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+# Minimal makefile for Sphinx documentation
+#
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+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
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+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
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diff --git a/docs/html/.buildinfo b/docs/html/.buildinfo
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: b5e755138676697d0972eed8cd45ecdd
+tags: 645f666f9bcd5a90fca523b33c5a78b7
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diff --git a/docs/html/.doctrees/pyenzyme.restful.validate.doctree b/docs/html/.doctrees/pyenzyme.restful.validate.doctree
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diff --git a/docs/html/.doctrees/pyenzyme.thinlayers.TL_Copasi.doctree b/docs/html/.doctrees/pyenzyme.thinlayers.TL_Copasi.doctree
diff --git a/docs/html/.doctrees/pyenzyme.thinlayers.TL_Pysces.doctree b/docs/html/.doctrees/pyenzyme.thinlayers.TL_Pysces.doctree
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diff --git a/docs/html/.nojekyll b/docs/html/.nojekyll
diff --git a/docs/html/_modules/index.html b/docs/html/_modules/index.html
@@ -0,0 +1,144 @@
+<!DOCTYPE html>
+<html >
+  <head>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width,initial-scale=1">
+      <title>Overview: module code</title>
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+      <p class="caption">
+        <span class="caption-text"><a href="../index.html#welcome-to-pyenzyme-s-documentation">Contents:</a></span>
+      </p>
+      <ul class="">
+
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+    </div>
+
+</div>
+        </sidebar>
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+      <page>
+          <div class="body-header" role="navigation" aria-label="navigation">
+
+  <ul class="breadcrumbs">
+    <li><a href="../index.html">Docs</a> &raquo;</li>
+
+    <li>Overview: module code</li>
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+
+  <ul class="page-nav">
+</ul>
+
+</div>
+<hr>
+          <div class="content" role="main" v-pre>
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="pyenzyme/enzymeml/core/abstract_classes.html">pyenzyme.enzymeml.core.abstract_classes</a></li>
+<li><a href="pyenzyme/enzymeml/core/creator.html">pyenzyme.enzymeml.core.creator</a></li>
+<li><a href="pyenzyme/enzymeml/core/enzymemlbase.html">pyenzyme.enzymeml.core.enzymemlbase</a></li>
+<li><a href="pyenzyme/enzymeml/core/enzymemldocument.html">pyenzyme.enzymeml.core.enzymemldocument</a></li>
+<li><a href="pyenzyme/enzymeml/core/enzymereaction.html">pyenzyme.enzymeml.core.enzymereaction</a></li>
+<li><a href="pyenzyme/enzymeml/core/exceptions.html">pyenzyme.enzymeml.core.exceptions</a></li>
+<li><a href="pyenzyme/enzymeml/core/measurement.html">pyenzyme.enzymeml.core.measurement</a></li>
+<li><a href="pyenzyme/enzymeml/core/measurementData.html">pyenzyme.enzymeml.core.measurementData</a></li>
+<li><a href="pyenzyme/enzymeml/core/ontology.html">pyenzyme.enzymeml.core.ontology</a></li>
+<li><a href="pyenzyme/enzymeml/core/protein.html">pyenzyme.enzymeml.core.protein</a></li>
+<li><a href="pyenzyme/enzymeml/core/reactant.html">pyenzyme.enzymeml.core.reactant</a></li>
+<li><a href="pyenzyme/enzymeml/core/replicate.html">pyenzyme.enzymeml.core.replicate</a></li>
+<li><a href="pyenzyme/enzymeml/core/unitdef.html">pyenzyme.enzymeml.core.unitdef</a></li>
+<li><a href="pyenzyme/enzymeml/core/utils.html">pyenzyme.enzymeml.core.utils</a></li>
+<li><a href="pyenzyme/enzymeml/core/vessel.html">pyenzyme.enzymeml.core.vessel</a></li>
+<li><a href="pyenzyme/enzymeml/databases/dataverse.html">pyenzyme.enzymeml.databases.dataverse</a></li>
+<li><a href="pyenzyme/enzymeml/models/kineticmodel.html">pyenzyme.enzymeml.models.kineticmodel</a></li>
+<li><a href="pyenzyme/enzymeml/models/michaelismenten.html">pyenzyme.enzymeml.models.michaelismenten</a></li>
+<li><a href="pyenzyme/enzymeml/tools/enzymemlreader.html">pyenzyme.enzymeml.tools.enzymemlreader</a></li>
+<li><a href="pyenzyme/enzymeml/tools/enzymemlwriter.html">pyenzyme.enzymeml.tools.enzymemlwriter</a></li>
+<li><a href="pyenzyme/enzymeml/tools/unitcreator.html">pyenzyme.enzymeml.tools.unitcreator</a></li>
+<li><a href="pyenzyme/enzymeml/tools/unitparser.html">pyenzyme.enzymeml.tools.unitparser</a></li>
+<li><a href="pyenzyme/restful/create.html">pyenzyme.restful.create</a></li>
+<li><a href="pyenzyme/restful/create_schema.html">pyenzyme.restful.create_schema</a></li>
+</ul>
+
+          </div>
+          <div class="page-nav">
+            <div class="inner"><ul class="page-nav">
+</ul><div class="footer" role="contentinfo">
+      &#169; Copyright 2021, Jan.
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+    Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.3.1 with <a href="https://github.com/schettino72/sphinx_press_theme">Press Theme</a> 0.8.0.
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+            </div>
+          </div>
+      </page>
+    </div></div>
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+
+  </body>
+</html>
diff --git a/docs/html/_modules/pyenzyme/enzymeml/core/abstract_classes.html b/docs/html/_modules/pyenzyme/enzymeml/core/abstract_classes.html
@@ -0,0 +1,173 @@
+<!DOCTYPE html>
+<html >
+  <head>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width,initial-scale=1">
+      <title>pyenzyme.enzymeml.core.abstract_classes</title>
+
+          <link rel="stylesheet" href="../../../../_static/pygments.css" type="text/css" />
+          <link rel="stylesheet" href="../../../../_static/theme.css " type="text/css" />
+          <link rel="stylesheet" href="../../../../_static/autodoc_pydantic.css" type="text/css" />
+          <link rel="stylesheet" href="../../../../_static/copybutton.css" type="text/css" />
+
+      <!-- sphinx script_files -->
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+
+
+      <!-- bundled in js (rollup iife) -->
+      <!-- <script src="../../../../_static/theme-vendors.js"></script> -->
+      <script src="../../../../_static/theme.js" defer></script>
+
+  <link rel="index" title="Index" href="../../../../genindex.html" />
+  <link rel="search" title="Search" href="../../../../search.html" /> 
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+
+  <body>
+    <div id="app">
+    <div class="theme-container" :class="pageClasses"><navbar @toggle-sidebar="toggleSidebar">
+  <router-link to="../../../../index.html" class="home-link">
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+          </navlinks><div id="searchbox" class="searchbox" role="search">
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+      <form class="search" action="../../../../search.html" method="get">
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+        <input type="hidden" name="check_keywords" value="yes" />
+        <input type="hidden" name="area" value="default" />
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+</div><div class="sidebar-links" role="navigation" aria-label="main navigation">
+
+    <div class="sidebar-group">
+      <p class="caption">
+        <span class="caption-text"><a href="../../../../index.html#welcome-to-pyenzyme-s-documentation">Contents:</a></span>
+      </p>
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+
+      </ul>
+    </div>
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+</div>
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+      <page>
+          <div class="body-header" role="navigation" aria-label="navigation">
+
+  <ul class="breadcrumbs">
+    <li><a href="../../../../index.html">Docs</a> &raquo;</li>
+
+      <li><a href="../../../index.html">Module code</a> &raquo;</li>
+
+    <li>pyenzyme.enzymeml.core.abstract_classes</li>
+  </ul>
+
+
+  <ul class="page-nav">
+</ul>
+
+</div>
+<hr>
+          <div class="content" role="main" v-pre>
+
+  <h1>Source code for pyenzyme.enzymeml.core.abstract_classes</h1><div class="highlight"><pre>
+<span></span><span class="kn">from</span> <span class="nn">pydantic</span> <span class="kn">import</span> <span class="n">BaseModel</span><span class="p">,</span> <span class="n">PositiveFloat</span><span class="p">,</span> <span class="n">PrivateAttr</span><span class="p">,</span> <span class="n">validator</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span>
+<span class="kn">from</span> <span class="nn">enum</span> <span class="kn">import</span> <span class="n">Enum</span>
+<span class="kn">from</span> <span class="nn">abc</span> <span class="kn">import</span> <span class="n">ABC</span><span class="p">,</span> <span class="n">abstractmethod</span>
+
+
+<div class="viewcode-block" id="AbstractSpeciesDataclass"><a class="viewcode-back" href="../../../../pyenzyme.enzymeml.core.html#pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesDataclass">[docs]</a><span class="k">class</span> <span class="nc">AbstractSpeciesDataclass</span><span class="p">(</span><span class="n">BaseModel</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;Abstract dataclass to describe an EnzymeML/SBML species.&quot;&quot;&quot;</span>
+
+    <span class="n">name</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="nb">id</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">meta_id</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">init_conc</span><span class="p">:</span> <span class="n">PositiveFloat</span>
+    <span class="n">constant</span><span class="p">:</span> <span class="nb">bool</span>
+    <span class="n">unit</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">ontology</span><span class="p">:</span> <span class="n">Enum</span>
+    <span class="n">_unit_id</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">PrivateAttr</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+    <span class="n">uri</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span>
+    <span class="n">creator_id</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span></div>
+
+
+<div class="viewcode-block" id="AbstractSpecies"><a class="viewcode-back" href="../../../../pyenzyme.enzymeml.core.html#pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies">[docs]</a><span class="k">class</span> <span class="nc">AbstractSpecies</span><span class="p">(</span><span class="n">ABC</span><span class="p">,</span> <span class="n">AbstractSpeciesDataclass</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;Due to inheritance and type-checking issues, the dataclass has to be mixed in.&quot;&quot;&quot;</span>
+
+<div class="viewcode-block" id="AbstractSpecies.set_unit_id"><a class="viewcode-back" href="../../../../pyenzyme.enzymeml.core.html#pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies.set_unit_id">[docs]</a>    <span class="k">def</span> <span class="nf">set_unit_id</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">unit_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s2">&quot;_unit_id&quot;</span><span class="p">,</span> <span class="n">unit_id</span><span class="p">)</span></div>
+
+    <span class="c1"># ! Validators</span>
+<div class="viewcode-block" id="AbstractSpecies.set_meta_id"><a class="viewcode-back" href="../../../../pyenzyme.enzymeml.core.html#pyenzyme.enzymeml.core.abstract_classes.AbstractSpecies.set_meta_id">[docs]</a>    <span class="nd">@validator</span><span class="p">(</span><span class="s2">&quot;id&quot;</span><span class="p">)</span>
+    <span class="k">def</span> <span class="nf">set_meta_id</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="nb">id</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">values</span><span class="p">:</span> <span class="nb">dict</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Sets the meta ID when an ID is provided&quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="nb">id</span><span class="p">:</span>
+            <span class="c1"># Set Meta ID with ID</span>
+            <span class="n">values</span><span class="p">[</span><span class="s2">&quot;meta_id&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;METAID_</span><span class="si">{</span><span class="nb">id</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span><span class="si">}</span><span class="s2">&quot;</span>
+
+        <span class="k">return</span> <span class="nb">id</span></div></div>
+
+
+<div class="viewcode-block" id="AbstractSpeciesFactory"><a class="viewcode-back" href="../../../../pyenzyme.enzymeml.core.html#pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesFactory">[docs]</a><span class="k">class</span> <span class="nc">AbstractSpeciesFactory</span><span class="p">(</span><span class="n">ABC</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Factory that returns a specific species instance.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">enzymeml_part</span><span class="p">:</span> <span class="nb">str</span>
+
+<div class="viewcode-block" id="AbstractSpeciesFactory.get_species"><a class="viewcode-back" href="../../../../pyenzyme.enzymeml.core.html#pyenzyme.enzymeml.core.abstract_classes.AbstractSpeciesFactory.get_species">[docs]</a>    <span class="nd">@abstractmethod</span>
+    <span class="k">def</span> <span class="nf">get_species</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">AbstractSpecies</span><span class="p">:</span>
+        <span class="sd">&quot;&quot;&quot;Return a new species object&quot;&quot;&quot;</span></div></div>
+</pre></div>
+
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