bad inchi for chiral S when the molecule is sanitized

[greglandrum]

[18]>>> print mb

  Mrv0541 07211416442D          

  7  6  0  0  1  0            999 V2000
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 S   0  0  1  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  1  6  0  0  0
  7  6  2  0  0  0  0
M  END


[19]>>> print Chem.MolToInchi(Chem.MolFromMolBlock(mb,sanitize=False))
InChI=1S/C5H12OS/c1-5(2,3)7(4)6/h1-4H3/t7-/m1/s1

[20]>>> print Chem.MolToInchi(Chem.MolFromMolBlock(mb,sanitize=True))
InChI=1S/C5H12OS/c1-5(2,3)7(4)6/h1-4H3/t7-/m0/s1

[21]>>> print Chem.MolToSmiles(Chem.MolFromMolBlock(mb,sanitize=True),True)
C[S@@](=O)C(C)(C)C

[22]>>> print Chem.MolToSmiles(Chem.MolFromMolBlock(mb,sanitize=False),True)
C[S@@](=O)C(C)(C)C

[23]>>> m1 = Chem.MolFromMolBlock(mb,sanitize=True)

[24]>>> m2 = Chem.MolFromMolBlock(mb,sanitize=False)

[25]>>> m1.Debug()
Atoms:
    0 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    1 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    2 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    3 6 C chg: 0  deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
    4 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    5 8 O chg: 0  deg: 1 exp: 2 imp: 0 hyb: 3 arom?: 0 chi: 0
    6 16 S chg: 0  deg: 3 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 1
Bonds:
    0 3->0 order: 1 conj?: 0 aromatic?: 0
    1 3->1 order: 1 conj?: 0 aromatic?: 0
    2 3->2 order: 1 conj?: 0 aromatic?: 0
    3 6->3 order: 1 conj?: 0 aromatic?: 0
    4 6->4 order: 1 conj?: 0 aromatic?: 0
    5 6->5 order: 2 conj?: 0 aromatic?: 0

[26]>>> m2.Debug()
Atoms:
    0 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0
    1 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0
    2 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0
    3 6 C chg: 0  deg: 4 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0
    4 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0
    5 8 O chg: 0  deg: 1 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0
    6 16 S chg: 0  deg: 3 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 1
Bonds:
    0 3->0 order: 1 conj?: 0 aromatic?: 0
    1 3->1 order: 1 conj?: 0 aromatic?: 0
    2 3->2 order: 1 conj?: 0 aromatic?: 0
    3 6->3 order: 1 conj?: 0 aromatic?: 0
    4 6->4 order: 1 dir: 2 conj?: 0 aromatic?: 0
    5 6->5 order: 2 conj?: 0 aromatic?: 0

[greglandrum]

It's not purely sanitization; it's one of the cleanup operations that the molfile parser does when it sanitizes:

In [17]: m3 = Chem.MolFromMolBlock(mb,sanitize=False)

In [18]: Chem.SanitizeMol(m3)
Out[18]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE

In [19]: print Chem.MolToInchi(m3)
InChI=1S/C5H12OS/c1-5(2,3)7(4)6/h1-4H3/t7-/m1/s1

In [20]: m3.Debug()
Atoms:
    0 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    1 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    2 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    3 6 C chg: 0  deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
    4 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    5 8 O chg: 0  deg: 1 exp: 2 imp: 0 hyb: 3 arom?: 0 chi: 0
    6 16 S chg: 0  deg: 3 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 1
Bonds:
    0 3->0 order: 1 conj?: 0 aromatic?: 0
    1 3->1 order: 1 conj?: 0 aromatic?: 0
    2 3->2 order: 1 conj?: 0 aromatic?: 0
    3 6->3 order: 1 conj?: 0 aromatic?: 0
    4 6->4 order: 1 dir: 2 conj?: 0 aromatic?: 0
    5 6->5 order: 2 conj?: 0 aromatic?: 0

[greglandrum]

Can be traced back to the bond direction:

In [21]: b=m3.GetBondWithIdx(4)

In [22]: b.SetBondDir(Chem.BondDir.NONE)

In [23]: print Chem.MolToInchi(m3)
InChI=1S/C5H12OS/c1-5(2,3)7(4)6/h1-4H3/t7-/m0/s1

[greglandrum]

further proof of this, adding bond wedging fixes the problem:

In [35]: Chem.WedgeMolBonds(m1,m1.GetConformer())

In [37]: m1.Debug()
Atoms:
    0 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    1 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    2 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    3 6 C chg: 0  deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
    4 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
    5 8 O chg: 0  deg: 1 exp: 2 imp: 0 hyb: 3 arom?: 0 chi: 0
    6 16 S chg: 0  deg: 3 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 1
Bonds:
    0 3->0 order: 1 conj?: 0 aromatic?: 0
    1 3->1 order: 1 conj?: 0 aromatic?: 0
    2 3->2 order: 1 conj?: 0 aromatic?: 0
    3 6->3 order: 1 dir: 2 conj?: 0 aromatic?: 0
    4 6->4 order: 1 conj?: 0 aromatic?: 0
    5 6->5 order: 2 conj?: 0 aromatic?: 0

In [38]: print Chem.MolToInchi(m1)
InChI=1S/C5H12OS/c1-5(2,3)7(4)6/h1-4H3/t7-/m1/s1

But this wouldn't be a general fix because molecules built from SMILES still won't have the correct InChI:

In [41]: print Chem.MolToSmiles(m2,True)
C[S@@](=O)C(C)(C)C

In [42]: print Chem.MolToInchi(Chem.MolFromSmiles('C[S@@](=O)C(C)(C)C'))
InChI=1S/C5H12OS/c1-5(2,3)7(4)6/h1-4H3/t7-/m0/s1