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[v2 Feature Request]: automated rdkit2d features #843
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Also got here looking for ways to use |
As far as 2D features go, we had originally not added this to v2 because we wanted people to calculate them on their own and pass them as extra features manually. Since it has now been requested to do this automatically here, in #864 (here: #864 (comment)), and in #849, we will put this feature on the TODO list. |
for now how do i manually calculate --features_generator rdkit_2d_normalized --no_features_scaling in V2? |
@KC-Zhang chemprop v1 generated feature by descriptastorus and it's simple to use. However, I didn't understand how to use those feature during training, as the example notebook from #772 doesn't work. |
@SteshinSS which specific notebook in 772 are you talking about? is it |
@KC-Zhang I think |
First install descriptastorus
Then run chemprop
Alternatively, you don't need to install descriptastorus if you use RDKit directly to make the descriptors
Note however that these descriptors are not scaled so the |
What are you trying to do?
I could run my first training/prediction following the tutorials in a notebook! I had a couple of questions on how to achieve the following:
rdkit2d
features? Based on the documentation, I think I should compute these and dump them into a file and then load them. Is that correct? I am unsure how to proceed.Thank you very much for this new version, it is very exciting. I look forward to hearing from you.
Best,
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