Fixed tutorial introduction

bioexcel · Sep 28, 2023 · 7fb344a · 7fb344a
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diff --git a/README.md b/README.md
@@ -24,9 +24,8 @@ The tutorials will guide you through the process of identifying the **active sit
 
 ### Auxiliar libraries used
 
-* [nb_conda_kernels](https://github.com/Anaconda-Platform/nb_conda_kernels): Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.
+* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.
 * [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
-* [ipywidgets](https://github.com/jupyter-widgets/ipywidgets): Interactive HTML widgets for Jupyter notebooks and the IPython kernel.
 
 ### Conda Installation
 
@@ -37,13 +36,6 @@ conda env create -f conda_env/environment.yml
 conda activate biobb_VS_tutorial
 ```
 
-Please execute the following commands before launching the Jupyter Notebook if you experience some issues with widgets such as NGL View (3D molecular visualization):
-
-```console
-jupyter-nbextension enable --py --user widgetsnbextension
-jupyter-nbextension enable --py --user nglview
-```
-
 ### Launch
 
 #### EBI REST API tutorial

diff --git a/biobb_wf_virtual-screening/docs/notebooks/wf_vs_clusterBindingSite.docs.ipynb b/biobb_wf_virtual-screening/docs/notebooks/wf_vs_clusterBindingSite.docs.ipynb
@@ -29,25 +29,17 @@
     " \n",
     "### Auxiliar libraries used\n",
     "\n",
-    " - [nb_conda_kernels](https://github.com/Anaconda-Platform/nb_conda_kernels): Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.\n",
-    " - [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.\n",
-    " - [ipywidgets](https://github.com/jupyter-widgets/ipywidgets): Interactive HTML widgets for Jupyter notebooks and the IPython kernel.\n",
+    "* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.\n",
+    "* [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.\n",
     "\n",
-    "### Conda Installation and Launch\n",
+    "### Conda Installation\n",
     "\n",
     "```console\n",
     "git clone https://github.com/bioexcel/biobb_wf_virtual-screening.git\n",
     "cd biobb_wf_virtual-screening\n",
     "conda env create -f conda_env/environment.yml\n",
     "conda activate biobb_VS_tutorial\n",
-    "jupyter-notebook biobb_wf_virtual-screening/notebooks/ebi_api/wf_vs_ebi_api.ipynb\n",
-    "``` \n",
-    "\n",
-    "Please execute the following commands before launching the Jupyter Notebook if you experience some issues with widgets such as NGL View (3D molecular visualization):\n",
-    "\n",
-    "```console\n",
-    "jupyter-nbextension enable --py --user widgetsnbextension\n",
-    "jupyter-nbextension enable --py --user nglview\n",
+    "jupyter-notebook biobb_wf_virtual-screening/notebooks/ebi_api/wf_vs_clusterBindingSite.ipynb\n",
     "```\n",
     "\n",
     "***\n",

diff --git a/biobb_wf_virtual-screening/docs/notebooks/wf_vs_ebi_api.docs.ipynb b/biobb_wf_virtual-screening/docs/notebooks/wf_vs_ebi_api.docs.ipynb
@@ -29,25 +29,17 @@
     " \n",
     "### Auxiliar libraries used\n",
     "\n",
-    " - [nb_conda_kernels](https://github.com/Anaconda-Platform/nb_conda_kernels): Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.\n",
-    " - [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.\n",
-    " - [ipywidgets](https://github.com/jupyter-widgets/ipywidgets): Interactive HTML widgets for Jupyter notebooks and the IPython kernel.\n",
+    "* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.\n",
+    "* [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.\n",
     "\n",
-    "### Conda Installation and Launch\n",
+    "### Conda Installation\n",
     "\n",
     "```console\n",
     "git clone https://github.com/bioexcel/biobb_wf_virtual-screening.git\n",
     "cd biobb_wf_virtual-screening\n",
     "conda env create -f conda_env/environment.yml\n",
     "conda activate biobb_VS_tutorial\n",
     "jupyter-notebook biobb_wf_virtual-screening/notebooks/ebi_api/wf_vs_ebi_api.ipynb\n",
-    "  ```\n",
-    "  \n",
-    "Please execute the following commands before launching the Jupyter Notebook if you experience some issues with widgets such as NGL View (3D molecular visualization):\n",
-    "\n",
-    "```console\n",
-    "jupyter-nbextension enable --py --user widgetsnbextension\n",
-    "jupyter-nbextension enable --py --user nglview\n",
     "```\n",
     "\n",
     "***\n",

diff --git a/biobb_wf_virtual-screening/docs/notebooks/wf_vs_fpocket.docs.ipynb b/biobb_wf_virtual-screening/docs/notebooks/wf_vs_fpocket.docs.ipynb
@@ -29,28 +29,70 @@
     " - [biobb_chemistry](https://github.com/bioexcel/biobb_chemistry): Tools to perform chemoinformatics processes.\n",
     " - [biobb_vs](https://github.com/bioexcel/biobb_vs): Tools to perform virtual screening studies.\n",
     " \n",
+    "# Protein-ligand Docking tutorial using BioExcel Building Blocks (biobb)\n",
+    "### -- *Fpocket Version* --\n",
+    "\n",
+    "***\n",
+    "This tutorial aims to illustrate the process of **protein-ligand docking**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Mitogen-activated protein kinase 14** (p38-α) protein (PDB code [3HEC](https://www.rcsb.org/structure/3HEC)), a well-known **Protein Kinase enzyme**, \n",
+    " in complex with the FDA-approved **Imatinib**, (PDB Ligand code [STI](https://www.rcsb.org/ligand/STI), DrugBank Ligand Code [DB00619](https://go.drugbank.com/drugs/DB00619)), a small molecule **kinase inhibitor** used to treat certain types of **cancer**. \n",
+    " \n",
+    "The tutorial will guide you through the process of identifying the **active site cavity** (pocket) without previous knowledge, and the final prediction of the **protein-ligand complex**. \n",
+    "\n",
+    "Please note that **docking algorithms**, and in particular, **AutoDock Vina** program used in this tutorial, are **non-deterministic**. That means that results obtained when running the workflow **could be diferent** from the ones we obtained during the writing of this tutorial (see [AutoDock Vina manual](http://vina.scripps.edu/manual.html)). We invite you to try the docking process several times to verify this behaviour. \n",
+    "***\n",
+    "\n",
+    "\n",
+    "<div style=\"background:#b5e0dd; padding: 15px;\"><strong>Important:</strong> it is recommended to execute this tutorial step by step (not as a single workflow execution, <strong><em>Run All</em></strong> mode), as it has interactive selections.</div>\n",
+    "\n",
+    "## Settings\n",
+    "\n",
+    "### Biobb modules used\n",
+    "\n",
+    " - [biobb_io](https://github.com/bioexcel/biobb_io): Tools to fetch biomolecular data from public databases.\n",
+    " - [biobb_structure_utils](https://github.com/bioexcel/biobb_structure_utils): Tools to modify or extract information from a PDB structure file.\n",
+    " - [biobb_chemistry](https://github.com/bioexcel/biobb_chemistry): Tools to perform chemoinformatics processes.\n",
+    " - [biobb_vs](https://github.com/bioexcel/biobb_vs): Tools to perform virtual screening studies.\n",
+    "\n",
     "### Auxiliar libraries used\n",
     "\n",
-    " - [nb_conda_kernels](https://github.com/Anaconda-Platform/nb_conda_kernels): Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.\n",
-    " - [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.\n",
-    " - [ipywidgets](https://github.com/jupyter-widgets/ipywidgets): Interactive HTML widgets for Jupyter notebooks and the IPython kernel.\n",
+    "* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.\n",
+    "* [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.\n",
     "\n",
-    "### Conda Installation and Launch\n",
+    "### Conda Installation\n",
     "\n",
     "```console\n",
     "git clone https://github.com/bioexcel/biobb_wf_virtual-screening.git\n",
     "cd biobb_wf_virtual-screening\n",
     "conda env create -f conda_env/environment.yml\n",
     "conda activate biobb_VS_tutorial\n",
     "jupyter-notebook biobb_wf_virtual-screening/notebooks/fpocket/wf_vs_fpocket.ipynb\n",
-    "  ``` \n",
+    "```\n",
     "\n",
-    "Please execute the following commands before launching the Jupyter Notebook if you experience some issues with widgets such as NGL View (3D molecular visualization):\n",
+    "***\n",
+    "## Pipeline steps\n",
+    " 1. [Input Parameters](#input)\n",
+    " 2. [Fetching PDB Structure](#fetch)\n",
+    " 3. [Extract Protein Structure](#extractProtein)\n",
+    " 4. [Computing Protein Cavities (fpocket)](#fpocket)\n",
+    " 5. [Filtering Protein Cavities (fpocket output)](#fpocketFilter)\n",
+    " 6. [Extract Pocket Cavity ](#fpocketSelect)\n",
+    " 7. [Generating Cavity Box ](#cavityBox)\n",
+    " 8. [Downloading Small Molecule](#downloadSmallMolecule)\n",
+    " 9. [Converting Small Molecule](#sdf2pdb)\n",
+    " 10. [Preparing Small Molecule (ligand) for Docking](#ligand_pdb2pdbqt)\n",
+    " 11. [Preparing Target Protein for Docking](#protein_pdb2pdbqt)\n",
+    " 12. [Running the Docking](#docking)\n",
+    " 13. [Extract a Docking Pose](#extractPose)\n",
+    " 14. [Converting Ligand Pose to PDB format](#pdbqt2pdb)\n",
+    " 15. [Superposing Ligand Pose to the Target Protein Structure](#catPdb)\n",
+    " 16. [Comparing final result with experimental structure](#viewFinal)\n",
+    " 17. [Questions & Comments](#questions)\n",
+    " \n",
+    "***\n",
+    "<img src=\"https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png\" alt=\"Bioexcel2 logo\"\n",
+    "\ttitle=\"Bioexcel2 logo\" width=\"400\" />\n",
+    "***\n",
     "\n",
-    "```console\n",
-    "jupyter-nbextension enable --py --user widgetsnbextension\n",
-    "jupyter-nbextension enable --py --user nglview\n",
-    "```\n",
     "\n",
     "***\n",
     "## Pipeline steps\n",

diff --git a/biobb_wf_virtual-screening/docs/source/cluster_bs_tutorial.md b/biobb_wf_virtual-screening/docs/source/cluster_bs_tutorial.md
@@ -1,5 +1,5 @@
 # Protein-ligand Docking tutorial using BioExcel Building Blocks (biobb)
-### -- *PDB Cluster90 Binding Site Version* --
+**-- *PDB Cluster90 Binding Site Version* --**
 
 ***
 This tutorial aims to illustrate the process of **protein-ligand docking**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Mitogen-activated protein kinase 14** (p38-α) protein (PDB code [3HEC](https://www.rcsb.org/structure/3HEC)), a well-known **Protein Kinase enzyme**, 
@@ -23,9 +23,8 @@ Please note that **docking algorithms**, and in particular, **AutoDock Vina** pr
 
 ### Auxiliar libraries used
 
- - [nb_conda_kernels](https://github.com/Anaconda-Platform/nb_conda_kernels): Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.
- - [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
- - [ipywidgets](https://github.com/jupyter-widgets/ipywidgets): Interactive HTML widgets for Jupyter notebooks and the IPython kernel.
+* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.
+* [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
 
 ### Conda Installation and Launch
 
@@ -37,13 +36,6 @@ conda activate biobb_VS_tutorial
 jupyter-notebook biobb_wf_virtual-screening/notebooks/ebi_api/wf_vs_ebi_api.ipynb
 ``` 
 
-Please execute the following commands before launching the Jupyter Notebook if you experience some issues with widgets such as NGL View (3D molecular visualization):
-
-```console
-jupyter-nbextension enable --py --user widgetsnbextension
-jupyter-nbextension enable --py --user nglview
-```
-
 ***
 ## Pipeline steps
  1. [Input Parameters](#input)

diff --git a/biobb_wf_virtual-screening/docs/source/ebi_api_tutorial.md b/biobb_wf_virtual-screening/docs/source/ebi_api_tutorial.md
@@ -1,5 +1,5 @@
 # Protein-ligand Docking tutorial using BioExcel Building Blocks (biobb)
-### -- *PDBe REST-API Version* --
+**-- *PDBe REST-API Version* --**
 
 ***
 This tutorial aims to illustrate the process of **protein-ligand docking**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Mitogen-activated protein kinase 14** (p38-α) protein (PDB code [3LFA](https://www.rcsb.org/structure/3LFA)), a well-known **Protein Kinase enzyme**, 
@@ -23,9 +23,8 @@ Please note that **docking algorithms**, and in particular, **AutoDock Vina** pr
 
 ### Auxiliar libraries used
 
- - [nb_conda_kernels](https://github.com/Anaconda-Platform/nb_conda_kernels): Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.
- - [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
- - [ipywidgets](https://github.com/jupyter-widgets/ipywidgets): Interactive HTML widgets for Jupyter notebooks and the IPython kernel.
+* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.
+* [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
 
 ### Conda Installation and Launch
 
@@ -37,13 +36,6 @@ conda activate biobb_VS_tutorial
 jupyter-notebook biobb_wf_virtual-screening/notebooks/ebi_api/wf_vs_ebi_api.ipynb
 ``` 
 
-Please execute the following commands before launching the Jupyter Notebook if you experience some issues with widgets such as NGL View (3D molecular visualization):
-
-```console
-jupyter-nbextension enable --py --user widgetsnbextension
-jupyter-nbextension enable --py --user nglview
-```
-
 ***
 ## Pipeline steps
  1. [Input Parameters](#input)

diff --git a/biobb_wf_virtual-screening/docs/source/fpocket_tutorial.md b/biobb_wf_virtual-screening/docs/source/fpocket_tutorial.md
@@ -1,5 +1,5 @@
 # Protein-ligand Docking tutorial using BioExcel Building Blocks (biobb)
-### -- *Fpocket Version* --
+**-- *Fpocket Version* --**
 
 ***
 This tutorial aims to illustrate the process of **protein-ligand docking**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **Mitogen-activated protein kinase 14** (p38-α) protein (PDB code [3HEC](https://www.rcsb.org/structure/3HEC)), a well-known **Protein Kinase enzyme**, 
@@ -21,28 +21,20 @@ Please note that **docking algorithms**, and in particular, **AutoDock Vina** pr
  - [biobb_structure_utils](https://github.com/bioexcel/biobb_structure_utils): Tools to modify or extract information from a PDB structure file.
  - [biobb_chemistry](https://github.com/bioexcel/biobb_chemistry): Tools to perform chemoinformatics processes.
  - [biobb_vs](https://github.com/bioexcel/biobb_vs): Tools to perform virtual screening studies.
- 
+
 ### Auxiliar libraries used
 
- - [nb_conda_kernels](https://github.com/Anaconda-Platform/nb_conda_kernels): Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.
- - [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
- - [ipywidgets](https://github.com/jupyter-widgets/ipywidgets): Interactive HTML widgets for Jupyter notebooks and the IPython kernel.
+* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.
+* [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
 
-### Conda Installation and Launch
+### Conda Installation
 
 ```console
 git clone https://github.com/bioexcel/biobb_wf_virtual-screening.git
 cd biobb_wf_virtual-screening
 conda env create -f conda_env/environment.yml
 conda activate biobb_VS_tutorial
 jupyter-notebook biobb_wf_virtual-screening/notebooks/fpocket/wf_vs_fpocket.ipynb
-  ``` 
-
-Please execute the following commands before launching the Jupyter Notebook if you experience some issues with widgets such as NGL View (3D molecular visualization):
-
-```console
-jupyter-nbextension enable --py --user widgetsnbextension
-jupyter-nbextension enable --py --user nglview
 ```
 
 ***

diff --git a/biobb_wf_virtual-screening/docs/source/readme.md b/biobb_wf_virtual-screening/docs/source/readme.md
@@ -24,9 +24,8 @@ The tutorials will guide you through the process of identifying the **active sit
 
 ### Auxiliar libraries used
 
-* [nb_conda_kernels](https://github.com/Anaconda-Platform/nb_conda_kernels): Enables a Jupyter Notebook or JupyterLab application in one conda environment to access kernels for Python, R, and other languages found in other environments.
+* [jupyter](https://jupyter.org/): Free software, open standards, and web services for interactive computing across all programming languages.
 * [nglview](http://nglviewer.org/#nglview): Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.
-* [ipywidgets](https://github.com/jupyter-widgets/ipywidgets): Interactive HTML widgets for Jupyter notebooks and the IPython kernel.
 
 ### Conda Installation
 
@@ -37,13 +36,6 @@ conda env create -f conda_env/environment.yml
 conda activate biobb_VS_tutorial
 ```
 
-Please execute the following commands before launching the Jupyter Notebook if you experience some issues with widgets such as NGL View (3D molecular visualization):
-
-```console
-jupyter-nbextension enable --py --user widgetsnbextension
-jupyter-nbextension enable --py --user nglview
-```
-
 ### Launch
 
 #### EBI REST API tutorial