title: How to save RDKit conformer object into a sdf file?
body: <p>I generated a bunch of conformers for a molecule. For each conformed, I want to save the coordinates in a SDF file. I tried the following, but the coordinates in the sdf file is different from that of the conformer.</p>
  <pre><code>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())
  </code></pre>
  <p>I get</p>
  <pre><code>[[ 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]]
  </code></pre>
  <p>But when I tried to save the molecule with this conformer structure into a SDF file with,</p>
  <pre><code>w = Chem.SDWriter('conformer.sdf')
  mol.AddConformer(conformer_i)
  w.write(mol)
  w.close()
  </code></pre>
  <p>I got the following:</p>
  <pre><code>
       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
  $$$$
  </code></pre>
  <p>The coordinates in the molecular sdf file is different from the coordinates in the <code>conformer_i</code>. Does anyone have a insight about this issue? Thank you!</p>