migrate from BasicPart.concentration() to BasicPart.clip_mass()

basicsynbio/cam/csv_export.py

@@ -43,8 +43,7 @@ def export_csvs(
             "Prefix ID",
             "Part ID",
             "Part Name",
-            "Part suggested stock concentration (ng/µL)",
-            "Part stock per 30 µL clip (µL)",
+            "Part mass for 30 μL clip reaction (ng)",
             "Suffix ID",
             "Total assemblies",
             "Assembly indexes",
@@ -59,10 +58,9 @@ def export_csvs(
                     "Prefix ID": clip_data[0]._prefix.prefix_id,
                     "Part ID": clip_data[0]._part.id,
                     "Part Name": clip_data[0]._part.name,
-                    "Part suggested stock concentration (ng/µL)": clip_data[
+                    "Part mass for 30 μL clip reaction (ng)": clip_data[
                         0
-                    ]._part.concentration(),
-                    "Part stock per 30 µL clip (µL)": 1,
+                    ]._part.clip_mass(),
                     "Suffix ID": clip_data[0]._suffix.suffix_id,
                     "Total assemblies": len(clip_data[1]),
                     "Assembly indexes": [

basicsynbio/cam/main.py

@@ -238,8 +238,7 @@ def unique_parts_json(obj):
                 "id": value["part"].id,
                 "name": value["part"].name,
                 "description": value["part"].description,
-                "suggested stock concentration (ng/µL)": value["part"].concentration(),
-                "stock per 30 µL clip (µL)": 1,
+                "Part mass for 30 μL clip reaction (ng)": value["part"].clip_mass(),
                 "clip reactions": [
                     "CR" + str(list(obj.clips_data.keys()).index(clip_reaction))
                     for clip_reaction in value["clip reactions"]

basicsynbio/main.py

@@ -102,19 +102,15 @@ def basic_slice(self) -> SeqRecord:
         else:
             raise ValueError("incorrect sequence used.")
 
-    def concentration(
+    def clip_mass(
         self,
-        stock: bool = True,
         clip_vol: float = 30,
         circular: bool = True,
         ndigit: int = None,
     ) -> Union[float, int]:
-        """Obtain the recommended concentration of part in ng/µL.
-
-        This can either be the recommended stock concentration of part or the final concentration of part in clip reactions.
+        """Obtain the recommended mass of part (ng) for a clip reaction.
 
         Args:
-            stock: If true, method returns the stock concentration required for adding 1 µL part to each clip reaction with volume = clip_vol. Else returns the suggested final concentration of part in a clip reaction (ng/µL).
             clip_vol: volume of the clip reaction (µL).
             circular: The part is circular or linear if False.
             ndigit: Refer to built-in round function documentation.
@@ -126,9 +122,7 @@ def concentration(
             )
             / 1e6
         )
-        if stock:
-            return round(final_concentration * clip_vol, ndigit)
-        return round(final_concentration, ndigit)
+        return round(final_concentration * clip_vol, ndigit)
 
     def domesticating_primers(
         self,

docs/_modules/basicsynbio/cam/main.html

@@ -272,8 +272,7 @@ <h1>Source code for basicsynbio.cam.main</h1><div class="highlight"><pre>
                 <span class="s2">&quot;id&quot;</span><span class="p">:</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;part&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">id</span><span class="p">,</span>
                 <span class="s2">&quot;name&quot;</span><span class="p">:</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;part&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
                 <span class="s2">&quot;description&quot;</span><span class="p">:</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;part&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">description</span><span class="p">,</span>
-                <span class="s2">&quot;suggested stock concentration (ng/µL)&quot;</span><span class="p">:</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;part&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">concentration</span><span class="p">(),</span>
-                <span class="s2">&quot;stock per 30 µL clip (µL)&quot;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
+                <span class="s2">&quot;Part mass for 30 μL clip reaction (ng)&quot;</span><span class="p">:</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;part&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">clip_mass</span><span class="p">(),</span>
                 <span class="s2">&quot;clip reactions&quot;</span><span class="p">:</span> <span class="p">[</span>
                     <span class="s2">&quot;CR&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">obj</span><span class="o">.</span><span class="n">clips_data</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">clip_reaction</span><span class="p">))</span>
                     <span class="k">for</span> <span class="n">clip_reaction</span> <span class="ow">in</span> <span class="n">value</span><span class="p">[</span><span class="s2">&quot;clip reactions&quot;</span><span class="p">]</span>

docs/_modules/basicsynbio/main.html

@@ -136,19 +136,15 @@ <h1>Source code for basicsynbio.main</h1><div class="highlight"><pre>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;incorrect sequence used.&quot;</span><span class="p">)</span></div>
 
-<div class="viewcode-block" id="BasicPart.concentration"><a class="viewcode-back" href="../../api.html#basicsynbio.main.BasicPart.concentration">[docs]</a>    <span class="k">def</span> <span class="nf">concentration</span><span class="p">(</span>
+<div class="viewcode-block" id="BasicPart.clip_mass"><a class="viewcode-back" href="../../api.html#basicsynbio.main.BasicPart.clip_mass">[docs]</a>    <span class="k">def</span> <span class="nf">clip_mass</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
-        <span class="n">stock</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
         <span class="n">clip_vol</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mi">30</span><span class="p">,</span>
         <span class="n">circular</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
         <span class="n">ndigit</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Union</span><span class="p">[</span><span class="nb">float</span><span class="p">,</span> <span class="nb">int</span><span class="p">]:</span>
-        <span class="sd">&quot;&quot;&quot;Obtain the recommended concentration of part in ng/µL.</span>
-
-<span class="sd">        This can either be the recommended stock concentration of part or the final concentration of part in clip reactions.</span>
+        <span class="sd">&quot;&quot;&quot;Obtain the recommended mass of part (ng) for a clip reaction.</span>
 
 <span class="sd">        Args:</span>
-<span class="sd">            stock: If true, method returns the stock concentration required for adding 1 µL part to each clip reaction with volume = clip_vol. Else returns the suggested final concentration of part in a clip reaction (ng/µL).</span>
 <span class="sd">            clip_vol: volume of the clip reaction (µL).</span>
 <span class="sd">            circular: The part is circular or linear if False.</span>
 <span class="sd">            ndigit: Refer to built-in round function documentation.</span>
@@ -160,9 +156,7 @@ <h1>Source code for basicsynbio.main</h1><div class="highlight"><pre>
             <span class="p">)</span>
             <span class="o">/</span> <span class="mf">1e6</span>
         <span class="p">)</span>
-        <span class="k">if</span> <span class="n">stock</span><span class="p">:</span>
-            <span class="k">return</span> <span class="nb">round</span><span class="p">(</span><span class="n">final_concentration</span> <span class="o">*</span> <span class="n">clip_vol</span><span class="p">,</span> <span class="n">ndigit</span><span class="p">)</span>
-        <span class="k">return</span> <span class="nb">round</span><span class="p">(</span><span class="n">final_concentration</span><span class="p">,</span> <span class="n">ndigit</span><span class="p">)</span></div>
+        <span class="k">return</span> <span class="nb">round</span><span class="p">(</span><span class="n">final_concentration</span> <span class="o">*</span> <span class="n">clip_vol</span><span class="p">,</span> <span class="n">ndigit</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="BasicPart.domesticating_primers"><a class="viewcode-back" href="../../api.html#basicsynbio.main.BasicPart.domesticating_primers">[docs]</a>    <span class="k">def</span> <span class="nf">domesticating_primers</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>

docs/_sources/echo_clips_1_csv.rst.txt

@@ -1,5 +1,5 @@
 echo_clips_1.csv
-==========
+================
 
 .. csv-table::
     :file: ./literal_includes/echo_clips_1.csv

docs/_sources/echo_water_buffer_1_csv.rst.txt

@@ -1,5 +1,5 @@
 echo_water_buffer_1.csv
-==========
+=======================
 
 .. csv-table::
     :file: ./literal_includes/echo_water_buffer_1.csv

docs/api.html

@@ -245,14 +245,12 @@ <h1>API reference<a class="headerlink" href="#api-reference" title="Permalink to
 </dd></dl>
 
 <dl class="py method">
-<dt id="basicsynbio.main.BasicPart.concentration">
-<code class="sig-name descname">concentration</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">stock</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">True</span></em>, <em class="sig-param"><span class="n">clip_vol</span><span class="p">:</span> <span class="n">float</span> <span class="o">=</span> <span class="default_value">30</span></em>, <em class="sig-param"><span class="n">circular</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">True</span></em>, <em class="sig-param"><span class="n">ndigit</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em><span class="sig-paren">)</span> &#x2192; Union<span class="p">[</span>float<span class="p">, </span>int<span class="p">]</span><a class="reference internal" href="_modules/basicsynbio/main.html#BasicPart.concentration"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#basicsynbio.main.BasicPart.concentration" title="Permalink to this definition">¶</a></dt>
-<dd><p>Obtain the recommended concentration of part in ng/µL.</p>
-<p>This can either be the recommended stock concentration of part or the final concentration of part in clip reactions.</p>
+<dt id="basicsynbio.main.BasicPart.clip_mass">
+<code class="sig-name descname">clip_mass</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">clip_vol</span><span class="p">:</span> <span class="n">float</span> <span class="o">=</span> <span class="default_value">30</span></em>, <em class="sig-param"><span class="n">circular</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">True</span></em>, <em class="sig-param"><span class="n">ndigit</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em><span class="sig-paren">)</span> &#x2192; Union<span class="p">[</span>float<span class="p">, </span>int<span class="p">]</span><a class="reference internal" href="_modules/basicsynbio/main.html#BasicPart.clip_mass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#basicsynbio.main.BasicPart.clip_mass" title="Permalink to this definition">¶</a></dt>
+<dd><p>Obtain the recommended mass of part (ng) for a clip reaction.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>stock</strong> – If true, method returns the stock concentration required for adding 1 µL part to each clip reaction with volume = clip_vol. Else returns the suggested final concentration of part in a clip reaction (ng/µL).</p></li>
 <li><p><strong>clip_vol</strong> – volume of the clip reaction (µL).</p></li>
 <li><p><strong>circular</strong> – The part is circular or linear if False.</p></li>
 <li><p><strong>ndigit</strong> – Refer to built-in round function documentation.</p></li>