Hi --

I recently struggled over the following results of a StandardizeCharges operation (from StandardizeMolecule component).

Example:

Both molecules are represented by different CTABs (which is correct, IMHO):

  SciTegic09281211082D

  4  2  0  0  0  0            999 V2000

   -3.8125    0.6875    0.0000 C   0  0

   -3.0980    1.1000    0.0000 C   0  0

   -2.3836    0.6875    0.0000 N   0  0

   -0.4375    0.7208    0.0000 Cl  0  0

  1  2  1  0

  2  3  1  0

M  END

\$\$\$\$

  SciTegic09281211082D

  5  3  0  0  0  0            999 V2000

   -3.8125    0.6875    0.0000 C   0  0

   -3.0980    1.1000    0.0000 C   0  0

   -2.3836    0.6875    0.0000 N   0  0

   -0.4667    0.7208    0.0000 H   0  0

    0.4103    0.7167    0.0000 Cl  0  0

  2  3  1  0

  1  2  1  0

  4  5  1  0

M  END

\$\$\$\$

Both "notations" of a HCl besides Ethylamine are encoded into identical canonical smiles, which is correct from my point of view (see picture above).

Now, if I do apply a StandardizeCharges operation, I'll end up with:

Hmm, I'm not sure wether this is a glitch or a feature that the first molecule will be standardized to become a negatively charged molecule (due to the lacking a NH3+ moiety).

IMHO the second molecule is standardized correctly and as advertised in the help text:

"Note that halogen acids with explicit hydrogens (H-X) are not modified."

But, I would have expected that a mixture of an uncharged structure with an additional "HCl" entry would have been unmodified as well. What is your opinion?

Regards,

Michael