PPIIMoL: Difference between revisions

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(Initial publication of PPIIMoL)
 
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= PPIIMoL =
= PPIIMoL =


'''PPIIMoL''' is a Python module designed to integrate with PyMOL and automate the detection of polyproline II (PPII) helices in proteins. This tool streamlines structural analysis by identifying characteristic torsional angles (phi and psi) and potential non-canonical hydrogen bonds (Cα-H···O=C).
'''PPIIMoL''' is a Python module for [[PyMOL]] that automates the detection of polyproline II (PPII) helices in proteins.
It streamlines structural analysis by:


Developed as part of a Bachelor's Thesis in Computer Engineering in collaboration with the CSIC neuroscience lab.
* Identifying characteristic torsional angles (phi and psi) of PPII helices.
* Detecting potential non-canonical hydrogen bonds (Cα-H···O=C) relevant to structural stability.
* Exporting results for further analysis.
* Providing direct, customizable visualization in PyMOL.
 
This tool was developed as part of a Bachelor's Thesis in Computer Engineering in collaboration with the CSIC neuroscience laboratory.


[[Category:Plugins]]
[[Category:Plugins]]
Line 13: Line 19:
* 🎨 Direct visualization in PyMOL with customizable color codes.
* 🎨 Direct visualization in PyMOL with customizable color codes.
* 🖱️ Simple GUI based on Tkinter.
* 🖱️ Simple GUI based on Tkinter.
== Requirements ==
* [[PyMOL]] 2.x or newer.
* Python with [https://docs.python.org/3/library/tkinter.html Tkinter] support enabled (for the GUI).


== Installation ==
== Installation ==
1. Clone this repository:
# Download or clone the repository:
  <syntaxhighlight lang="bash">
<pre>
  git clone https://github.com/silviaenma/PPIIMoL.git
git clone https://github.com/silviaenma/PPIIMoL.git
  </syntaxhighlight>
</pre>
 
# Start PyMOL and load the module:
2. Open PyMOL and load the module:
<pre>
  <syntaxhighlight lang="python">
run PPIIMoL/PPIIMoL.py
  run PPIIMoL/PPIIMoL.py
</pre>
  </syntaxhighlight>
# (Optional) Install permanently as a plugin:
* In PyMOL, go to: '''Plugin → Plugin Manager → Install New Plugin'''.
* Select the file `PPIIMoL.py` or the full `PPIIMoL` folder.
* Restart PyMOL to complete installation.


== Example Usage ==
== Example Usage ==
<syntaxhighlight lang="python">
<pre>
# Load the module in PyMOL
# Load the module in PyMOL
run PPIIMoL/PPIIMoL.py
run PPIIMoL/PPIIMoL.py


# Detect PPII helices in a PDB file
# Load a structure
load 3bog.pdb
load 3bog.pdb
# Detect PPII helices
ppii_detect()
ppii_detect()
</syntaxhighlight>
</pre>


📂 Results will be automatically exported in a dated folder.
Results will be automatically exported in a folder named with the current date, containing CSV files with detected segments and interactions. 
Detected PPII helices will be highlighted in the PyMOL viewer according to the selected color scheme in the GUI.


== Repository ==
== Repository ==
The project is hosted on GitHub:
The project is hosted on GitHub: [https://github.com/silviaenma/PPIIMoL PPIIMoL on GitHub]
[https://github.com/silviaenma/PPIIMoL PPIIMoL on GitHub]


== License ==
== License ==
This project is licensed under the GNU GPLv3.
This project is licensed under the [https://www.gnu.org/licenses/gpl-3.0.html GNU GPLv3].
 
[[Category:Plugins]]

Revision as of 04:10, 14 August 2025

PPIIMoL

PPIIMoL is a Python module for PyMOL that automates the detection of polyproline II (PPII) helices in proteins. It streamlines structural analysis by:

  • Identifying characteristic torsional angles (phi and psi) of PPII helices.
  • Detecting potential non-canonical hydrogen bonds (Cα-H···O=C) relevant to structural stability.
  • Exporting results for further analysis.
  • Providing direct, customizable visualization in PyMOL.

This tool was developed as part of a Bachelor's Thesis in Computer Engineering in collaboration with the CSIC neuroscience laboratory.

Features

  • 🔍 Automatic detection of PPII segments via phi/psi angle analysis.
  • 🧬 Identification of Cα-H···O=C interactions relevant to structural stability.
  • 📊 Export of results in CSV format for further analysis.
  • 🎨 Direct visualization in PyMOL with customizable color codes.
  • 🖱️ Simple GUI based on Tkinter.

Requirements

  • PyMOL 2.x or newer.
  • Python with Tkinter support enabled (for the GUI).

Installation

  1. Download or clone the repository:
git clone https://github.com/silviaenma/PPIIMoL.git
  1. Start PyMOL and load the module:
run PPIIMoL/PPIIMoL.py
  1. (Optional) Install permanently as a plugin:
  • In PyMOL, go to: Plugin → Plugin Manager → Install New Plugin.
  • Select the file `PPIIMoL.py` or the full `PPIIMoL` folder.
  • Restart PyMOL to complete installation.

Example Usage

# Load the module in PyMOL
run PPIIMoL/PPIIMoL.py

# Load a structure
load 3bog.pdb

# Detect PPII helices
ppii_detect()

Results will be automatically exported in a folder named with the current date, containing CSV files with detected segments and interactions. Detected PPII helices will be highlighted in the PyMOL viewer according to the selected color scheme in the GUI.

Repository

The project is hosted on GitHub: PPIIMoL on GitHub

License

This project is licensed under the GNU GPLv3.

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