SmiNav

SMILES visualization with Godot

SmiNav (SMILES Navigator) is a GUI visualizer for parts of the SMILES syntax (atoms, neighbors, and rings). It was inspired by Andrew Dalke's smiview. It uses the RDKit library in Python to parse the SMILES string and return mol coordinates and properties that are then used to create a 2D or 3D visualization of the molecule. The visualization is done using the Godot game engine.

To use SmiNav, input a SMILES string, then click the visualization dimension you wish to view. Upon clicking on an atom in the string, the corresponding atom in the depiction will then get highlighted. The reverse works as well; that is, click on an atom in the depiction and the corresponding atom in the SMILES string will get highlighted.

We did this for fun and to learn how to create interfaces in Godot. Any feedback and bug reports are very much welcome.

Features

• 2D and 3D visualization of SMILES strings
• Interactive highlighting of atoms in the SMILES string and depiction
• Atom properties (e.g., charge, SMILES Index) are shown in the SMILES string and depiction
• Ring properties (e.g., aromaticity) and ring closures are shown in the SMILES string and depiction
• Branches of the SMILES string are shown in the depiction
• Highlighting of explicit hydrogens in the SMILES string and depiction

Main Screen

2D

3D

Installation of source code in godot

1. Download the source code from the repository git clone https://github.com/ualibweb/sminav.git
2. Open Godot and click on Import
3. Navigate to the SmiNav folder and click on Open on the project.godot file

To run the program

In the Godot editor, click on the Play button to run ► the program on the top right corner of the window.

Downlad binaries from Releases

For Linux x86, download the base SmiNav_Linux.zip

For Arm64 Linux systems like Raspi, download the SmiNav_LinuxArm.zip

For Windows systems, download the SmiNav_Windows.zip

Running Binaries

1. Linux x86 - Open binary in file navigator or start from terminal (e.g., ./SmiNav.x86_64)

2. Linux ARM64 - Open binary in file navigator or start from terminal with (e.g., ./SmiNav.arm64)

   • If needed, use opengl3_es, ./SmiNav.arm64 --rendering-driver opengl3_es

3. Windows - Click on SmiNav.exe

NOTE: On all platforms, SmiNav will try to detect a .venv enviroment and if it has Python3 and RDKit installed. If not, you are given the option with "Install Requirements" to set this up for you. Alternatively, see below for manual instructions on how to setup your own virtual Python environment, if you do not want SmiNav to do this for you. SmiNav creates the .venv folder in the SmiNav folder (you may need to show hidden files to see it).

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For the program to run, you must have Python 3.7 or greater installed and Python virtual environments installed:

Ubuntu/Debian Systems or Arm Linux Systems (like Raspberry Pi)

Install Python 3.7 or greater and Virtual Environment:

• Most modern Ubuntu/Debian systems come with Python 3 already installed. You can check your Python version by running:

  python3 --version

• If you don't have Python 3.7 or greater, install it:

  sudo apt-get install python3

• Install python3-venv to use virtual environments:

  sudo apt-get install python3-venv

Windows Systems

1. Install Python 3.7 or greater:

   • Download the Python installer from the official Python website. Make sure to download a version that is 3.7 or greater.
   • Run the installer. Ensure you check the box that says "Add Python 3.x to PATH" to make Python accessible from the command line.

2. Install Virtual Environment:

   • Open Command Prompt and install the virtual environment package:

     pip install virtualenv

Advanced Installation

Manually Setting Up a Virtual Environment

If you prefer to manually set up a virtual environment within the SmiNav folder, follow these steps:

1. Create a Virtual Environment:

   • Open a terminal or command prompt and navigate to the project directory.
   • Run the following command to create a virtual environment (Windows users should replace python3 with python):

     python3 -m venv .venv

   • This will create a new directory called .venv in your project folder. This directory contains a local Python environment that is isolated from your system-wide Python installation.

2. Activate the Virtual Environment:

   • Once the virtual environment is created, you need to activate it. Run the following command:
     • On Ubuntu/Debian:

       source .venv/bin/activate

     • On Windows:

       .venv\Scripts\activate

   • When the virtual environment is activated, your terminal or command prompt will show the name of the environment at the beginning of the command line. This indicates that you are now working within the virtual environment.

3. Install Dependencies:

   • With the virtual environment activated, you can install the required Python packages using pip. Run the following command:

     pip install rdkit

   • This will install all the necessary Python packages for the project within the virtual environment, ensuring that they do not interfere with your system-wide Python installation.

FAQ

1. If Python dependencies installation fails with SmiNav, delete the created .venv folder before trying again. Typical failure is not having Python 3 or Python venv installed.

2. Testing - We have last tested SmiNav with Godot v.4.2.1, RDKit 2023.09.05, and Python 3.11. See also the Godot minimum requirements: https://docs.godotengine.org/en/stable/about/system_requirements.html

Known Limitations

1. In the 2D depictions, stereochemistry is not shown
2. Currently only the atom Symbols are interactive in the SMILES string.
3. Only explict hydrogens are shown in the depictions. Valences are not automatically filled with H (e.g., an alcohol functional group would show up as -O, and not -OH)
4. Does not support individual explicit hydrogens in the SMILES string (e.g., [H] or [H][O][H]). However, explicit hydrogens are supported when attached to atoms within brackets (e.g., [CH4] as an atom property)