Molecule Visualizer

Molecule Visualizer is an innovative data structures and algorithms initiative designed to represent and manipulate chemical molecules in a three-dimensional space using graph data structures. Each atom is represented as a node, and each bond as an edge, allowing for a flexible and dynamic representation of molecular structures. The construction of the molecular graph employs Breadth-First Search (BFS) to ensure comprehensive and systematic node traversal, facilitating the accurate assembly of the molecule. Depth-First Search (DFS) is implemented for cycle detection, crucial for identifying rings and complex substructures within the molecule.

Key Features

• Detailed information sharing about the constructed molecules Physical and Chemical Properties.
• Bond angle calculations and molecular geometry analysis.
• Algorithmic efficiency for real-time updates and smooth interactions.

Tech Stack

Client: React JS, Material UI, Tailwind CSS

Server: Node JS, Express JS

Plotting: Plotly JS

Contributing

Contributions are always welcome!

See contributing.md for ways to get started.

Please adhere to this project's code of conduct.

API Utilized

Gemini 1.5 Flash

API Documentation

API-Reference

Environment Variables

To run this project, you will need to add the following environment variables to your .env file

PORT

API_KEY

Developers

• Tharun Kumarr A
• Naganathan M R
• Lowkik Sai P
• Praveen K
• Bharath S
• Hariprasath M

Future Ideas for Molecule Visualizer:

• Validation of the compounds that has be entered by the user.
• Extending the available hybridisation of molecules to sp3d and sp3d2.
• Allowing for various type of elements available in the periodic table.

FAQ

How to build the Molecule ?

• Add Atoms: Navigate to the menu bar at the right side of the page. Initially you need to add all the atoms with respective hybridisations that are present in your molecule using the Add Atoms menu.

• Add Bond: Menu in the right side will be comprising a option named Add Bond. Using this option select respective two atoms and the type of bond Single, Double, Triple. Then add bond will connect those two atoms in the 3d space.

What are these Examples ?

• These are prebuilt molecule templates for visualizing. These include the most common Organic and Inorganic compounds for fast visualization.

How to find if a Molecule is Cyclic/Acyclic ?

• Once you constructed the molecule using the option available, you can see the Check Cycle information in the bottom of the menu bar present at the right. This indicates whether the constructed molecule is Cyclic or Acyclic.

How get properties of constructed moelcule ?

• Once you have constrcuted the molecule, use the option Get Data available at the top left. This option when trigerred whill fetch you all the Chemical and Physical Properties of the molecule that has been constrcuted.

graph TD
    A[Start] --> B[Add Atoms]
    B --> C[Add Bond]
    C --> D{Cycle Detection}
    D -->|Cyclic| E[Identify Rings]
    D -->|Acyclic| F[Proceed]
    E --> F
    F --> G[Calculate Bond Angles]
    G --> H[Analyze Molecular Geometry]
    H --> I[Get Physical/Chemical Properties]
    I --> J[Display Results]
    J --> K[Real-time Updates]
    K --> L[End]

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