Xibin Bayes Zhou

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icon company @westlake-repl icon location Hangzhou, Zhejiang, China icon location Ph.D. candidate of AI+Biology in Westlake University.

Results 2 issues of Xibin Bayes Zhou

Exception using `notebooks/unimol_mol_repr_demo.ipynb`

3 comment

Hi there, While using your `notebooks/unimol_mol_repr_demo.ipynb`, my molecules result in an Exception from `smi2coords` function. My molecules are following: ``` smi_list = [ "CC(C)CC(C(=O)NC(C(C)C)C(=O)O)NC(=O)CNC(=O)C(CCC(=O)N)NC(=O)C(CC(C)C)NC(=O)C(CC(C)C)NC(=O)C(CCCNC(=N)N)NC(=O)C(CCC(=O)N)NC(=O)C(CC(C)C)NC(=O)C(CCCNC(=N)N)NC(=O)C(C)NC(=O)C(CO)NC(=O)C(CC(=O)O)NC(=O)C(CCCNC(=N)N)NC(=O)C(CC(C)C)NC(=O)C(CCCNC(=N)N)NC(=O)C(CO)NC(=O)C(CC(C)C)NC(=O)C(CCC(=O)O)NC(=O)C(CO)NC(=O)C(C(C)O)NC(=O)C(CC1=CC=CC=C1)NC(=O)C(C(C)O)NC(=O)CNC(=O)C(CC(=O)O)NC(=O)C(CO)NC(=O)C(CC2=NC=CN2)N", "CC(C)CC1C(=O)NC(C(=O)NC(C(=O)NC(CSSCC(C(=O)NC(C(=O)NC(C(=O)N1)CC(=O)N)CO)N)C(=O)NC(C(C)C)C(=O)NC(CC(C)C)C(=O)NCC(=O)NC(CCCCN)C(=O)NC(CC(C)C)C(=O)NC(CO)C(=O)NC(CCC(=O)N)C(=O)NC(CCC(=O)O)C(=O)NC(CC(C)C)C(=O)NC(CC2=CN=CN2)C(=O)NC(CCCCN)C(=O)NC(CC(C)C)C(=O)NC(CCC(=O)N)C(=O)NC(C(C)O)C(=O)NC(CC3=CC=C(C=C3)O)C(=O)N4CCCC4C(=O)NC(CCCNC(=N)N)C(=O)NC(C(C)O)C(=O)NC(CC(=O)N)C(=O)NC(C(C)O)C(=O)NCC(=O)NC(CO)C(=O)NCC(=O)NC(C(C)O)C(=O)N5CCCC5C(=O)N)C(C)O)CO", "C(C1C(C(C(C(O1)OC2(C(C(C(O2)CO)O)O)COC3(C(C(C(O3)CO)O)O)COC4(C(C(C(O4)CO)O)O)COC5(C(C(C(O5)CO)O)O)COC6(C(C(C(O6)CO)O)O)COC7(C(C(C(O7)CO)O)O)COC8(C(C(C(O8)CO)O)O)COC9(C(C(C(O9)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)COC1(C(C(C(O1)CO)O)O)CO)O)O)O)O", ] ``` Error Stack...

Difference of embedding layer dimension between pretrained model and dict.txt

4 comment

Hi there, I'm trying to load pretrained weights of `molecular pretrain`(https://github.com/dptech-corp/Uni-Mol/releases/download/v0.1/mol_pre_no_h_220816.pt), but using the `example_data/molecule/dict.txt` leads to an Exception below. ``` RuntimeError: Error(s) in loading state_dict for MoleculeEmbeddingModel: size mismatch...