Supporting SMILES str or rdkit Mol object in the `MainWindow` class

[Ruibin-Liu]

Currently, we can use MainWindow in custom code but the class only support empty or file_name argument. I looked through the code briefly and thought it would not be too hard to add supporting for a SMILES string or even better a rdkit Mol object as an argument.

Do you already have a plan to support that? If not I can help if you think it is useful.

[EBjerrum]

Thanks for reaching out. It's not something I had planned immediately, but I did think about if it could be made easier to reuse in embedded mode. The thing that was done with Metis could have been a bit smoother and I also had other applications in mind. Could you maybe tell a bit more what you had in mind?

[Ruibin-Liu]

I haven't tried Metis but only read through the repo homepage. It is similar idea but my use case is to pop out a rdeditor edit window along with the passed-in rdkit Mol or SMILES in my program so that the user can change the molecule if needed, and after the user closes the window the edit is saved back to my program for later use.

The change in the MainWindow class is quite simple:

1. The __init__ function should accept 'rdkit_mol' and 'smiles' keyword arguments, defaulting to None.
2. self.editor = MolEditWidget(rdkit_mol) where rdkit_mol is passed in directly or obtained through the passed-in 'smiles'.
3. Adapt the closeEvent, exitFile, and (user's) launch funcitons so that the edited self.editor.mol is passed back to the invoking code when the window is closed.

The first two steps are easy but I am not familiar with Qt or PySide programming so there might be a better way for the thrid step.

[EBjerrum]

I think you changes sound very backward compatible and not too complicated. Not sure how 3 is going to be implemented, but your idea was to stop program execution in the parent program, until the rdEditor window is closed? Is your main program in PySide or something else?
I suggest you fork the repository, and then implement your changes and make a pull request, then we can eventual discuss if there's a need for adjustments. How does that sound?

I was contemplating something a bit more elaborate, e.g. creating an "embedded mode", which would change some of the menu's (e.g. save may not make sense, there's instead a lack of "update" that pushes changes to parent, and also a reset that reloads from parent. There has also been some issues with the theme and settings management, that suddenly interfered with the main applications. It was actually an original use-case to allow for use as a library, but the application was then developed as a standalone for a long time. A simple use-case to develop the capabilities would be an SdEditor application, that can browse through an SD file, and then pop-out rdEditor to update the current molecule. E.g. something like this, which was a predecessor to rdEditor: https://www.cheminformania.com/rdkit-gui-browser-with-mvc-using-pyside/ But currently I don't have a lot of spare time on my hands.