OrganoMind 0.1.1

Cheminformatics tools for molecular analysis

OrganoMind

📚General informations📚

OrganoMind is a project developped as part of Practical Progamming in chemistry EPFL (2026) during second year of study. OrganoMind is thought as an organic chemistry assistant that allows 3D visualization of molecules with built-in features that give both chemical and stereochemical properties that allows better understanding of chemical processes.

💪Features💪

• 3D visualization of molecules and IUPAC naming.
• Detection and 2D visualization of functionnal groups.
• Detection of aromatic groups and nomenclature of the group.
• Detection of chiral centers, number of isomers and 2D visualization of the chiral center.
• Detection of acidic and basic groups, and estimation of the pKa of the molecule.
• Detection of the most nucleophilic and electrophilic sites in the molecule.
• Determination of molecule's point group.

👥Contributions👥

Théo Vienne

Noam Balter-Dejeux

Tolga Seckin

Théo Morales Crassier

📈A useful assistant📈

Organomind is thought as a tool to simplify the understanding of the reactivity of complex chemical compounds. By either putting directly the structure or the name or the formula or even the smile of a molecule, organomind will give you all the characteritics you need to work on your problem.

You need compute a reaction path for a synthesis ?

Put your reactants in organomind and it will tell you which group of your molecule are nucleophilic and electrophilic with all functional groups, allowing you to determine accuratly which part will react and with what.

Struggle with a MO diagram ?

Organomind will give you the point group allowing to simplify your work and focus on the important part of your search.

Working on a stereospcific synthesis ?

Organomind will give you the number of chiral centers and 2D view of them with the number of stable isomers which then allow you properly classify the stereo-isomers of your molecule.

Already convinced ? Let us show you how to install it and enjoy all the features of this framework ! 🎉

⚙️ Installation ⚙️

Prerequisites

• Python 3.10.20
• pip

Steps

1. Create a CONDA virtual environment (recommended)

#Open bash or terminal
#Name the environment as you wish and specify python 3.10
conda create -n env.name python=3.10

#Activate your environment
conda activate env.name

2. Two ways to proceed

A. Using the repo:

#Clone the repository
git clone https://github.com/TheoV19/OrganoMind.git

#Naviguate to the OrganoMind folder
cd path/to/organomind

#Install the dependencies locally as a user, make sure to activate your environment before doing so 
pip install .
    or
#Install the dependencies locally in editable mode, make sure to activate your environment before doing so
pip install -e . 

B. Only using the package:

pip install organomind 
    or
pip install git+https://github.com/TheoV19/OrganoMind.git

3. Run the app

#In your terminal, you can now run the program with:
organomind-ui

The app will open automatically in your browser at http://localhost:8501.

🧠How to use🧠

✍️Write your molecule anyway you want✍️

OrganoMind supports multiple input formats. In the Search tab, select your search type and enter your query:

Input type	Example
Name	aspirin
Formula	C9H8O4
SMILES	CC(=O)Oc1ccccc1C(=O)O
InChI	InChI=1S/C9H8O4/...
InChIKey	BSYNRYMUTXBXSQ-UHFFFAOYSA-N

Tip: SMILES input gives the most accurate structure results.

🎨Draw a molecule🎨

Switch to the Draw tab to use the built-in Ketcher molecular editor. Draw your molecule directly on the canvas and OrganoMind will automatically identify and analyze it.

Select the information to display

Use the sidebar on the left to select which properties you want to compute:

• Molecular formula / weight / IUPAC name / SMILES / CAS — General information
• Rotatable bonds — Conformational flexibility
• Stereochemistry — Chiral centers, number of stable isomers, 2D view
• Functional groups — Detection and 2D visualization
• Aromaticity — Aromatic ring detection and nomenclature
• Acidity / Basicity — Acidic and basic site detection with pKa estimation
• Nucleophilicity / Electrophilicity — Reactive site detection with HSAB-based level attribution
• Point groups — Symmetry group determination
• 3D drawing — Interactive 3D visualization

Requirements

OrganoMind requires the following dependencies, which are automatically installed when you install the package:

• rdkit
• pubchempy
• streamlit
• pandas
• py3dmol
• streamlit-ketcher
• pillow
• plotly
• pymatgen
• watchdog

If you encounter missing package errors, you can install them manually:

pip install rdkit pubchempy streamlit pandas py3dmol streamlit-ketcher pillow plotly pymatgen

Need help ?

If you encounter issues or the program doesn't work, try the following steps:

1. Verify your active environment

Make sure you are working in the environment where OrganoMind is installed.

# Check which Python executable is currently active
which python

If it's not the correct environment, activate it:

# Activate your conda environment
conda activate your_env_name

2. Check and update OrganoMind

pip show organomind

If needed, update to the latest version:

pip install --upgrade git+https://github.com/TheoV19/OrganoMind.git

If problems continue, try uninstalling and reinstalling OrganoMind:

pip uninstall organomind
pip install git+https://github.com/TheoV19/OrganoMind.git
or
pip install organomind

3. Update pip if necessary

Sometimes, issues may arise due to an outdated pip. Thus, to update pip:

• For virtual environments

pip install --upgrade pip

• For Linux or macOS systems

python3 -m pip install --upgrade pip

📄 License

MIT License