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package ADGenKinetics "Implementation of generalized kinetics for modeling biochemical reaction networks"
package UsersGuide "User Guide"
extends Modelica.Icons.Information;
model Overview
extends Modelica.Icons.Information;
annotation(
Documentation(info = "<html>
<p><img src=\"icons/logo.jpg\"/></p>
<p><br/><h4><font color=\"#008000\">About</font></h4></p>
<p><br/><i>ADGenKinetics</i> contains an implementation of a specific set of reaction kinetics, namely, generalized simplified kinetic formats. It follows many of the guidelines recommended by the <a href=\"https://modelica.org/publications/papers/2005-05-LarsdotterNilsson-Fritzson-BioMedSim2005-MetabolicModeling.pdf\">Biochem library</a>. The underlying simplified kinetics formats are represented by generalized structured kinetics formulas suitable for arbitrary biochemical reactions with arbitrary number of substrates, products, inhibitors and activators. In this way, matabolic reaction networks can be easily assembled using a few number of reaction kinetics.</p>
<p><i>ADGenKinetics</i> is the first algorithmically differentiated Modelica library. Constructed models can also be used for computing parameter sensitivities with little modifications to the used interfaces and by initializing the input Jacobian, i.e. the parameters w.r.t. derivatives are sought. </p>
<p><br/><b><font style=\"color: #008000; \">Structure of the Library</font></b></p>
<p><br/>The following packages are available: </p>
<p><ul>
<li><i>Interfaces</i>: connectors and icons </li>
<li><i>NodeElements</i>: interfaces and components for nodes </li>
<li><i>Reactions</i>: interfaces and components for reactions </li>
<li><i>Derivatives</i>: for computing parameter sensitivities</li>
<li><i>Examples</i>: biochemical network models</li>
</ul></p>
<p>Further two subpackages within <i>NodeElements</i> and <i>Reactions</i> exist corresponding to two ways of declaration of connectors within components: </p>
<p><ul>
<li><i>dynamic</i>: dynamic parameterized number of connections </li>
<li><i>static</i>: static fixed number of connections </li>
</ul></p>
<p><br/>The main differences of both ways and their advantages and disadvantages are emphasized in this section along with the given examples. </p>
<p>Common interfaces and abstract classes are located above these packages. </p>
<p><h4><font color=\"#008000\">Connections</font></h4></p>
<p><br/>That is concentration of a substance is the potential variable while the flow rate of materials (i.e. the chemical transformation process) represents the flow variables when connecting nodes and reactions together, cf. <i><a href=\"ADGenKinetics.Interfaces.ChemicalPort\">ADGenKinetics.Interfaces.ChemicalPort</a></i>. Further subtypes of connectors exist: </p>
<p><ul>
<li><i><a href=\"
ADGenKinetics.Intefaces.ChemicalPort_S\">ADGenKinetics.Intefaces.ChemicalPort_S</a></i>: for reactions from the substrate side</li>
<li><i><a href=\"
ADGenKinetics.Interfaces.ChemicalPort_P\">ADGenKinetics.Interfaces.ChemicalPort_P</a></i>: for reactions from the product side</li>
<li><i><a href=\"
ADGenKinetics.Interfaces.ModifierChemicalPort\">ADGenKinetics.Interfaces.ModifierChemicalPort</a></i>: connecting reactions and effector nodes</li>
<li><i><a href=\"
ADGenKinetics.Interfaces.MModifierChemicalPort_I\">ADGenKinetics.Interfaces.ModifierChemicalPort_I</a></i>: for inhibiting reactions</li>
<li><i><a href=\"
ADGenKinetics.Interfaces.MModifierChemicalPort_A\">ADGenKinetics.Interfaces.MModifierChemicalPort_A</a></i>: for activating reactions<br/></li>
</ul></p>
<p><h4><font color=\"#008000\">Interfaces and abstract classes</font></h4></p>
<p><br/>Further interfaces and abstract classes are used within implemented reactions for simplifying their implementations and emphasizing their classification. The most important of which are: </p>
<p><i><a href=\"ADGenKinetics.Interfaces.Reversible.ReactionReversibility\">ADGenKinetics.Interfaces.Reversible.ReactionReversibility</a></i>: for determining the reversibility of reactions. The extended interfaces OneWay, TwoWay are used for irreversible, reversible reactions, respectively:</p>
<p><ul>
<li><i><a href=\"
ADGenKinetics.Interfaces.static.NodeConnections\">ADGenKinetics.Interfaces.static.NodeConnections</a></i>: fixed number of connections for nodes</li>
<li><i><a href=\"
ADGenKinetics.Interfaces.dynamic.NodeConnections\">ADGenKinetics.Interfaces.dynamic.NodeConnections</a></i>: parameterized number of connections for nodes.</li>
<li><i><a href=\"
ADGenKinetics.Interfaces.dynamic.Dimension.ReactionDimension\">ADGenKinetics.Interfaces.dynamic.Dimension.ReactionDimension</a></i>: parameterized number of connections for nodes. This interface can be used for specializing further classes of specific dimension, e.g. <i><a href=\"
ADGenKinetics.Interfaces.dynamic.Dimension.ReactionDimension\">ADGenKinetics.Interfaces.dynamic.Dimension.UniUni</a> .</i> </li>
<li><i><a href=\"
ADGenKinetics.Interfaces.static\">ADGenKinetics.Interfaces.static</a></i>.{<i><a href=\"ADGenKinetics.Interfaces.static.Reaction1S\">ReactionXS</a>, <a href=\"
ADGenKinetics.Interfaces.static.Reaction2P\">ReactionXP</a></i>, <i><a href=\"
ADGenKinetics.Interfaces.static.Reaction1I\">ReactionXI</a>,</i> <i><a href=\"Reaction1A\">ReactionXA</a></i>}: icons and connections for reactions with X number of connections.</li>
</ul></p>
<p><h4><font color=\"#008000\">Nodes</font></h4></p>
<p><br/>Typically, the component <i><a href=\"ADGenKinetics.NodeElements.dynamic.Node\">ADGenKinetics.NodeElements.dynamic.Node</a></i> or <i><a href=\"ADGenKinetics.NodeElements.static.Node\">ADGenKinetics.NodeElements.static.Node</a> </i>is the basic one needed for constructing biochemical reaction networks. Further types can be also imported from available implementation of the Biochem library. </p>
<p><h4><font color=\"#008000\">Reactions </font></h4></p>
<p><br/>Reaction kinetics are available in the packages<i><a href=\" ADGenKinetics.Reactions.convenience.\"> </a><a href=\" ADGenKinetics.Reactions.convenience\">ADGenKinetics.Reactions.convenience</a><a href=\" ADGenKinetics.Reactions.convenience.\">.</a>{<a href=\"ADGenKinetics.Reactions.convenience.dynamic\">dynamic</a></i>.<i><a href=\"ADGenKinetics.Reactions.convenience.static\">static</a></i>}. </p>
<p><br/>For instance,<i><a href=\" ADGenKinetics.Reactions.convenience.dynamic.IrrKinetic\"> ADGenKinetics.Reactions.convenience.dynamic.IrrKinetic</a></i> is used for irreversible reactions with arbitrary number of substrates and products, while <i><a href=\"ADGenKinetics.Reactions.convenience.dynamic.InhRevKinetic\">ADGenKinetics.Reactions.convenience.dynamic.InhRevKinetic</a></i> for reversible inhibited reactions with arbitrary number of substrates, products and inhibitors. </p>
<p><br/>Static packages provide reaction kinetics with fixed reaction structure. For instance <i><a href=\"ADGenKinetics.Reactions.convenience.static.IrrKinetic2S1P1I\">ADGenKinetics.Reactions.convenience.static.IrrKinetic2S1P1I</a></i>. </p>
<p><br/>Examples of constructing biochemical networks are given in <i><a href=\"ADGenKinetics.Examples.Spirallusdyn\">ADGenKinetics.Examples.Spirallusdyn</a> and <a href=\"ADGenKinetics.Examples.Spirallustatic\">ADGenKinetics.Examples.Spirallustatic</a>. </i></p>
<p><h4><font color=\"#008000\">Computation of parameter sensitivities</font></h4></p>
<p><br/>Given a biochemical reaction network model, the same model can be used for computing parameter sensitivities by additional slight modification in the declaration part: </p>
<p><ol>
<li>Importing <i><a href=\"
ADGenKinetics.Derivatives.NodeElements.*\">ADGenKinetics.Derivatives.NodeElements.*</a></i> and <i><a href=\"
ADGenKinetics.Derivatives.Reactions.convenience\">ADGenKinetics.Derivatives.Reactions.convenience.*</a></i> types for nodes and reaction kinetics.</li>
<li>Initializing the input Jacobian specifying active parameter with respect to which derivatives are sought. </li>
</ol></p>
<p>For instance compare the model given in <i><a href=\"ADGenKinetics.Examples.Spirallusdyn\">ADGenKinetics.Examples.Spirallusdyn</a> with <a href=\"ADGenKinetics.Derivatives.Examples.SpirallusdynAll \">ADGenKinetics.Derivatives.Examples.SpirallusdynAll </a></i></p>
</html>"));
end Overview;
model Contributors
extends Modelica.Icons.Information;
annotation(
Documentation(info = "<html>
<p>Author: Atiyah Elsheikh </p>
<p>Contact details: <i><a href=\"ADGenKinetics.UsersGuide.Contact\">ADGenKinetics.UsersGuide.Contact</a></i></p>
</html>"));
end Contributors;
model Contact
extends Modelica.Icons.Contact;
annotation(
Documentation(info = "<html><head></head><body><p>Atiyah Elsheikh : <a href=\"a.m.g.elsheikh@gmail.com\">a.m.g.elsheikh-at-gmail.com</a></p>
</body></html>"));
end Contact;
class ModelicaLicense2 "Modelica License 2"
extends Modelica.Icons.Information;
annotation(
Documentation(info = "<html>
<head>
<title>The Modelica License 2</title>
<style type=\"text/css\">
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h6 { font-size: 10pt; font-weight: bold; color: green; }
h5 { font-size: 11pt; font-weight: bold; color: green; }
h4 { font-size: 13pt; font-weight: bold; color: green; }
address { font-weight: normal}
td { solid #000; vertical-align:top; }
th { solid #000; vertical-align:top; font-weight: bold; }
table { solid #000; border-collapse: collapse;}
</style>
</head>
<body lang=\"en-US\">
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\"Modelica/Resources/C-Sources/win32_dirent.*\").</p>
<p style=\"margin-left: 40px;\"><b>Licensor:</b><br>
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Licensor grants You a worldwide, royalty-free, non-exclusive, sublicensable license,
under patent claims owned by the Licensor or licensed to the Licensor by
the owners of the Original Work that are embodied in the Original Work
as furnished by the Licensor, for the duration of the patents,
to make, use, sell, offer for sale, have made, and import the Original Work
and Derivative Works under the conditions as given in Section 2.
For the matter of clarity, the license regarding Derivative Works covers
patent claims to the extent as they are embodied in the Original Work only.</p>
<p>
<b>6. Provision of Source Code.</b> Licensor agrees to provide
You with a copy of the Source Code of the Original Work but reserves
the right to decide freely on the manner of how the Original Work is
provided.<br>
For the matter of clarity, Licensor might provide only a binary
representation of the Original Work. In that case, You may (a) either
reproduce the Source Code from the binary representation if this is
possible (e.g., by performing a copy of an encrypted Modelica
package, if encryption allows the copy operation) or (b) request the
Source Code from the Licensor who will provide it to You.</p>
<p>
<b>7. Exclusions from License Grant.</b> Neither the names of
Licensor, nor the names of any contributors to the Original Work, nor
any of their trademarks or service marks, may be used to endorse or
promote products derived from this Original Work without express
prior permission of the Licensor. Except as otherwise expressly
stated in this License and in particular in Sections 2 and 5, nothing
in this License grants any license to Licensor’s trademarks,
copyrights, patents, trade secrets or any other intellectual
property, and no patent license is granted to make, use, sell, offer
for sale, have made, or import embodiments of any patent claims.<br>
No license is granted to the trademarks of
Licensor even if such trademarks are included in the Original Work,
except as expressly stated in this License. Nothing in this License
shall be interpreted to prohibit Licensor from licensing under terms
different from this License any Original Work that Licensor otherwise
would have a right to license.</p>
<p>
<b>8. Attribution Rights.</b> You must retain in the Source
Code of the Original Work and of any Derivative Works that You
create, all author, copyright, patent, or trademark notices, as well
as any descriptive text identified therein as an "Attribution
Notice". The same applies to the licensing notice of this
License in the Original Work. For the matter of clarity, “author
notice” means the notice that identifies the original
author(s). <br>
You must cause the Source Code for any Derivative
Works that You create to carry a prominent Attribution Notice
reasonably calculated to inform recipients that You have modified the
Original Work. <br>
In case the Original Work or Derivative Work is not provided in
Source Code, the Attribution Notices shall be appropriately
displayed, e.g., in the documentation of the Derivative Work.</p>
<p><b>9. Disclaimer
of Warranty. <br></b><u><b>The Original Work is provided under this
License on an "as is" basis and without warranty, either
express or implied, including, without limitation, the warranties of
non-infringement, merchantability or fitness for a particular
purpose. The entire risk as to the quality of the Original Work is
with You.</b></u> This disclaimer of warranty constitutes an
essential part of this License. No license to the Original Work is
granted by this License except under this disclaimer.</p>
<p>
<b>10. Limitation of Liability.</b> Under no circumstances and
under no legal theory, whether in tort (including negligence),
contract, or otherwise, shall the Licensor, the owner or a licensee
of the Original Work be liable to anyone for any direct, indirect,
general, special, incidental, or consequential damages of any
character arising as a result of this License or the use of the
Original Work including, without limitation, damages for loss of
goodwill, work stoppage, computer failure or malfunction, or any and
all other commercial damages or losses. This limitation of liability
shall not apply to the extent applicable law prohibits such
limitation.</p>
<p>
<b>11. Termination.</b> This License conditions your rights to
undertake the activities listed in Section 2 and 5, including your
right to create Derivative Works based upon the Original Work, and
doing so without observing these terms and conditions is prohibited
by copyright law and international treaty. Nothing in this License is
intended to affect copyright exceptions and limitations. This License
shall terminate immediately and You may no longer exercise any of the
rights granted to You by this License upon your failure to observe
the conditions of this license.</p>
<p>
<b>12. Termination for Patent Action.</b> This License shall
terminate automatically and You may no longer exercise any of the
rights granted to You by this License as of the date You commence an
action, including a cross-claim or counterclaim, against Licensor,
any owners of the Original Work or any licensee alleging that the
Original Work infringes a patent. This termination provision shall
not apply for an action alleging patent infringement through
combinations of the Original Work under combination with other
software or hardware.</p>
<p>
<b>13. Jurisdiction.</b> Any action or suit relating to this
License may be brought only in the courts of a jurisdiction wherein
the Licensor resides and under the laws of that jurisdiction
excluding its conflict-of-law provisions. The application of the
United Nations Convention on Contracts for the International Sale of
Goods is expressly excluded. Any use of the Original Work outside the
scope of this License or after its termination shall be subject to
the requirements and penalties of copyright or patent law in the
appropriate jurisdiction. This section shall survive the termination
of this License.</p>
<p>
<b>14. Attorneys’ Fees.</b> In any action to enforce the
terms of this License or seeking damages relating thereto, the
prevailing party shall be entitled to recover its costs and expenses,
including, without limitation, reasonable attorneys' fees and costs
incurred in connection with such action, including any appeal of such
action. This section shall survive the termination of this License.</p>
<p>
<b>15. Miscellaneous.</b>
</p>
<ol type=\"a\">
<li>If any
provision of this License is held to be unenforceable, such
provision shall be reformed only to the extent necessary to make it
enforceable.</li>
<li>No verbal
ancillary agreements have been made. Changes and additions to this
License must appear in writing to be valid. This also applies to
changing the clause pertaining to written form.</li>
<li>You may use the
Original Work in all ways not otherwise restricted or conditioned by
this License or by law, and Licensor promises not to interfere with
or be responsible for such uses by You.</li>
</ol>
<hr>
<h5><a name=\"Frequently_Asked_Questions-outline\"></a>
Frequently Asked Questions</h5>
<p>This
section contains questions/answer to users and/or distributors of
Modelica packages and/or documents under Modelica License 2. Note,
the answers to the questions below are not a legal interpretation of
the Modelica License 2. In case of a conflict, the language of the
license shall prevail.</p>
<h6>Using or Distributing a Modelica <u>Package</u> under the Modelica License 2</h6>
<p><b>What are the main
differences to the previous version of the Modelica License?</b></p>
<ol>
<li><p>
Modelica License 1 is unclear whether the licensed Modelica package
can be distributed under a different license. Version 2 explicitly
allows that “Derivative Work” can be distributed under
any license of Your choice, see examples in Section 1d) as to what
qualifies as Derivative Work (so, version 2 is clearer).</p>
<li><p>
If You modify a Modelica package under Modelica License 2 (besides
fixing of errors, adding vendor specific Modelica annotations, using
a subset of the classes of a Modelica package, or using another
representation, e.g., a binary representation), you must rename the
root-level name of the package for your distribution. In version 1
you could keep the name (so, version 2 is more restrictive). The
reason of this restriction is to reduce the risk that Modelica
packages are available that have identical names, but different
functionality.</p>
<li><p>
Modelica License 1 states that “It is not allowed to charge a
fee for the original version or a modified version of the software,
besides a reasonable fee for distribution and support”.
Version 2 has a similar intention for all Original Work under
<u>Modelica License 2</u> (to remain free of charge and open source)
but states this more clearly as “No fee, neither as a
copyright-license fee, nor as a selling fee for the copy as such may
be charged”. Contrary to version 1, Modelica License 2 has no
restrictions on fees for Derivative Work that is provided under a
different license (so, version 2 is clearer and has fewer
restrictions).</p>
<li><p>
Modelica License 2 introduces several useful provisions for the
licensee (articles 5, 6, 12), and for the licensor (articles 7, 12,
13, 14) that have no counter part in version 1.</p>
<li><p>
Modelica License 2 can be applied to all type of work, including
documents, images and data files, contrary to version 1 that was
dedicated for software only (so, version 2 is more general).</p>
</ol>
<p><b>Can I distribute a
Modelica package (under Modelica License 2) as part of my commercial
Modelica modeling and simulation environment?</b></p>
<p>Yes,
according to Section 2c). However, you are not allowed to charge a
fee for this part of your environment. Of course, you can charge for
your part of the environment.
</p>
<p><b>Can I distribute a
Modelica package (under Modelica License 2) under a different
license?</b></p>
<p>No.
The license of an unmodified Modelica package cannot be changed
according to Sections 2c) and 2d). This means that you cannot <u>sell</u>
copies of it, any distribution has to be free of charge.</p>
<p><b>Can I distribute a
Modelica package (under Modelica License 2) under a different license
when I first encrypt the package?</b></p>
<p>No.
Merely encrypting a package does not qualify for Derivative Work and
therefore the encrypted package has to stay under Modelica License 2.</p>
<p><b>Can I distribute a
Modelica package (under Modelica License 2) under a different license
when I first add classes to the package?</b></p>
<p>No.
The package itself remains unmodified, i.e., it is Original Work, and
therefore the license for this part must remain under Modelica
License 2. The newly added classes can be, however, under a different
license.
</p>
<p><b>Can
I copy a class out of a Modelica package (under Modelica License 2)
and include it </b><u><b>unmodified</b></u><b> in a Modelica package
under a </b><u><b>commercial/proprietary license</b></u><b>?</b></p>
<p>No,
according to article 2c). However, you can include model, block,
function, package, record and connector classes in your Modelica
package under <u>Modelica License 2</u>. This means that your
Modelica package could be under a commercial/proprietary license, but
one or more classes of it are under Modelica License 2.<br>Note, a
“type” class (e.g., type Angle = Real(unit=”rad”))
can be copied and included unmodified under a commercial/proprietary
license (for details, see the next question).</p>
<p><b>Can
I copy a type class or </b><u><b>part</b></u><b> of a model, block,
function, record, connector class, out of a Modelica package (under
Modelica License 2) and include it modified or unmodified in a
Modelica package under a </b><u><b>commercial/proprietary</b></u><b>
license</b></p>
<p>Yes,
according to article 2d), since this will in the end usually qualify
as Derivative Work. The reasoning is the following: A type class or
part of another class (e.g., an equation, a declaration, part of a
class description) cannot be utilized “by its own”. In
order to make this “usable”, you have to add additional
code in order that the class can be utilized. This is therefore
usually Derivative Work and Derivative Work can be provided under a
different license. Note, this only holds, if the additional code
introduced is sufficient to qualify for Derivative Work. Merely, just
copying a class and changing, say, one character in the documentation
of this class would be no Derivative Work and therefore the copied
code would have to stay under Modelica License 2.</p>
<p><b>Can
I copy a class out of a Modelica package (under Modelica License 2)
and include it in </b><u><b>modified </b></u><b>form in a
</b><u><b>commercial/proprietary</b></u><b> Modelica package?</b></p>
<p>Yes.
If the modification can be seen as a “Derivative Work”,
you can place it under your commercial/proprietary license. If the
modification does not qualify as “Derivative Work” (e.g.,
bug fixes, vendor specific annotations), it must remain under
Modelica License 2. This means that your Modelica package could be
under a commercial/proprietary license, but one or more parts of it
are under Modelica License 2.</p>
<p><b>Can I distribute a
“save total model” under my commercial/proprietary
license, even if classes under Modelica License 2 are included?</b></p>
<p>Your
classes of the “save total model” can be distributed
under your commercial/proprietary license, but the classes under
Modelica License 2 must remain under Modelica License 2. This means
you can distribute a “save total model”, but some parts
might be under Modelica License 2.</p>
<p><b>Can I distribute a
Modelica package (under Modelica License 2) in encrypted form?</b></p>
<p>Yes.
Note, if the encryption does not allow “copying” of
classes (in to unencrypted Modelica source code), you have to send
the Modelica source code of this package to your customer, if he/she
wishes it, according to article 6.</p>
<p><b>Can I distribute an
executable under my commercial/proprietary license, if the model from
which the executable is generated uses models from a Modelica package
under Modelica License 2?</b></p>
<p>Yes,
according to article 2d), since this is seen as Derivative Work. The
reasoning is the following: An executable allows the simulation of a
concrete model, whereas models from a Modelica package (without
pre-processing, translation, tool run-time library) are not able to
be simulated without tool support. By the processing of the tool and
by its run-time libraries, significant new functionality is added (a
model can be simulated whereas previously it could not be simulated)
and functionality available in the package is removed (e.g., to build
up a new model by dragging components of the package is no longer
possible with the executable).</p>
<p><b>Is my modification to
a Modelica package (under Modelica License 2) a Derivative Work?</b></p>
<p>It
is not possible to give a general answer to it. To be regarded as "an
original work of authorship", a derivative work must be
different enough from the original or must contain a substantial
amount of new material. Making minor changes or additions of little
substance to a preexisting work will not qualify the work as a new
version for such purposes.
</p>
<h6>Using or Distributing a Modelica <u>Document</u> under the Modelica License 2</h6>
<p>This
section is devoted especially for the following applications:</p>
<ol type=\"a\">
<li><p>
A Modelica tool extracts information out of a Modelica package and
presents the result in form of a “manual” for this
package in, e.g., html, doc, or pdf format.</p>
<li><p>
The Modelica language specification is a document defining the
Modelica language. It will be licensed under Modelica License 2.</p>
<li><p>
Someone writes a book about the Modelica language and/or Modelica
packages and uses information which is available in the Modelica
language specification and/or the corresponding Modelica package.</p>
</ol>
<p><b>Can I sell a manual
that was basically derived by extracting information automatically
from a Modelica package under Modelica License 2 (e.g., a “reference
guide” of the Modelica Standard Library):</b></p>
<p>Yes.
Extracting information from a Modelica package, and providing it in a
human readable, suitable format, like html, doc or pdf format, where
the content is significantly modified (e.g. tables with interface
information are constructed from the declarations of the public
variables) qualifies as Derivative Work and there are no restrictions
to charge a fee for Derivative Work under alternative 2d).</p>
<p><b>Can
I copy a text passage out of a Modelica document (under Modelica
License 2) and use it </b><u><b>unmodified</b></u><b> in my document
(e.g. the Modelica syntax description in the Modelica Specification)?</b></p>
<p>Yes.
In case you distribute your document, the copied parts are still
under Modelica License 2 and you are not allowed to charge a license
fee for this part. You can, of course, charge a fee for the rest of
your document.</p>
<p><b>Can
I copy a text passage out of a Modelica document (under Modelica
License 2) and use it in </b><u><b>modified</b></u><b> form in my
document?</b></p>
<p>Yes,
the creation of Derivative Works is allowed. In case the content is
significantly modified this qualifies as Derivative Work and there
are no restrictions to charge a fee for Derivative Work under
alternative 2d).</p>
<p><b>Can I sell a printed
version of a Modelica document (under Modelica License 2), e.g., the
Modelica Language Specification?</b></p>
<p>No,
if you are not the copyright-holder, since article 2c) does not allow
a selling fee for a (in this case physical) copy. However, mere
printing and shipping costs may be recovered.</p>
</body>
</html>"));
end ModelicaLicense2;
model ReleaseNotes
extends Modelica.Icons.ReleaseNotes;
annotation(
Documentation(info = "<html>
<p><b><font style=\"color: #008000; \">R23 </font></b>27th August 2012 </p>
<p>first published release of the library with Basic phyiscial units, basic components for nodes and reactions both with parameterized and static number of connections. Examples and algorithmically differentiated components available. </p>
</html>"));
end ReleaseNotes;
model References
extends Modelica.Icons.References;
end References;
model CopyRight
extends Modelica.Icons.Information;
annotation(
Documentation(info = "<html><head></head><body><p><span style=\"font-size: 12px;\">Licensed under the Modelica License 2</span></p><p><b style=\"color: rgb(170, 0, 0); font-size: x-large;\">Copyright © <2011>-<2018>, <Atiyah Elsheikh>.</b></p><p><i>This Modelica package is <u>free</u> software and the use is completely at <u>your own risk</u>; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see <a href=\"modelica://Modelica.UsersGuide.ModelicaLicense2\">Modelica.UsersGuide.ModelicaLicense2</a> or visit<a href=\"http://www.modelica.org/licenses/ModelicaLicense2\">http://www.modelica.org/licenses/ModelicaLicense2</a>.</i></p></body></html>"));
end CopyRight;
annotation(
Documentation);
end UsersGuide;
package Units "Physical units"
type Concentration = Modelica.Icons.TypeReal(final quantity = "Concentration", final unit = "mol/l", min = 0);
type VolumetricReactionRate = Modelica.Icons.TypeReal(final quantity = "Volumetric reaction rate", final unit = "mol/(s.l)");
type MolarFlowRate = Modelica.Icons.TypeReal(final unit = "mol/s");
type ReactionCoef = Modelica.Icons.TypeReal(final unit = "1/s");
type StoichiometricCoef = Modelica.Icons.TypeReal(final unit = "1");
type ReactionCoef1st = Units.ReactionCoef;
type ReactionCoef2nd = Modelica.Icons.TypeReal(final unit = "l/(mol.s)");
type AffinityConst = Modelica.Icons.TypeReal(final unit = "mol/l");
type Elasticity = Modelica.Icons.TypeReal(final quantity = "Elasticity", final unit = "1");
type Volume = Modelica.SIunits.Conversions.NonSIunits.Volume_litre annotation(
Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, initialScale = 0.1, grid = {10, 10})),
Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, initialScale = 0.1, grid = {10, 10})));
annotation(
Documentation(info = "<html><head></head><body><p>This subpackage contains basic physical units describing main entitites of a biochemical reaction network model. </p>
<p><br>Licensed under the Modelica License 2</p><p><br>Copyright © <a href=\"ADGenKinetics.UserGuide.CopyRight\">ADGenKinetics.UserGuide.CopyRight</a></p>
<p><i>This Modelica package is <u>free</u> software and the use is completely at <u>your own risk</u>; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see <a href=\"modelica://Modelica.UsersGuide.ModelicaLicense2\">Modelica.UsersGuide.ModelicaLicense2</a> or visit <a href=\"http://www.modelica.org/licenses/ModelicaLicense2\">http://www.modelica.org/licenses/ModelicaLicense2</a>.</i> </p>
</body></html>"));
end Units;
package Interfaces "Typical interfaces"
connector ChemicalPort "reaction connector from a node to a reaction, declared within the node side"
Units.Concentration c "concentration";
flow Units.VolumetricReactionRate r "reaction rate";
annotation(
Icon(graphics = {Bitmap(extent = {{-75, 75}, {75, -75}}, fileName = "icons/reactionconnection.gif")}),
Diagram(graphics));
end ChemicalPort;
connector ModifierChemicalPort "connector that connects a node to a reaction. The node is supposed to effects (activate or inhibit) the reaction"
input Units.Concentration c "concentration";
annotation(
Icon(graphics = {Bitmap(extent = {{-80, 84}, {100, -98}}, fileName = "icons/modifierconnection.gif")}));
end ModifierChemicalPort;
connector ChemicalPort_S "connector from a reactant substrate node to a reaction, declared within the reaction side"
extends ADGenKinetics.Interfaces.ChemicalPort;
annotation(
Icon(graphics = {Bitmap(extent = {{-80, 80}, {82, -82}}, fileName = "icons/reactionconnection_S.gif")}),
Diagram(graphics));
end ChemicalPort_S;
connector ChemicalPort_P "connector from a reactant substrate node to a reaction, declared within the reaction side"
extends ADGenKinetics.Interfaces.ChemicalPort;
annotation(
Icon(graphics = {Bitmap(extent = {{-88, 106}, {94, -104}}, fileName = "icons/reactionconnection_P2.gif")}));
end ChemicalPort_P;
connector ModifierChemicalPort_I "connection from a reaction to an inhibition node"
extends ADGenKinetics.Interfaces.ModifierChemicalPort;
annotation(
Icon(coordinateSystem(preserveAspectRatio = true, extent = {{-100, -100}, {100, 100}}), graphics = {Bitmap(extent = {{-80, 80}, {84, -80}}, fileName = "icons/modifierconnection_I2.gif")}));
end ModifierChemicalPort_I;
connector ModifierChemicalPort_A "connection from a reaction to an activation node"
extends ADGenKinetics.Interfaces.ModifierChemicalPort;
annotation(
Icon(graphics = {Bitmap(extent = {{-96, 100}, {124, -120}}, fileName = "icons/modifierconnection_A2.gif")}));
end ModifierChemicalPort_A;
package Reversible "Interfaces describing reversibility of a reaction"
partial model ReactionReversibility "Base Type for describing Reversability of a reaction"
parameter Units.ReactionCoef Vfwdmax = 1 "maximal forward reaction rate";
end ReactionReversibility;
class OneWay "Irreversible Reaction"
extends ReactionReversibility;
annotation(
Icon(graphics = {Bitmap(extent = {{-78, 80}, {86, -80}}, fileName = "icons/OneWay.gif")}));
end OneWay;
class TwoWay "Reversible Reaction"
extends ReactionReversibility;
parameter Units.ReactionCoef Vbwdmax = 1 "backward maximal reaction rate";
annotation(
Icon(graphics = {Bitmap(extent = {{-110, 100}, {90, -100}}, fileName = "icons/TwoWay.gif")}));
end TwoWay;
annotation(
Documentation(info = "<html><head></head><body><p>This subpackage contains basic interfaces describing the reversibility of a reaction</p>
<p><br>Licensed under the Modelica License 2</p><p><br>Copyright © <a href=\"ADGenKinetics.UserGuide.CopyRight\" style=\"font-size: 12px;\">ADGenKinetics.UserGuide.CopyRight</a></p>
<p><i>This Modelica package is <u>free</u> software and the use is completely at <u>your own risk</u>; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see <a href=\"modelica://Modelica.UsersGuide.ModelicaLicense2\">Modelica.UsersGuide.ModelicaLicense2</a> or visit <a href=\"http://www.modelica.org/licenses/ModelicaLicense2\">http://www.modelica.org/licenses/ModelicaLicense2</a>.</i> </p>
</body></html>"));
end Reversible;
package static "Interfaces for components consisting of a fixed number of connections"
partial model NodeConnections "Metabolite connections to reactions"
ADGenKinetics.Interfaces.ChemicalPort rc1 annotation(
extent = [-60, 80; -40, 100],
Placement(transformation(extent = {{-84, 54}, {-14, 124}}), iconTransformation(extent = {{-86, 48}, {10, 148}})));
ADGenKinetics.Interfaces.ChemicalPort rc2 annotation(
extent = [-60, 80; -40, 100],
Placement(transformation(extent = {{-84, 54}, {-14, 124}}), iconTransformation(extent = {{-8, 48}, {88, 148}})));
ADGenKinetics.Interfaces.ChemicalPort rc3 annotation(
extent = [-60, 80; -40, 100],
Placement(transformation(extent = {{-84, 54}, {-14, 124}}), iconTransformation(extent = {{52, -12}, {148, 88}})));
ADGenKinetics.Interfaces.ChemicalPort rc4 annotation(
extent = [-60, 80; -40, 100],
Placement(transformation(extent = {{-84, 54}, {-14, 124}}), iconTransformation(extent = {{52, -90}, {148, 10}})));
ADGenKinetics.Interfaces.ChemicalPort rc5 annotation(
extent = [-60, 80; -40, 100],
Placement(transformation(extent = {{-84, 54}, {-14, 124}}), iconTransformation(extent = {{-8, -150}, {88, -50}})));
ADGenKinetics.Interfaces.ChemicalPort rc6 annotation(
extent = [-60, 80; -40, 100],
Placement(transformation(extent = {{-84, 54}, {-14, 124}}), iconTransformation(extent = {{-86, -150}, {10, -50}})));
ADGenKinetics.Interfaces.ChemicalPort rc7 annotation(
extent = [-60, 80; -40, 100],
Placement(transformation(extent = {{-84, 54}, {-14, 124}}), iconTransformation(extent = {{-146, -90}, {-50, 10}})));
ADGenKinetics.Interfaces.ChemicalPort rc8 annotation(
extent = [-60, 80; -40, 100],
Placement(transformation(extent = {{-84, 54}, {-14, 124}}), iconTransformation(extent = {{-146, -12}, {-50, 88}})));
ADGenKinetics.Interfaces.ModifierChemicalPort mc1 annotation(
Placement(transformation(extent = {{-30, 44}, {30, 104}}), iconTransformation(extent = {{-128, 68}, {-68, 128}})));
ADGenKinetics.Interfaces.ModifierChemicalPort mc2 annotation(
Placement(transformation(extent = {{-30, 44}, {30, 104}}), iconTransformation(extent = {{72, 68}, {132, 128}})));
ADGenKinetics.Interfaces.ModifierChemicalPort mc3 annotation(
Placement(transformation(extent = {{-30, 44}, {30, 104}}), iconTransformation(extent = {{70, -130}, {130, -70}})));
ADGenKinetics.Interfaces.ModifierChemicalPort mc4 annotation(
Placement(transformation(extent = {{-30, 44}, {30, 104}}), iconTransformation(extent = {{-130, -130}, {-70, -70}})));
annotation(
Line(points = {{-43, 73}, {-43, 90.5}, {-43, 90.5}, {-43, 73}}, color = {0, 0, 255}, smooth = Smooth.None),
Diagram(graphics),
Icon(graphics = {Rectangle(extent = {{-100, 100}, {100, -100}}, lineColor = {0, 0, 255})}));
end NodeConnections;
model Reaction "icon for a reaction"
annotation(
Icon(graphics = {Bitmap(extent = {{-106, 110}, {134, -130}}, fileName = "icons/reaction.gif")}));
end Reaction;
partial model Reaction1S "basic declaration of a reaction with one substrate"
ADGenKinetics.Interfaces.ChemicalPort_S rc_S1 annotation(
Placement(transformation(extent = {{-36, 50}, {-16, 70}}), iconTransformation(extent = {{-60, 72}, {-20, 112}})));
annotation(
Diagram(graphics),
Icon(graphics = {Rectangle(extent = {{-100, 100}, {98, -100}}, lineColor = {0, 0, 255})}));
end Reaction1S;
partial model Reaction2S "basic declaration of a reaction with two substrates"
extends Interfaces.static.Reaction1S;
ADGenKinetics.Interfaces.ChemicalPort_S rc_S2 annotation(
Placement(transformation(extent = {{-36, 50}, {-16, 70}}), iconTransformation(extent = {{20, 72}, {60, 112}})));
annotation(
Diagram(graphics),
Icon(graphics = {Rectangle(extent = {{-100, 100}, {98, -100}}, lineColor = {0, 0, 255})}));
end Reaction2S;
partial model Reaction1P "basic declaration of a reaction with one product"
ADGenKinetics.Interfaces.ChemicalPort_P rc_P1 annotation(
Placement(transformation(extent = {{-50, 6}, {-10, 46}}), iconTransformation(extent = {{-58, -112}, {-18, -72}})));
equation
annotation(
Diagram(graphics),
Icon(graphics = {Rectangle(extent = {{-100, 100}, {98, -100}}, lineColor = {0, 0, 255})}));
end Reaction1P;
partial model Reaction2P "basic declaration of a reaction with two products"
extends Interfaces.static.Reaction1P;
ADGenKinetics.Interfaces.ChemicalPort_P rc_P2 annotation(
Placement(transformation(extent = {{-50, 6}, {-10, 46}}), iconTransformation(extent = {{22, -112}, {62, -72}})));
annotation(
Diagram(graphics),
Icon(graphics = {Rectangle(extent = {{-100, 100}, {98, -100}}, lineColor = {0, 0, 255})}));
end Reaction2P;
partial model Reaction1A "interface for activating a reaction"
ADGenKinetics.Interfaces.ModifierChemicalPort_A mc_A1 annotation(
Placement(transformation(extent = {{-40, 80}, {0, 120}}), iconTransformation(extent = {{-120, -18}, {-80, 22}})));
annotation(
Icon(graphics));
end Reaction1A;
partial model Reaction1I "interface for inhibiting a reaction"
ADGenKinetics.Interfaces.ModifierChemicalPort_I mc_I1 annotation(
Placement(transformation(extent = {{-108, -12}, {-88, 8}}), iconTransformation(extent = {{76, -20}, {116, 20}})));
annotation(
Icon(graphics));
end Reaction1I;
annotation(
Documentation(info = "<html><head></head><body><p>This subpackage contains basic icons for nodes and reactions. The nodes and the reactions are declared with a \"static\" fixed number of connectors. </p>
<p><br>Licensed under the Modelica License 2</p><p><br>Copyright © <a href=\"ADGenKinetics.UserGuide.CopyRight\" style=\"font-size: 12px;\">ADGenKinetics.UserGuide.CopyRight</a></p>
<p><i>This Modelica package is <u>free</u> software and the use is completely at <u>your own risk</u>; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see <a href=\"modelica://Modelica.UsersGuide.ModelicaLicense2\">Modelica.UsersGuide.ModelicaLicense2</a> or visit <a href=\"http://www.modelica.org/licenses/ModelicaLicense2\">http://www.modelica.org/licenses/ModelicaLicense2</a>.</i> </p>
</body></html>"));
end static;
package dynamic "Interfaces with parameterized number of connections for textual implementation and automatic model generation"
package Dimension "Reaction Dimension and Molecularity"
class ReactionDimension "Dimension and structure of a reaction"
parameter Integer NS = 1 "number of substrates";
parameter Units.StoichiometricCoef n_S[NS] = ones(NS) "stoichiometry of all subtrates";
parameter Integer NP = 1 "number of products";
parameter Units.StoichiometricCoef n_P[NP] = ones(NP) "stoichiometry of all products";
end ReactionDimension;
class UniUni "S => P"
extends ReactionDimension(redeclare final parameter Integer NS = 1, redeclare final parameter Integer NP = 1);
end UniUni;
annotation(
Documentation(info = "<html><head></head><body><p>This subpackage contains basic interface for specifying the dimension of the reaction, see <a href=\"GenKinetics.Interfaces.dynamic.Dimension.ReactionDimension\">GenKinetics.Interfaces.dynamic.Dimension.ReactionDimension</a> . Out of this interface, specialized reaction types can be created as a syntactic sugar, e.g. <a href=\"GenKinetics.Interfaces.dynamic.Dimension.UniUni\">GenKinetics.Interfaces.dynamic.Dimension.UniUni</a> . </p>
<p><br>Licensed under the Modelica License 2</p>
<p><br>Copyright © <a href=\"ADGenKinetics.UserGuide.CopyRight\" style=\"font-size: 12px;\">ADGenKinetics.UserGuide.CopyRight</a></p>
<p><i>This Modelica package is <u>free</u> software and the use is completely at <u>your own risk</u>; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see <a href=\"modelica://Modelica.UsersGuide.ModelicaLicense2\">Modelica.UsersGuide.ModelicaLicense2</a> or visit <a href=\"http://www.modelica.org/licenses/ModelicaLicense2\">http://www.modelica.org/licenses/ModelicaLicense2</a>.</i> </p>
<p></p><h4>Package Content</h4><p></p>
</body></html>"));
end Dimension;
package Structure "Reaction Structure reversibility and dimension"
class ReactionStructure "The structure of a reaction reversibility, molecularity and order"
replaceable class Reversibility = Reversible.ReactionReversibility constrainedby Reversible.ReactionReversibility;
extends Reversibility;
replaceable class Dimensionality = ADGenKinetics.Interfaces.dynamic.Dimension.ReactionDimension constrainedby ADGenKinetics.Interfaces.dynamic.Dimension.ReactionDimension;
extends Dimensionality;
end ReactionStructure;
class StrUniUni "Structure Uni Uni "
extends ReactionStructure(redeclare final class Dimensionality = Dimension.UniUni);
end StrUniUni;
class StrOneWay "Structure Uni Uni "
extends ReactionStructure(redeclare final class Reversibility = Reversible.OneWay);
end StrOneWay;
annotation(
Documentation(info = "<html><head></head><body><p>This subpackage contains basic interface for specifying the structure of a reaction, i.e. its dimension and reversibility see <a href=\"ADGenKinetics.Interfaces.dynamic.Dimension.ReactionStructure\">ADGenKinetics.Interfaces.dynamic.Dimension.ReactionStructure</a> . Out of this interface, specialized reaction types can be created as a syntactic sugar, e.g. <a href=\"ADGenKinetics.Interfaces.dynamic.Dimension.StrOneWay\">GenKinetics.Interfaces.dynamic.Dimension.StrOneWay</a> . </p>
<p><br>Licensed under the Modelica License 2</p>
<p><br>Copyright © <a href=\"ADGenKinetics.UserGuide.CopyRight\" style=\"font-size: 12px;\">ADGenKinetics.UserGuide.CopyRight</a></p>
<p><i>This Modelica package is <u>free</u> software and the use is completely at <u>your own risk</u>; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see <a href=\"modelica://Modelica.UsersGuide.ModelicaLicense2\">Modelica.UsersGuide.ModelicaLicense2</a> or visit <a href=\"http://www.modelica.org/licenses/ModelicaLicense2\">http://www.modelica.org/licenses/ModelicaLicense2</a>.</i> </p>
</body></html>"));
end Structure;
partial model NodeConnections "Metabolite connections to reactions wuth one connector only"
ADGenKinetics.Interfaces.ChemicalPort rc "connection to any reaction " annotation(
Placement(transformation(extent = {{-50, -50}, {50, 50}}), iconTransformation(extent = {{-114, -40}, {122, 154}})));
ADGenKinetics.Interfaces.ModifierChemicalPort mc "connection to a modifier" annotation(
Placement(transformation(extent = {{-50, -50}, {50, -50}}), iconTransformation(extent = {{-64, -122}, {72, 2}})));
annotation(
Icon(graphics));
end NodeConnections;
annotation(
Documentation(info = "<html><head></head><body><p>This subpackage contains basic interfaces for nodes and reactions. The nodes and the reactions are declared with a \"dynamic\" parameterized number of connectors. </p>
<p><br>Licensed under the Modelica License 2</p>
<p><br>Copyright © <a href=\"ADGenKinetics.UserGuide.CopyRight\" style=\"font-size: 12px;\">ADGenKinetics.UserGuide.CopyRight</a></p>
<p><i>This Modelica package is <u>free</u> software and the use is completely at <u>your own risk</u>; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see <a href=\"modelica://Modelica.UsersGuide.ModelicaLicense2\">Modelica.UsersGuide.ModelicaLicense2</a> or visit <a href=\"http://www.modelica.org/licenses/ModelicaLicense2\">http://www.modelica.org/licenses/ModelicaLicense2</a>.</i> </p>
<p><br></p><font style=\"font-size: 19pt; \">
</font></body></html>"));
end dynamic;
annotation(
Documentation(info = "<html><head></head><body><p>This subpackage contains all interfaces, abstract models, connectors etc. utilized by the components of the library. </p>
<p><br>Licensed under the Modelica License 2</p><p><br>Copyright © <a href=\"ADGenKinetics.UserGuide.CopyRight\" style=\"font-size: 12px;\">ADGenKinetics.UserGuide.CopyRight</a></p>
<p><i>This Modelica package is <u>free</u> software and the use is completely at <u>your own risk</u>; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see <a href=\"modelica://Modelica.UsersGuide.ModelicaLicense2\">Modelica.UsersGuide.ModelicaLicense2</a> or visit <a href=\"http://www.modelica.org/licenses/ModelicaLicense2\">http://www.modelica.org/licenses/ModelicaLicense2</a>.</i> </p>
</body></html>", revisions = "<html>
</html>"));
end Interfaces;
package NodeElements "Metabolites"
package dynamic "Nodes with parameterized interfaces and connections"
partial model BasicNode "Basic declarations of any Metabolite"
extends ADGenKinetics.Interfaces.dynamic.NodeConnections;
parameter Units.Concentration c_0 = 0 "initial concentration";
Units.Concentration c(start = c_0) "substance concentration";
Units.VolumetricReactionRate r_net "net reaction rate";
equation
r_net = rc.r;
rc.c = c;
mc.c = c;
end BasicNode;
partial model BasicModifierNode "Deprecated: Basic declarations of any Metabolite, which effects at least one reaction"
extends BasicNode;
end BasicModifierNode;
model Node "Metabolite with dynamic rate"
extends ADGenKinetics.NodeElements.dynamic.BasicNode;
//parameter Units.Concentration tolerance=1e-6;
equation
//der(c) = if(c < tolerance) then 0 else r_net;
der(c) = r_net;
end Node;
model ModifierNode "Deprecated: Metabolite with dynamic rate, that effects at least one reaction"
extends ADGenKinetics.NodeElements.dynamic.BasicModifierNode;
//parameter Units.Concentration tolerance=1e-6;
equation
//der(c) = if (c < tolerance) then 0 else r_net;
der(c) = r_net;
end ModifierNode;
model FixedConcentrationNode "Metabolite with fixed concentration"
extends ADGenKinetics.NodeElements.dynamic.BasicNode;
parameter Units.Concentration c_fixed = 1.0;
equation
c = c_fixed;
end FixedConcentrationNode;
annotation(
Documentation(info = "<html><head></head><body><p>This subpackage contains implmentation for nodes, chemical substances, which can be connected to arbitrary number of reactions. Typically the component <a href=\"ADGenKinetics.NodeElements.dynamic.Node\">ADGenKinetics.NodeElements.dynamic.Node</a> is the one which will be used at most. The component <a href=\"ADGenKinetics.NodeElements.dynamic.ModifierNode\">ADGenKinetics.NodeElements.dynamic.ModifierNode</a> is exactly the same and does not really provide additional functionalities (it is here only for backword compatibility reasons with older versions of this implementation). This component will mostly get removed in later versions. </p>
<p><br>Licensed under the Modelica License 2</p>
<p><br>Copyright © <a href=\"ADGenKinetics.UserGuide.CopyRight\" style=\"font-size: 12px;\">ADGenKinetics.UserGuide.CopyRight</a></p>
<p><i>This Modelica package is <u>free</u> software and the use is completely at <u>your own risk</u>; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see <a href=\"modelica://Modelica.UsersGuide.ModelicaLicense2\">Modelica.UsersGuide.ModelicaLicense2</a> or visit <a href=\"http://www.modelica.org/licenses/ModelicaLicense2\">http://www.modelica.org/licenses/ModelicaLicense2</a>.</i> </p>
</body></html>"));
end dynamic;
package static "Node elements with a static number of interfaces and icons"
partial model BasicNode "Basic declarations of any Metabolite"
extends ADGenKinetics.Interfaces.static.NodeConnections;
parameter ADGenKinetics.Units.Concentration c_0 = 0 "initial reaction rate";
ADGenKinetics.Units.Concentration c(start = c_0) "dynamic concentration";
ADGenKinetics.Units.VolumetricReactionRate r_net "net reaction rate";
equation
r_net = rc1.r + rc2.r + rc3.r + rc4.r + rc5.r + rc6.r + rc7.r + rc8.r;
rc1.c = c;
rc2.c = c;
rc3.c = c;
rc4.c = c;
rc5.c = c;
rc6.c = c;
rc7.c = c;
rc8.c = c;
mc1.c = c;
mc2.c = c;
mc3.c = c;
mc4.c = c;
annotation(
Line(points = {{50, 90}, {50, 90}}, color = {0, 0, 255}, smooth = Smooth.None),
Icon(graphics = {Rectangle(extent = {{-100, 100}, {100, -100}}, lineColor = {0, 0, 255})}),
Diagram(graphics));
end BasicNode;
partial model BasicModifierNode "Deprecated: Basic declarations of any Metabolite / exactly like BasicNode for declaration symmetry reasons"