Closed MachineGUN001 closed 9 months ago
Hi, thanks for your interest in the work. We have uploaded relevant code for sampling with a specific protein and scaffold and provided some examples. Additionally, regarding the single_train.smi
in process_and_prepare.py
, it is created by Lib-INVENT-dataset repo (https://github.com/MolecularAI/Lib-INVENT-dataset). We also provide corresponding examples for it.
hi, @XJJBot thanks for your kind explanation.
I also noted that the smi file as the output SMILES file
in lib-INVENT repo that will contain three columns including scaffolds
, decorations
and the original compounds
.
however, the lib-INVENT needs to be implemented in linux, and I have some trouble in runing that.
thus, could you please provide some expamles for single_train.smi
generated by Lib-INVENT-dataset repo?
it'd be great to try your codes mainly for testing if that works on the specific proteins with specific new molecules.
many many thanks,
Best, Sh-Y
You may try the newly uploaded codes sample_single_for_specific_context.py
and sample_multi_for_specific_context.py
, and the relevant instructions are updated in README
accordingly.
You may try the newly uploaded codes
sample_single_for_specific_context.py
andsample_multi_for_specific_context.py
, and the relevant instructions are updated inREADME
accordingly.
that works well,
Thank you very much for your help, your code is very high quality and clear!!
many thanks,
ShY
hi,
Thanks a lot for offering such an interesting program, very good work. Acknowledgement. Here is the question, I would like to ask how to make R group changes for a specific protein pocket and for a specific molecule as you have shown in your article, such as PDB , 4iiy and 4ja8. if I want to change to another protein structure as well as to a new compound, how should I use the run script? coud you please provide an example or tutorial for the process? or could you pleaes provide the example data with scaffolds/Rgroups/protein pdb file etc for format exaplanation? in the line of process_and_prepare.py,single_train.smi,what format is it?
Thank you very much!
Best,
S-y