Are you tired of creating one molecule at a time using Marvin View? I know the struggle. My folder was overflowing with individual molecule files, and it was becoming a nightmare to efficiently dock them against my target protein. But fear not, because I have found a solution, with the help of a research member from my group, George Van Den Driessche.
So, here’s what you need to do to streamline your molecule compilation process. First things first, let’s get you set up with Knime. It’s a fantastic and free software that will make your life so much easier. You can download it from the official website: https://www.knime.org/downloads/overview.
Once you have Knime installed, make sure you also install all the necessary extensions and update the software to the latest version. We want to make the most of its capabilities, right?
Now, let’s dive into the exciting part. On the left bottom of the Knime interface, you’ll find the Note Repository. Go ahead and search for “Molfile Reader” in that handy search bar. Once you spot it, simply drag it onto your workspace. Remember, we’ll be using .mol files to convert them into a single .sdf file.
Need to import your files? No problem. Select the Molfile Reader, and drag and drop your files into the workspace nearby. Right-click on the icon in the workspace, and choose the “configure” option. A dialogue box will appear, allowing you to browse and select the directory or folder containing your precious mol files. Depending on your requirements, tweak the options accordingly. In this tutorial, we’ll leave the options unchecked. Once you’re all set, click “apply” and then “ok” to confirm.
Next stop, the Note Repository on the left side. Search for the file format you wish to use. In our case, we’re converting to an sdf file, so locate the sdf writer. Remember, when exporting, you’ll need to choose “writer” instead of “reader.”
Right-click on the sdf writer icon, and select the “configure” option. 
HHere, you’ll choose the destination folder for your output file. Browse through your directories, pick a location, and give your output file a meaningful name. Don’t forget to add the file extension to the name. We don’t want any confusion here!
Make sure to add the extension in the file name. 
Feel free to adjust the other settings based on your specific needs. Once you’re satisfied, hit “apply” and then “ok” to confirm your configuration.
Now, let’s connect the two nodes to make the magic happen. Simply drag from one arrowhead to another, linking the Molfile Reader and the sdf writer.
With everything set up, it’s time to run the process. Select both nodes, and click on the green arrow located in the top bar. Sit back, relax, and let Knime do its thing.
If you did the steps correctly, you should have the output file in your destination folder. 
If you followed the steps correctly, you’ll find your shiny new output file waiting for you in the designated destination folder. Congratulations! You’ve successfully converted a bunch of individual mol files into a single sdf file. Isn’t that satisfying?
Oh, and one more thing. If you’re looking for an even easier solution, I’ve got you covered. I’ve written a program called “mergefile.py” that performs similar functions. It’s a breeze to use and has been tested to combine individual files and convert them into sdf, mol, and txt formats. You can find it on my GitHub page under my name: zinph.
Now go ahead and enjoy the efficiency and simplicity of compiling your molecules with Knime or my handy “mergefile.py” program. Happy molecule merging!