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