Load JNK3 Oracle Error about tdc

[yuanqidu]

sklearn.ensemble.forest was renamed to sklearn.ensemble._forest in scikit-learn/scikit-learn@437ca05 on Oct 16, 2019. It requires us to compile the old version from sources, e.g. 0.21.3. I suspect the problem was due to a name change in scikit-learn versions?

[yuanqidu]

Another error I found was in the Deco Hop oracle (below). But the errors did not occur in a similar function Scaffold Hop. I suspect that it was caused by https://github.com/mims-harvard/TDC/blob/master/tdc/chem_utils.py#L1395-L1399 and https://github.com/mims-harvard/TDC/blob/master/tdc/chem_utils.py#L1367 (the if statement).

Traceback (most recent call last):
File "/home/yqdu/moflow-master/data/process_property.py", line 36, in
deco_hop.append(deco_oracle(smile))
File "/home/yqdu/anaconda3/envs/rdkit/lib/python3.9/site-packages/tdc/oracles.py", line 251, in call
return self.evaluator_func(*args, **kwargs)
File "/home/yqdu/anaconda3/envs/rdkit/lib/python3.9/site-packages/tdc/chem_utils.py", line 1382, in deco_hop
deco1_score = deco1_smarts_scoring(molecule)
NameError: name 'deco1_smarts_scoring' is not defined

[kexinhuang12345]

Hi yuanqi, this is indeed due to a version issue with sklearn. We will change the requirements file in the next version. For the next error, @futianfan could you take a look?

[futianfan]

sure

[yuanqidu]

It looks like the old version is no longer supported by scikit-learn. Could you/May I help to update the function to support the latest scikit-learn version? But it seems like the errors happened during loading the model. Is it possible to re-dump the model with the latest scikit-learn and I believe it will be fixed.

[futianfan]

i fixed them, thanks for pointing out!

[yuanqidu]

Thanks!

[futianfan]

will address the version issue later.