Umar "Reversible mixed activation kinetics"
annotation(Documentation(info="<html>
<p>
Reversible mixed activation kinetics.
</p>
</html>"), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
extends BioChem.Interfaces.Reactions.Uur;
extends BioChem.Interfaces.Reactions.Modifiers.Activator;
parameter BioChem.Units.Concentration Kas=1 "Activation constant";
Expand All @@ -27,14 +12,14 @@ This package contains models for irreversible and reversible activation reaction
parameter BioChem.Units.ReactionRate vR=1 "Backward maximum velocity";
equation
rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + Kas/a1.c + (s1.c/KmS + p1.c/KmP)*(1 + Kac/a1.c));
end Umar;

model Umai "Irreversible mixed activation kinetics"
annotation(Documentation(info="<html>
<p>
Irreversible mixed activation kinetics.
Reversible mixed activation kinetics.
</p>
</html>"), 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"
extends BioChem.Interfaces.Reactions.Uui;
extends BioChem.Interfaces.Reactions.Modifiers.Activator;
parameter BioChem.Units.Concentration Kac=1 "Activation constant";
Expand All @@ -43,14 +28,14 @@ This package contains models for irreversible and reversible activation reaction
parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity";
equation
rr=vF*s1.c*a1.c/(s1.c*(a1.c + Kac) + KmS*(a1.c + Kas));
end Umai;

model Uctr "Reversible catalytic activation"
annotation(Documentation(info="<html>
<p>
Reversible catalytic activation.
Irreversible mixed activation kinetics.
</p>
</html>"), 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"
extends BioChem.Interfaces.Reactions.Uur;
extends BioChem.Interfaces.Reactions.Modifiers.Activator;
parameter BioChem.Units.Concentration Ka=1 "Activation constant";
Expand All @@ -60,29 +45,29 @@ This package contains models for irreversible and reversible activation reaction
parameter BioChem.Units.ReactionRate vR=1 "Backward maximum velocity";
equation
rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + Ka/a1.c + (s1.c/KmS + p1.c/KmP)*(1 + Ka/a1.c));
end Uctr;

model Ucti "Irreversible catalytic activation"
annotation(Documentation(info="<html>
<p>
Irreversible catalytic activation.
Reversible catalytic activation.
</p>
</html>"), 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"
extends BioChem.Interfaces.Reactions.Uui;
extends BioChem.Interfaces.Reactions.Modifiers.Activator;
parameter BioChem.Units.Concentration Ka=1 "Activation constant";
parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant";
parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity";
equation
rr=vF*s1.c*a1.c/((a1.c + Ka)*(s1.c + KmS));
end Ucti;

model Uar "Reversible specific activation kinetics"
annotation(Documentation(info="<html>
<p>
Reversible specific activation kinetics.
Irreversible catalytic activation.
</p>
</html>"), 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"
extends BioChem.Interfaces.Reactions.Uur;
extends BioChem.Interfaces.Reactions.Modifiers.Activator;
parameter BioChem.Units.Concentration Ka=1 "Activation constant";
Expand All @@ -92,35 +77,50 @@ This package contains models for irreversible and reversible activation reaction
parameter BioChem.Units.ReactionRate vR=1 "Backward maximum velocity";
equation
rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + s1.c/KmS + p1.c/KmP + Ka/a1.c);
end Uar;

model Uaii "Irreversible specific activation kinetics"
annotation(Documentation(info="<html>
<p>
Irreversible specific activation kinetics.
Reversible specific activation kinetics.
</p>
</html>"), 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"
extends BioChem.Interfaces.Reactions.Uui;
extends BioChem.Interfaces.Reactions.Modifiers.Activator;
parameter BioChem.Units.Concentration Ka=1 "Activation constant";
parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant";
parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity";
equation
rr=vF*s1.c*a1.c/(a1.c*(KmS + s1.c) + KmS*Ka);
end Uaii;

model Uai "Irreversible substrate activation"
annotation(Documentation(info="<html>
<p>
Irreversible substrate activation.
Irreversible specific activation kinetics.
</p>
</html>"), 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"
extends BioChem.Interfaces.Reactions.Uui;
parameter BioChem.Units.Concentration KSa=1 "Dissociation constant of substrate-activation site";
parameter BioChem.Units.Concentration KSc=1 "Dissociation constant of substrate-active site";
parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity";
equation
rr=vF*s1.c/KSa*s1.c/KSa/(1 + s1.c/KSc + s1.c/KSa*s1.c/KSa + s1.c/KSa);
annotation(Documentation(info="<html>
<p>
Irreversible substrate activation.
</p>
</html>"), 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="<html>
<h1>Activation</h1>
<p>
This package contains models for irreversible and reversible activation reaction kinetics.
</p>

<br>
<img src=\"modelica://BioChem/Resources/Images/Activation.png\" >
<br>
</html>", 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 Activation;
54 changes: 27 additions & 27 deletions BioChem/Reactions/BiSubstrate/package.mo
Original file line number Diff line number Diff line change
@@ -1,22 +1,7 @@
within BioChem.Reactions;
package BiSubstrate "Bi-substrate reactions"
extends Icons.Library;
annotation(Documentation(info="<html>
<h1>BiSubstrate</h1>
<p>
This package contains models for bi-substrate reactions.
</p>
<br>
<img src=\"modelica://BioChem/Resources/Images/BiSubstrate.png\" >
<br>

</html>", 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})));
model Ppbr "Ping pong bi-bi kinetics"
annotation(Documentation(info="<html>
<p>
Ping pong bi-bi kinetics.
</p>
</html>"), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
extends BioChem.Interfaces.Reactions.Basics.Reaction;
extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible;
extends BioChem.Interfaces.Reactions.Basics.TwoProducts;
Expand All @@ -38,14 +23,14 @@ package BiSubstrate "Bi-substrate reactions"
p2.r=-rr;
K1=vF/(vR*Keq)*(KmP2*p1.c*(1 + s1.c/KiS1) + p2.c*(KmP1 + p1.c));
rr=vF*(s1.c*s2.c - p1.c*p2.c/Keq)/(s1.c*s2.c + KmS2*s1.c + KmS1*s2.c*(1 + p2.c/KiP2) + K1);
end Ppbr;

model Ordubr "Ordered uni-bi kinetics"
annotation(Documentation(info="<html>
<p>
Ordered uni-bi kinetics.
Ping pong bi-bi kinetics.
</p>
</html>"), 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"
extends BioChem.Interfaces.Reactions.Basics.Reaction;
extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible;
extends BioChem.Interfaces.Reactions.Basics.TwoProducts;
Expand All @@ -61,14 +46,14 @@ package BiSubstrate "Bi-substrate reactions"
p1.r=-rr;
p2.r=-rr;
rr=vF*(s1.c - p1.c*p2.c/Keq)/(KmS1 + s1.c*(1 + p1.c/KiP1) + vF/(vR*Keq)*(KmP2*p1.c + KmP1*p2.c + p1.c*p2.c));
end Ordubr;

model Ordbur "Ordered bi-uni kinetics"
annotation(Documentation(info="<html>
<p>
Ordered bi-uni kinetics.
Ordered uni-bi kinetics.
</p>
</html>"), 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"
extends BioChem.Interfaces.Reactions.Basics.Reaction;
extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible;
extends BioChem.Interfaces.Reactions.Basics.OneProduct;
Expand All @@ -84,14 +69,14 @@ package BiSubstrate "Bi-substrate reactions"
s2.r=rr;
p1.r=-rr;
rr=vF*(s1.c*s2.c - p1.c/Keq)/(s1.c*s2.c + KmS1*s2.c + KmS2*s1.c + vF/(vR*Keq)*(KmP1 + p1.c*(1 + s1.c/KiS1)));
end Ordbur;

model Ordbbr "Ordered bi-bi kinetics"
annotation(Documentation(info="<html>
<p>
Ordered bi-bi kinetics.
Ordered bi-uni kinetics.
</p>
</html>"), 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"
extends BioChem.Interfaces.Reactions.Basics.Reaction;
extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible;
extends BioChem.Interfaces.Reactions.Basics.TwoProducts;
Expand All @@ -116,6 +101,21 @@ package BiSubstrate "Bi-substrate reactions"
K1=vF/(vR*Keq)*(KmP2*p1.c*(1 + s1.c/KiS1) + p2.c*K2);
K2=KmP1*(1 + KmS1*s2.c/(KiS1*KmS2) + p1.c*(1 + s2.c/KiS2));
rr=vF*(s1.c*s2.c - p1.c*p2.c/Keq)/(s1.c*s2.c*(1 + p1.c/KiP1) + KmS2*(s1.c + KiS1) + KmS1*s2.c + K1);
annotation(Documentation(info="<html>
<p>
Ordered bi-bi kinetics.
</p>
</html>"), 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="<html>
<h1>BiSubstrate</h1>
<p>
This package contains models for bi-substrate reactions.
</p>
<br>
<img src=\"modelica://BioChem/Resources/Images/BiSubstrate.png\" >
<br>

</html>", 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 BiSubstrate;
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