Allow systems like C/C=N/[H] to be stereogenic with the new chirality code

[greglandrum]

The old stereo perception code handled these cases, as does InChI, so we shouldn't reject them.

This was raised in discussion #6291 here:
#6291 (comment)

[ricrogz]

LGTM, but do we need to worry about the failed tests?

[greglandrum]

LGTM, but do we need to worry about the failed tests?

Yes, yes we do. I hadn't notice those; thanks for pointing them out.
I will figure out what's going on and update the PR.

[greglandrum]

LGTM, but do we need to worry about the failed tests?

Yes, yes we do. I hadn't notice those; thanks for pointing them out. I will figure out what's going on and update the PR.

@ricrogz : the test failures here are not connected with this PR. These now seem to be popping up on all CI builds and must be due to something having changed with the linux_py311 build env. I will try to track this down separately.

[ricrogz]

@ricrogz : the test failures here are not connected with this PR. These now seem to be popping up on all CI builds and must be due to something having changed with the linux_py311 build env. I will try to track this down separately.

Sounds good!

[ptosco]

@greglandrum @ricrogz
After this commit, a guanidine-containing molecule as simple as

fails to build. Here's a simple reproducible:

from rdkit import Chem

mb = """
     RDKit          2D

  6  5  0  0  0  0  0  0  0  0999 V2000
    2.0443    0.2759    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7038    2.5963    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3828    2.5961    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0444    1.8228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6359    1.8229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3827   -0.4985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0
  4  2  1  0
  4  3  2  0
  2  5  1  0
  6  1  1  0
M  END
"""

Chem.SetUseLegacyStereoPerception(False)
mol = Chem.MolFromMolBlock(mb)
assert mol
AssertionError

Chem.SetUseLegacyStereoPerception(True)
mol = Chem.MolFromMolBlock(mb)
assert mol

The molecule builds as expected with the new stereo perception code after reverting this commit.

[ricrogz]

Oh, I see the issue here. I'll post a PR in a sec.