无法生成3D构象

[sunyrain]

import numpy as np
from unimol_tools import UniMolRepr
# single smiles unimol representation
clf = UniMolRepr(data_type='molecule', 
                 remove_hs=False,
                 model_name='unimolv1', # avaliable: unimolv1, unimolv2
                 model_size='84m', # work when model_name is unimolv2. avaliable: 84m, 164m, 310m, 570m, 1.1B.
                 )
smiles = 'CCCCCCCCC(CCCCCC)Cn1nc2c(-c3ccc(C)s3)c(F)c(F)c(-c3ccc(-c4cc5c(-c6ccc(CC(CC)CCCC)s6)c6sc(C)cc6c(-c6ccc(CC(CC)CCCC)s6)c5s4)s3)c2n1'
smiles_list = [smiles]
unimol_repr = clf.get_repr(smiles_list, return_atomic_reprs=True)
# CLS token repr
print(np.array(unimol_repr['cls_repr']).shape)
# atomic level repr, align with rdkit mol.GetAtoms()
print(np.array(unimol_repr['atomic_reprs']).shape)

运行这段代码，输出结果如下

2024-12-19 18:26:08 | unimol_tools/data/conformer.py | 126 | INFO | Uni-Mol Tools | Succeeded in generating conformers for 100.00% of molecules.
2024-12-19 18:26:08 | unimol_tools/data/conformer.py | 128 | INFO | Uni-Mol Tools | Succeeded in generating 3d conformers for 0.00% of molecules.

[Naplessss]

It seems CCCCCCCCC(CCCCCC)Cn1nc2c(-c3ccc(C)s3)c(F)c(F)c(-c3ccc(-c4cc5c(-c6ccc(CC(CC)CCCC)s6)c6sc(C)cc6c(-c6ccc(CC(CC)CCCC)s6)c5s4)s3)c2n1 is to hard for rdkit with MMFF. you can use other methods for conformation generation, unimol-tools also support to fit with custom conformations with coordinates provided.