biobb_dna updated to 4.2.2

.gitignore

@@ -20,6 +20,7 @@ log*.*
 .ipynb_checkpoints/
 biobb_wf_dna_helparms/notebooks/*/
 !biobb_wf_dna_helparms/notebooks/TRAJ/
+!biobb_wf_dna_helparms/notebooks/.curvesplus/
 biobb_wf_dna_helparms/notebooks/*.jpg
 biobb_wf_dna_helparms/notebooks/*.gif
 biobb_wf_dna_helparms/notebooks/*.web.ipynb

binder/environment.yml

@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - biobb_dna==4.2.1
+  - biobb_dna==4.2.2
   - matplotlib

biobb_wf_dna_helparms/docs/source/tutorial.md

@@ -53,7 +53,58 @@ jupyter-notebook biobb_wf_dna_helparms/notebooks/biobb_wf_dna_helparms.ipynb
 	title="Bioexcel2 logo" width="400" />
 ***
 
+***
+
+## Initializing colab
+The two cells below are used only in case this notebook is executed via **Google Colab**. Take into account that, for running conda on **Google Colab**, the **condacolab** library must be installed. As [explained here](https://pypi.org/project/condacolab/), the installation requires a **kernel restart**, so when running this notebook in **Google Colab**, don't run all cells until this **installation** is properly **finished** and the **kernel** has **restarted**.
+
+
+```python
+# Only executed when using google colab
+import sys
+if 'google.colab' in sys.modules:
+  import subprocess
+  from pathlib import Path
+  try:
+    subprocess.run(["conda", "-V"], check=True)
+  except FileNotFoundError:
+    subprocess.run([sys.executable, "-m", "pip", "install", "condacolab"], check=True)
+    import condacolab
+    condacolab.install()
+    # Clone repository
+    repo_URL = "https://github.com/bioexcel/biobb_wf_dna_helparms.git"
+    repo_name = Path(repo_URL).name.split('.')[0]
+    if not Path(repo_name).exists():
+      subprocess.run(["mamba", "install", "-y", "git"], check=True)
+      subprocess.run(["git", "clone", repo_URL], check=True)
+      print("⏬ Repository properly cloned.")
+    # Install environment
+    print("⏳ Creating environment...")
+    env_file_path = f"{repo_name}/conda_env/environment.yml"
+    subprocess.run(["mamba", "env", "update", "-n", "base", "-f", env_file_path], check=True)
+    print("👍 Conda environment successfully created and updated.")
+```
+
 
+```python
+# Enable widgets for colab
+if 'google.colab' in sys.modules:
+  from google.colab import output
+  output.enable_custom_widget_manager()
+  # Change working dir
+  import os
+  os.chdir("biobb_wf_dna_helparms/biobb_wf_dna_helparms/notebooks/abc_setup")
+  print(f"📂 New working directory: {os.getcwd()}")
+```
+
+<a id="input"></a>
+## Input parameters
+**Input parameters** needed:
+ - **seq**: Sequence of the DNA structure (e.g. CGCGAATTCGCG)
+ - **seq_comp**: Complementary sequence of the given DNA structure (e.g. CGCGAATTCGCG)
+
+ - **traj**: Trajectory for a 500ns Drew Dickerson Dodecamer MD simulation (taken from [BigNASim](https://mmb.irbbarcelona.org/BIGNASim/)) 
+ - **top**: Associated topology for the MD trajectory 
 
 ```python
 # Auxiliary libraries
@@ -71,16 +122,6 @@ import ipywidgets
 
 ```
 
-<a id="input"></a>
-## Input parameters
-**Input parameters** needed:
- - **seq**: Sequence of the DNA structure (e.g. CGCGAATTCGCG)
- - **seq_comp**: Complementary sequence of the given DNA structure (e.g. CGCGAATTCGCG)
-
- - **traj**: Trajectory for a 500ns Drew Dickerson Dodecamer MD simulation (taken from [BigNASim](https://mmb.irbbarcelona.org/BIGNASim/)) 
- - **top**: Associated topology for the MD trajectory 
-
-
 ```python
 # Input parameters
 seq = "CGCGAATTCGCG"
@@ -146,7 +187,9 @@ curves_out_cda = "curves.out.cda"
 
 prop = {
     's1range' : '1:12',
-    's2range' : '24:13'
+    's2range' : '24:13',
+    # uncomment when running in google colab
+    # 'stdlib_path': '.curvesplus/standard'
 }
 
 biobb_curves(

biobb_wf_dna_helparms/html/biobb_wf_dna_helparms.web.html

@@ -14564,33 +14564,78 @@ <h2 id="Pipeline-steps">Pipeline steps<a class="anchor-link" href="#Pipeline-ste
     title="Bioexcel2 logo" width="400" /></p>
 <hr>
 
-</div>
-</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
-<div class="jp-Cell-inputWrapper">
-<div class="jp-InputArea jp-Cell-inputArea">
-<div class="jp-InputPrompt jp-InputArea-prompt">In&nbsp;[1]:</div>
-<div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
-     <div class="CodeMirror cm-s-jupyter">
-<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Auxiliary libraries</span>
-
-<span class="kn">import</span> <span class="nn">os</span>
-<span class="kn">import</span> <span class="nn">shutil</span>
-<span class="kn">import</span> <span class="nn">glob</span>
-<span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span><span class="p">,</span> <span class="n">PurePath</span>
-<span class="kn">import</span> <span class="nn">zipfile</span>
-<span class="kn">import</span> <span class="nn">matplotlib.image</span> <span class="k">as</span> <span class="nn">mpimg</span>
-<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
-<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
-<span class="kn">from</span> <span class="nn">IPython.display</span> <span class="kn">import</span> <span class="n">Image</span>
-<span class="kn">import</span> <span class="nn">ipywidgets</span>
-</pre></div>
-
-     </div>
-</div>
 </div>
 </div>
 
-</div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+  <div class="jp-Cell-inputWrapper" tabindex="0">
+  <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+  </div>
+  <div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+  </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+  <h2 id="Initializing-colab">Initializing colab<a class="anchor-link" href="#Initializing-colab">¶</a></h2><p>The two cells below are used only in case this notebook is executed via <strong>Google Colab</strong>. Take into account that, for running conda on <strong>Google Colab</strong>, the <strong>condacolab</strong> library must be installed. As <a href="https://pypi.org/project/condacolab/">explained here</a>, the installation requires a <strong>kernel restart</strong>, so when running this notebook in <strong>Google Colab</strong>, don't run all cells until this <strong>installation</strong> is properly <strong>finished</strong> and the <strong>kernel</strong> has <strong>restarted</strong>.</p>
+  </div>
+  </div>
+  </div>
+  </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+  <div class="jp-Cell-inputWrapper" tabindex="0">
+  <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+  </div>
+  <div class="jp-InputArea jp-Cell-inputArea">
+  <div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+  <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+  <div class="cm-editor cm-s-jupyter">
+  <div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Only executed when using google colab</span>
+  <span class="kn">import</span> <span class="nn">sys</span>
+  <span class="k">if</span> <span class="s1">'google.colab'</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">subprocess</span>
+    <span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span>
+    <span class="k">try</span><span class="p">:</span>
+      <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="s2">"conda"</span><span class="p">,</span> <span class="s2">"-V"</span><span class="p">],</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+    <span class="k">except</span> <span class="ne">FileNotFoundError</span><span class="p">:</span>
+      <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="n">sys</span><span class="o">.</span><span class="n">executable</span><span class="p">,</span> <span class="s2">"-m"</span><span class="p">,</span> <span class="s2">"pip"</span><span class="p">,</span> <span class="s2">"install"</span><span class="p">,</span> <span class="s2">"condacolab"</span><span class="p">],</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+      <span class="kn">import</span> <span class="nn">condacolab</span>
+      <span class="n">condacolab</span><span class="o">.</span><span class="n">install</span><span class="p">()</span>
+      <span class="c1"># Clone repository</span>
+      <span class="n">repo_URL</span> <span class="o">=</span> <span class="s2">"https://github.com/bioexcel/biobb_wf_dna_helparms.git"</span>
+      <span class="n">repo_name</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">repo_URL</span><span class="p">)</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'.'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+      <span class="k">if</span> <span class="ow">not</span> <span class="n">Path</span><span class="p">(</span><span class="n">repo_name</span><span class="p">)</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+        <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="s2">"mamba"</span><span class="p">,</span> <span class="s2">"install"</span><span class="p">,</span> <span class="s2">"-y"</span><span class="p">,</span> <span class="s2">"git"</span><span class="p">],</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="s2">"git"</span><span class="p">,</span> <span class="s2">"clone"</span><span class="p">,</span> <span class="n">repo_URL</span><span class="p">],</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="nb">print</span><span class="p">(</span><span class="s2">"⏬ Repository properly cloned."</span><span class="p">)</span>
+      <span class="c1"># Install environment</span>
+      <span class="nb">print</span><span class="p">(</span><span class="s2">"⏳ Creating environment..."</span><span class="p">)</span>
+      <span class="n">env_file_path</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">repo_name</span><span class="si">}</span><span class="s2">/conda_env/environment.yml"</span>
+      <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">([</span><span class="s2">"mamba"</span><span class="p">,</span> <span class="s2">"env"</span><span class="p">,</span> <span class="s2">"update"</span><span class="p">,</span> <span class="s2">"-n"</span><span class="p">,</span> <span class="s2">"base"</span><span class="p">,</span> <span class="s2">"-f"</span><span class="p">,</span> <span class="n">env_file_path</span><span class="p">],</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+      <span class="nb">print</span><span class="p">(</span><span class="s2">"👍 Conda environment successfully created and updated."</span><span class="p">)</span>
+  </pre></div>
+  </div>
+  </div>
+  </div>
+  </div>
+  </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs">
+  <div class="jp-Cell-inputWrapper" tabindex="0">
+  <div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+  </div>
+  <div class="jp-InputArea jp-Cell-inputArea">
+  <div class="jp-InputPrompt jp-InputArea-prompt">In [ ]:</div>
+  <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+  <div class="cm-editor cm-s-jupyter">
+  <div class="highlight hl-ipython3"><pre><span></span><span class="c1"># Enable widgets for colab</span>
+  <span class="k">if</span> <span class="s1">'google.colab'</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">:</span>
+    <span class="kn">from</span> <span class="nn">google.colab</span> <span class="kn">import</span> <span class="n">output</span>
+    <span class="n">output</span><span class="o">.</span><span class="n">enable_custom_widget_manager</span><span class="p">()</span>
+    <span class="c1"># Change working dir</span>
+    <span class="kn">import</span> <span class="nn">os</span>
+    <span class="n">os</span><span class="o">.</span><span class="n">chdir</span><span class="p">(</span><span class="s2">"biobb_wf_dna_helparms/biobb_wf_dna_helparms/notebooks"</span><span class="p">)</span>
+    <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"📂 New working directory: </span><span class="si">{</span><span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">()</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+  </pre></div>
+  </div>
+  </div>
+  </div>
+  </div>
+  </div>
+
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <p><a id="input"></a></p>
@@ -14605,7 +14650,34 @@ <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-pa
 </ul>
 
 </div>
-</div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
+</div>
+<div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
+  <div class="jp-Cell-inputWrapper">
+  <div class="jp-InputArea jp-Cell-inputArea">
+  <div class="jp-InputPrompt jp-InputArea-prompt">In&nbsp;[1]:</div>
+  <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
+       <div class="CodeMirror cm-s-jupyter">
+  <div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># Auxiliary libraries</span>
+
+  <span class="kn">import</span> <span class="nn">os</span>
+  <span class="kn">import</span> <span class="nn">shutil</span>
+  <span class="kn">import</span> <span class="nn">glob</span>
+  <span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span><span class="p">,</span> <span class="n">PurePath</span>
+  <span class="kn">import</span> <span class="nn">zipfile</span>
+  <span class="kn">import</span> <span class="nn">matplotlib.image</span> <span class="k">as</span> <span class="nn">mpimg</span>
+  <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
+  <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+  <span class="kn">from</span> <span class="nn">IPython.display</span> <span class="kn">import</span> <span class="n">Image</span>
+  <span class="kn">import</span> <span class="nn">ipywidgets</span>
+  </pre></div>
+
+       </div>
+  </div>
+  </div>
+  </div>
+
+  </div>
+<div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
 <div class="jp-Cell-inputWrapper">
 <div class="jp-InputArea jp-Cell-inputArea">
 <div class="jp-InputPrompt jp-InputArea-prompt">In&nbsp;[2]:</div>
@@ -14685,7 +14757,9 @@ <h3 id="Step-1:-Curves+">Step 1: Curves+<a class="anchor-link" href="#Step-1:-Cu
 
 <span class="n">prop</span> <span class="o">=</span> <span class="p">{</span>
     <span class="s1">&#39;s1range&#39;</span> <span class="p">:</span> <span class="s1">&#39;1:12&#39;</span><span class="p">,</span>
-    <span class="s1">&#39;s2range&#39;</span> <span class="p">:</span> <span class="s1">&#39;24:13&#39;</span>
+    <span class="s1">&#39;s2range&#39;</span> <span class="p">:</span> <span class="s1">&#39;24:13&#39;</span><span class="p">,</span>
+    <span class="c1"># uncomment when running in google colab</span>
+    <span class="c1"># 'stdlib_path': '.curvesplus/standard'</span>
 <span class="p">}</span>
 
 <span class="n">biobb_curves</span><span class="p">(</span>

biobb_wf_dna_helparms/notebooks/.curvesplus/standard_b.lib

@@ -0,0 +1,91 @@
+# This file defines the bases recognized by Cur+ and gives the coordinates
+# of the standard bases used for least squres fitting
+#
+# Each base begins with a one letter name code in col.1 and R (purine)
+# or Y (pyrimidine) in col.3, followed by number of atoms in the base and
+# the full base name (<= 8 chars)
+#
+# Each atom line gives x,y,z coordinates followed by the atom name (<= 4 chars)
+#
+# The first 2 atoms should define the bond from the backbone to the base
+# The third atom defines the standard base normal as a cross product (1-2)x(3-2)
+#
+# The fourth atom is used for defining groove depth, C8 for purines and C6 for pyrimidines.
+# It should be the atom that defines the center of the base pair for Watson-Crick pairing
+#
+G R 10 'Guanine'
+ 1.58195 -2.39594 -0.12320 'C1*'
+ 0.37714 -1.52785 -0.00520 'N9'
+ 0.37551 -0.14975 -0.04020 'C4'
+-0.94239 -1.88689  0.15880 'C8'
+-0.10165  2.41153 -0.05020 'N1'
+ 1.18367  1.92662 -0.18720 'C2'
+ 1.47916  0.62851 -0.18920 'N3'
+-0.93480  0.24071  0.10280 'C5'
+-1.25149  1.62390  0.10480 'C6'
+-1.76708 -0.87080  0.22880 'N7'
+I R 10 'Inosine'
+ 1.58195 -2.39594 -0.12320 'C1*'
+ 0.37714 -1.52785 -0.00520 'N9'
+ 0.37551 -0.14975 -0.04020 'C4'
+-0.94239 -1.88689  0.15880 'C8'
+-0.10165  2.41153 -0.05020 'N1'
+ 1.18367  1.92662 -0.18720 'C2'
+ 1.47916  0.62851 -0.18920 'N3'
+-0.93480  0.24071  0.10280 'C5'
+-1.25149  1.62390  0.10480 'C6'
+-1.76708 -0.87080  0.22880 'N7'
+Y R 10 'Y-base'
+ 1.58195 -2.39594 -0.12320 'C1*'
+ 0.37714 -1.52785 -0.00520 'N9'
+ 0.37551 -0.14975 -0.04020 'C4'
+-0.94239 -1.88689  0.15880 'C8'
+-0.10165  2.41153 -0.05020 'N1'
+ 1.18367  1.92662 -0.18720 'C2'
+ 1.47916  0.62851 -0.18920 'N3'
+-0.93480  0.24071  0.10280 'C5'
+-1.25149  1.62390  0.10480 'C6'
+-1.76708 -0.87080  0.22880 'N7'
+A R 10 'Adenine'
+ 1.57340 -2.41044 -0.12190 'C1*'
+ 0.37786 -1.52945 -0.00531 'N9'
+ 0.38110 -0.16006 -0.04011 'C4'
+-0.94428 -1.87750  0.15888 'C8'
+-0.11123  2.43959 -0.04964 'N1'
+ 1.10298  1.90641 -0.17768 'C2'
+ 1.45731  0.64079 -0.18694 'N3'
+-0.91754  0.23706  0.10110 'C5'
+-1.16848  1.61858  0.09523 'C6'
+-1.75109 -0.86494  0.22638 'N7'
+C Y 7 'Cytosine'
+ 1.94866 -1.45161 -0.19029 'C1*'
+ 0.74385 -0.58352 -0.07229 'N1'
+ 0.93020  0.79520 -0.12929 'C2'
+-0.49500 -1.12092  0.08671 'C6'
+-0.15547  1.60399 -0.02329 'N3'
+-1.37969  1.08626  0.13371 'C4'
+-1.59254 -0.32937  0.19471 'C5'
+T Y 7 'Thymine'
+ 1.95363 -1.45659 -0.19073 'C1*'
+ 0.75787 -0.57587 -0.07419 'N1'
+ 0.97215  0.78019 -0.13405 'C2'
+-0.49400 -1.10811  0.08633 'C6'
+-0.15841  1.56515 -0.02137 'N3'
+-1.45350  1.11665  0.14102 'C4'
+-1.57773 -0.32139  0.19302 'C5'
+U Y 7 'Uracil'
+ 1.95363 -1.45659 -0.19073 'C1*'
+ 0.75787 -0.57587 -0.07419 'N1'
+ 0.97215  0.78019 -0.13405 'C2'
+-0.49400 -1.10811  0.08633 'C6'
+-0.15841  1.56515 -0.02137 'N3'
+-1.45350  1.11665  0.14102 'C4'
+-1.57773 -0.32139  0.19302 'C5'
+P Y 7 'Pseudo-U'
+-1.24071 -2.10001 -0.01015 'C1*'
+-0.48272 -0.82819 -0.00729 'C5'
+-1.20770  0.33858  0.00979 'C4'
+ 0.89420 -0.82819 -0.00729 'C6'
+ 1.59022  0.32075 -0.00729 'N1'
+ 0.91535  1.59602  0.00679 'C2'
+-0.46861  1.50106  0.01545 'N3'

biobb_wf_dna_helparms/notebooks/.curvesplus/standard_i.lib

@@ -0,0 +1,14 @@
+# Ion library
+# Each line gives the ion/atom name (in signle quotes) and its formal charge
+# Up to 40 ion type are allowed in this library file
+'Na+' 1
+'K+' 1
+'K' 1
+'Cl' -1
+'Cl-' -1
+'CL' -1
+'P' -1
+'C1*' 0
+'NH1' 1
+'NH2' 1
+'NZ' 1