如何将 RDKit conformer 对象保存到 sdf 文件中？

Question

我为一个分子生成了一堆构象异构体。对于每个符合的，我想将坐标保存在 SDF 文件中。我尝试了以下，但sdf文件中的坐标与conformer的坐标不同。

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers
from rdkit.Chem.EnumerateStereoisomers import StereoEnumerationOptions


aspirin = '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)  # This is the conformer that I wanted to save in a SDF file.
print(conformer_i.GetPositions())

我明白了

[[ 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]]

但是当我试图将具有这种构象异构体结构的分子保存到 SDF 文件中时，

w = Chem.SDWriter('conformer.sdf')
mol.AddConformer(conformer_i)
w.write(mol)
w.close()

我得到以下信息：


     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  0
M  END
$$$$

分子 sdf 文件中的坐标与 conformer_i 中的坐标不同。有没有人对这个问题有洞察力？谢谢！

Answer 1

当您使用 SDWriter.write 时，您需要提供您希望写入文件的符合者 ID：

writer = Chem.SDWriter('aspirin_confs.sdf')
for cid in range(mol.GetNumConformers()):
    writer.write(mol, confId=cid)

编辑：

如果您只对将此属性写入文件感兴趣，那么为什么不在每次迭代时覆盖分子属性即

writer = Chem.SDWriter('aspirin_confs.sdf')
for cid in range(mol.GetNumConformers()):
    mol.SetProp('ID', f'aspirin_conformer_{cid}')
    writer.write(mol, confId=cid)

如何将 RDKit conformer 对象保存到 sdf 文件中？

How to save RDKit conformer object into a sdf file?

python

machine-learning

chemistry

rdkit

cheminformatics