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问题请教 #300

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buyudaren3 opened this issue Dec 14, 2024 · 2 comments
Open

问题请教 #300

buyudaren3 opened this issue Dec 14, 2024 · 2 comments

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@buyudaren3
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您好,我在使用命令:
df = pd.read_csv(csv_file)
smiles1_list = df['Smiles#1'].tolist()
smiles2_list = df['Smiles#2'].tolist()
clf = UniMolRepr(data_type='molecule')
repr1 = np.array(clf.get_repr(smiles1_list)['cls_repr'])
repr2 = np.array(clf.get_repr(smiles2_list)['cls_repr'])
得到unimol分子描述符的时候,输出结果中先后有这样的信息:
2024-12-14 19:45:11 | unimol_tools\data\conformer.py | 126 | INFO | Uni-Mol Tools | Succeeded in generating conformers for 97.44% of molecules.
2024-12-14 19:45:11 | unimol_tools\data\conformer.py | 128 | INFO | Uni-Mol Tools | Succeeded in generating 3d conformers for 95.86% of molecules.
2024-12-14 19:45:35 | unimol_tools\data\conformer.py | 126 | INFO | Uni-Mol Tools | Succeeded in generating conformers for 100.00% of molecules.
2024-12-14 19:45:36 | unimol_tools\data\conformer.py | 128 | INFO | Uni-Mol Tools | Succeeded in generating 3d conformers for 100.00% of molecules.
这里的意思是分子1的构象没有找到,而不是没有生成unimol分子描述符是吗?
该如何找出是哪个分子的这个信息缺失了呢?

@Naplessss
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Initially, we attempt to generate 3D conformations. If this process fails, we then try to generate 2D conformations. If both attempts fail, we fill the data with zeros. In your case, the process succeeded with a 97.44% overall conformation success rate, including a 95.86% success rate for 3D conformations.

Thank you for your advice. We will add logging information for failed SMILES ASAP.

@buyudaren3
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Initially, we attempt to generate 3D conformations. If this process fails, we then try to generate 2D conformations. If both attempts fail, we fill the data with zeros. In your case, the process succeeded with a 97.44% overall conformation success rate, including a 95.86% success rate for 3D conformations.

Thank you for your advice. We will add logging information for failed SMILES ASAP.

Thank you very much!

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