Try the Materials Informatics Toolkit, which is designed to easily handle SMILES data. This and other helpful add-ins are available in the JMP® Marketplace
JMP® Marketplace feature: The Materials Informatics Toolkit
Created:
Dec 5, 2024 09:57 AMLast Modified: Dec 5, 2024 10:04 AM
The Materials Informatics Toolkit is a powerful, user-friendly JMP add-in designed to provide an interface for using the RDKit package to calculate descriptors from Simplified Molecular Input Line Entry System (SMILES). I developed the add-in after numerous conversations with JMP users who were working with molecular structures and using Python for their analyses. They needed to be able to perform complex analyses – but without extensive coding.
The Materials Informatics Toolkit offers a point-and-click option for anyone who wants to use JMP to handle chemical structure data. It's helpful in a variety of instances, from searching for new molecular candidates that meet specific requirements to analyzing relationships between molecular structures and physical properties.
Before getting started, please remember that this add-in assumes that you already have SMILES data to analyze. SMILES represents molecular structures using strings.
How to use the Materials Informatics Toolkit
After downloading and installing the add-in:
In JMP, open the Add-Ins menu in the top navigation and click Toolkit for Materials Informatics.
Click Descriptor Calculation.
Select the column containing SMILES.
Calculate molecular descriptors
Select the features you want to generate.
Click OK to send the data from JMP to Python. Python generates features and sends the data back to JMP. Creating a model with these features allows you to predict the characteristic values of a certain substance.
To draw a picture from this molecular information, go back to the add-in menu and click Drawing Molecules.
Select the SMILES column and click OK. This sends the data from JMP to Python, creates a Python diagram, and sends the data back to JMP. The resulting images are stored in a column in the table.
Draw molecule from SMILES
Watch the demo
This video demonstrates how to use the Materials Informatics Toolkit:
MIT Tutorial - Yuichi - V2.mp4
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Here are a few helpful hints as you use the Materials Informatics Toolkit:
This add-in uses a Python integration feature. RDKit must be installed before using this add-in.
Once you have created the descriptors using this add-in, you can use this information to build the model to predict molecular properties and so on. If you have JMP Pro, you can use Model Screening and/or another platform as usual (you can also build the model using JMP).
This add-in can create a molecular image using SMILES. You can create a new column that contains images and then use that as your label column.
The JMP Marketplace has add-ins that use Python integration that open doors to new possibilities. Please give this and other add-ins a try and then share any ideas you have for improvements with us.