Uni-Mol

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Exception using `notebooks/unimol_mol_repr_demo.ipynb`

3

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...

zhoubay

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

4

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...

zhoubay

run unimol_mol_repr_demo.ipynb got error "KeyError: 'unimol'"

1

line 21, in setup_task return TASK_REGISTRY[args.task].setup_task(args, **kwargs) KeyError: 'unimol'

bowen-gao

传入参数出现下面的报错，请问是什么原因

3

error: argument --seed: invalid int value: '$seed'

dfaqw

Running inference outside of pre-computed datasets

4

Dear authors, Congratulations on Uni-Mol! This is truly exciting work 🥇 I'm writing to express interest in running inference outside of the pre-computed datasets. For example: 1.) Running docking from...

cyrusmaher

Correting patoms

1

Thanks for sharing your awesome work. I have a question about the pre-processing stage of protein data for Uni-Mol input (more specifically, tokenizing protein atoms). As described in your paper...

Bae-SungHan

Create unimol+ embeddings

1

I am trying to create unimol+ embeddings from a SMILES dataset. Is there a way to just infer this without having to train the model? how should I go about...

maxime-duchateau

uni_mol_tools weight

1

Thanks for sharing unimol_tools.I find No such file or directory: 'D:\\anaconda3\\Lib\\site-packages\\unimol_tools\\weights\\mol_pre_all_h_220816.pt',I found that the weights file is not mol_pre_all_h_220816.pt now.Can you share your weight file.Thank you .

JJFORJEY

The Colab notebook has lmdb error

6


ryan-pauling-ai

some confusion about installation

1

Hi, thanks a lot for your code. My question is: I intend to use **uni-mol**, and whether it's enough to prepare the env by singly pulling **docker image unimol**, or...

koalaaaaaaaaa