我为一个分子生成了许多构象。我想为每个构象将其坐标保存到一个SDF文件中。我尝试了以下方法，但sdf文件中的坐标与构象的坐标不同。
from rdkit import Chemfrom rdkit.Chem import AllChemfrom rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomersfrom rdkit.Chem.EnumerateStereoisomers import StereoEnumerationOptionsaspirin = 'CC(=O)OC1=CC=CC=C1C(=O)O'mol = Chem.AddHs(Chem.MolFromSmiles(aspirin))conformers = AllChem.EmbedMultipleConfs(mol, numConfs=8)conformer_i = mol.GetConformer(0) # 这是我想保存到SDF文件中的构象。print(conformer_i.GetPositions())我得到的输出是
[[ 3.55910965 0.20840444 0.20174025] [ 2.13148034 -0.07274183 -0.11680036] [ 1.81233825 -0.09134332 -1.32465968] [ 1.16950868 -0.30747936 0.83214171] [-0.12944319 -0.55824117 0.41262056] [-0.53676538 -1.86517356 0.15656512] [-1.82111824 -2.14574436 -0.26154327] [-2.69581394 -1.09437287 -0.4203516 ] [-2.35275981 0.20578091 -0.18448083] [-1.05455197 0.45649503 0.23480361] [-0.64543959 1.83612099 0.49878179] [ 0.50523818 2.10782743 0.87545738] [-1.54126908 2.879518 0.33273924] [ 4.15835976 -0.73143248 0.14404327] [ 3.62587517 0.63489849 1.2047807 ] [ 3.98056046 0.90402053 -0.55673262] [ 0.20229068 -2.6478098 0.3014611 ] [-2.09903401 -3.17965212 -0.45066362] [-3.71036497 -1.30377103 -0.74938855] [-3.04003996 1.04851376 -0.30756941] [-1.51816102 3.71618233 0.87474425]]但是当我尝试使用以下代码将带有此构象结构的分子保存到SDF文件中时，
w = Chem.SDWriter('conformer.sdf')mol.AddConformer(conformer_i)w.write(mol)w.close()我得到的结果是
RDKit 3D 21 21 0 0 0 0 0 0 0 0999 V2000 -2.8028 -2.2971 0.2528 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9196 -1.1193 0.3821 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9380 -0.4309 1.4053 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0329 -0.6957 -0.5799 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2038 0.3759 -0.5076 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5008 1.6592 -0.9114 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4068 2.6946 -0.8011 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6647 2.4889 -0.2762 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9781 1.2093 0.1330 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0695 0.1765 0.0217 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4778 -1.1541 0.4786 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6542 -2.1230 0.3851 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7241 -1.3647 1.0002 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9017 -2.5297 -0.8210 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7860 -2.0195 0.6858 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4405 -3.1762 0.7986 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4956 1.7914 -1.3196 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1087 3.6835 -1.1386 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3837 3.2960 -0.1858 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9838 1.0330 0.5554 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5700 -1.4979 0.4428 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 11 13 1 0 10 5 1 0 1 14 1 0 1 15 1 0 1 16 1 0 6 17 1 0 7 18 1 0 8 19 1 0 9 20 1 0 13 21 1 0M END$$$$分子sdf文件中的坐标与conformer_i中的坐标不同。有人对这个问题有见解吗？谢谢！
回答：
当你使用SDWriter.write时，你需要提供你希望写入文件的构象的ID：
writer = Chem.SDWriter('aspirin_confs.sdf')for cid in range(mol.GetNumConformers()): writer.write(mol, confId=cid)编辑：
如果你只对将此属性写入文件感兴趣，为什么不在每次迭代时只覆盖分子属性呢，例如：
writer = Chem.SDWriter('aspirin_confs.sdf')for cid in range(mol.GetNumConformers()): mol.SetProp('ID', f'aspirin_conformer_{cid}') writer.write(mol, confId=cid)