So, I’ve found the source of the problem - not the stereochemistry, but the ‘Cl’ atom. For reasons I don’t remember, our Mol-block parsing code converts the whole line to uppercase each time, so the line:
M V30 16 Cl 2.18109 3.09803 -0.113906 0
M V30 16 CL 2.18109 3.09803 -0.113906 0
The code to look up the atomic weight, which is required for the PMI calculations then fails to find anything for the element with the symbol ‘CL’. I will do a bit more checking to try to figure out if fixing this breaks anything else, add a ‘chloro’ example to the test cases and hopefully get a bug fix pushed out later today or tomorrow.
Thanks again for reporting this, and for your patience and help getting us to the bottom of the problem!