search

rxn4chemistry / rxn_yields

Code complementing our manuscript on the prediction of chemical reaction yields (https://iopscience.iop.org/article/10.1088/2632-2153/abc81d) and data augmentation strategies (https://doi.org/10.26434/chemrxiv.13286741).
https://rxn4chemistry.github.io/rxn_yields/
MIT License
107 stars 26 forks source link

Changing Reaction forward template #2

Closed atharvapurdue closed 3 years ago

atharvapurdue commented 3 years ago

How to make a reaction template to use the bert model for a different dataset

pschwllr commented 3 years ago

Depends on the data set, but what you could do is to atom-map some of the reactions with http://rxnmapper.ai (https://github.com/rxn4chemistry/rxnmapper). -> https://chemrxiv.org/articles/Unsupervised_Attention-Guided_Atom-Mapping/12298559

Then extract the templates with the tools by Thakkar et al. / Coley et al. (https://github.com/reymond-group/CASP-and-dataset-performance). -> https://pubs.rsc.org/en/content/articlelanding/2019/sc/c9sc04944d#!divAbstract and https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00286

The resulting templates might need some additional modifications but are a good starting point.