MolToMolBlock writes "either" stereo for double bonds which shouldn't be stereo

[ricrogz]

I think this was introduced in #6387 .

An example:

# coding: utf-8
from rdkit import Chem

mb = """
  MJ230800                      

 16 16  0  0  0  0  0  0  0  0999 V2000
  -12.8296    1.4763    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  -13.5918    1.1606    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -13.9075    0.3984    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  -13.5918   -0.3638    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -12.8296   -0.6795    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0674    1.1606    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7516    0.3984    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0674   -0.3638    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4647    2.2162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.1945    2.2162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0118    0.0335    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0118    0.7632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.1945   -1.4194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4647   -1.4194    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -14.6474    0.7632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.6474    0.0335    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  8  1  0  0  0  0
  6  7  1  0  0  0  0
  8  7  2  0  0  0  0
  1  9  1  0  0  0  0
  7 12  1  0  0  0  0
  5 13  1  0  0  0  0
  3 15  1  0  0  0  0
  1 10  1  0  0  0  0
  7 11  1  0  0  0  0
  5 14  1  0  0  0  0
  3 16  1  0  0  0  0
M  END
"""

m = Chem.MolFromMolBlock(mb)
print(Chem.MolToV3KMolBlock(m))

This prints:

     RDKit          2D

  0  0  0  0  0  0  0  0  0  0999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 16 16 0 0 0
M  V30 BEGIN ATOM
M  V30 1 P -12.829600 1.476300 0.000000 0
M  V30 2 N -13.591800 1.160600 0.000000 0
M  V30 3 P -13.907500 0.398400 0.000000 0
M  V30 4 N -13.591800 -0.363800 0.000000 0
M  V30 5 P -12.829600 -0.679500 0.000000 0
M  V30 6 N -12.067400 1.160600 0.000000 0
M  V30 7 P -11.751600 0.398400 0.000000 0
M  V30 8 N -12.067400 -0.363800 0.000000 0
M  V30 9 C -12.464700 2.216200 0.000000 0
M  V30 10 O -13.194500 2.216200 0.000000 0
M  V30 11 O -11.011800 0.033500 0.000000 0
M  V30 12 C -11.011800 0.763200 0.000000 0
M  V30 13 C -13.194500 -1.419400 0.000000 0
M  V30 14 O -12.464700 -1.419400 0.000000 0
M  V30 15 C -14.647400 0.763200 0.000000 0
M  V30 16 O -14.647400 0.033500 0.000000 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 2 1 6 CFG=2
M  V30 2 1 1 2
M  V30 3 2 2 3 CFG=2
M  V30 4 1 3 4
M  V30 5 2 4 5 CFG=2
M  V30 6 1 5 8
M  V30 7 1 6 7
M  V30 8 2 8 7 CFG=2
M  V30 9 1 1 9
M  V30 10 1 7 12
M  V30 11 1 5 13
M  V30 12 1 3 15
M  V30 13 1 1 10
M  V30 14 1 7 11
M  V30 15 1 5 14
M  V30 16 1 3 16
M  V30 END BOND
M  V30 END CTAB
M  END

None of these double bonds should have the "CFG=2" specification, since the P atoms on one side of the bond are pentavalent, so CIS/TRANS stereo does not apply.

[ricrogz]

It's easier to see with a SMILES:

m2 = Chem.MolFromSmiles('CP1(O)=NP(C)(O)=NP(C)(O)=NP(C)(O)=N1')
print(Chem.MolToV3KMolBlock(m2))
----------------------------------------------------------------

     RDKit          2D

  0  0  0  0  0  0  0  0  0  0999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 16 16 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C 3.149874 0.913142 0.000000 0
M  V30 2 P 1.959844 0.000000 0.000000 0
M  V30 3 O 3.149874 -0.913142 0.000000 0
M  V30 4 N 1.385819 -1.385819 0.000000 0
M  V30 5 P -0.000000 -1.959844 0.000000 0
M  V30 6 C 0.913142 -3.149874 0.000000 0
M  V30 7 O -0.913142 -3.149874 0.000000 0
M  V30 8 N -1.385819 -1.385819 0.000000 0
M  V30 9 P -1.959844 0.000000 0.000000 0
M  V30 10 C -3.149874 -0.913142 0.000000 0
M  V30 11 O -3.149874 0.913142 0.000000 0
M  V30 12 N -1.385819 1.385819 0.000000 0
M  V30 13 P 0.000000 1.959844 0.000000 0
M  V30 14 C -0.913142 3.149874 0.000000 0
M  V30 15 O 0.913142 3.149874 0.000000 0
M  V30 16 N 1.385819 1.385819 0.000000 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 2 3
M  V30 3 2 2 4 CFG=2
M  V30 4 1 4 5
M  V30 5 1 5 6
M  V30 6 1 5 7
M  V30 7 2 5 8 CFG=2
M  V30 8 1 8 9
M  V30 9 1 9 10
M  V30 10 1 9 11
M  V30 11 2 9 12 CFG=2
M  V30 12 1 12 13
M  V30 13 1 13 14
M  V30 14 1 13 15
M  V30 15 2 13 16 CFG=2
M  V30 16 1 16 2
M  V30 END BOND
M  V30 END CTAB
M  END