AddHs creates H atom with nan coordinates on edge case 2D structure

[ricrogz]

This illustrates the problem:

In [1]: from rdkit import Chem 
   ...: mol = Chem.MolFromMolBlock(""" 
   ...:      RDKit          2D 
   ...:  
   ...:   7  8  0  0  1  0  0  0  0  0999 V2000 
   ...:     5.0014    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0 
   ...:     4.1764    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0 
   ...:     3.3514    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0 
   ...:     2.9389    1.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0 
   ...:     3.3514    1.8412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0 
   ...:     4.1764    1.8412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0 
   ...:     4.5889    1.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0 
   ...:   2  1  1  1 
   ...:   7  1  1  1 
   ...:   2  3  1  0 
   ...:   2  7  1  0 
   ...:   3  4  1  0 
   ...:   4  5  1  0 
   ...:   5  6  1  0 
   ...:   7  6  1  0 
   ...: M  END 
   ...: """) 
   ...: res = Chem.AddHs(mol, explicitOnly=False, addCoords=True, onlyOnAtoms=[1, 6]) 
   ...: print(Chem.MolToMolBlock(res))                                                                                                                                              

     RDKit          2D

  9 10  0  0  1  0  0  0  0  0999 V2000
    5.0014    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1764    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3514    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9389    1.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3514    1.8412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1764    1.8412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5889    1.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
       nan       nan       nan H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7229    0.6270    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0
  7  1  1  0
  2  3  1  0
  2  7  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  7  6  1  0
  2  8  1  1
  7  9  1  6
M  END

This is apparently happening because atoms 0, 1 and 6 are perfectly aligned:

If coordinates are regenerated, so that they are no longer perectly aligned, all is fine:

In [2]: params = Chem.rdCoordGen.CoordGenParams() 
   ...: Chem.rdCoordGen.AddCoords(mol, params) 
   ...: print(Chem.MolToMolBlock(mol))                                                                                                                                              

     RDKit          2D

  7  8  0  0  1  0  0  0  0  0999 V2000
   -1.4846   -0.0011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6190    0.4995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2466    1.0003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1130    0.5009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1138   -0.4991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2482   -0.9997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6182   -0.5005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1
  7  1  1  1
  2  3  1  0
  2  7  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  7  6  1  0
M  END


In [3]: res = Chem.AddHs(mol, explicitOnly=False, addCoords=True, onlyOnAtoms=[1, 6]) 
   ...: print(Chem.MolToMolBlock(res))                                                                                                                                              

     RDKit          2D

  9 10  0  0  1  0  0  0  0  0999 V2000
   -1.4846   -0.0011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6190    0.4995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2466    1.0003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1130    0.5009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1138   -0.4991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2482   -0.9997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6182   -0.5005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1197    1.3651    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1189    0.3659    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0
  7  1  1  0
  2  3  1  0
  2  7  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  7  6  1  0
  2  8  1  6
  7  9  1  6
M  END