Example of adding a new linker group

[djcole56]

Request to provide an example showing how to modify or update the available linkers dataset in FEGrow.

[djcole56]

If you have your required linkers in smiles format, then there is an example showing how add the linker in the tutorial:
https://github.com/cole-group/FEgrow/blob/master/tutorials/1_tutorial_introduce_chemspace.ipynb

Ie something like this should work:
rcor_linker = Chem.AddHs(Chem.MolFromSmiles("[*:0]CO[*:1]"))
Though I suggest to check the protonation of the linker carefully. When constructing the full library I believe we used obabel to generate the 3D coordinates of the linker. Alternatively if you have these, you should be able to append them to the sdf file here: https://github.com/cole-group/FEgrow/tree/master/fegrow/data/linkers

Much easier though is just to generate smiles strings for the full molecule that you'd like to build. FEgrow will then use a substructure search on the supplied scaffold to assign the flexible R-group without any need for linkers. We're in the process of adding a tutorial on this. An early version is here, which will be updated in the new year: https://github.com/AsmaFeriel000/FEgrow/blob/feature-smiles-tutorial-2/tutorials/3_tutorial_read_from_smiles.ipynb

@BenCree might have additional comments.