Predict MeSH Classes
You can find the example file here . It has only three columns 1) compound_name 2) pubchem_id 3 ) smiles. Use the PubChem Identifier Exchange service to obtain the SMILES code and/or PubChem IDs for your compound list.
Create a new folder "MeSh prediction" somewhere on your computer. Download and copy the example file to this folder. Now in RStudio, setup that folder as the working directory. Now, run the below code to predict chemical classes for the input compound list.
If completed, the code will generate the "MeSh_Prediction_Results.xlsx" file. Which has the MeSH Class column.
Warning : Since, these are the predicted MeSH classes, there is always some errors. You should carefully review the predicted classes with help of a biochemistry expert to make sure that there are no errors.
To check if there are incorrect SMILES code in the input file, you can use this function "checkSmiles() ". It will tell the line numbers which have a problematic SMILES meaning rCDK cannot parse them.