I'm trying to generate reaction CXSMARTS for a reaction that includes explicit H atoms in the form of H-I or H-H molecules.
When I try molconvert.bat cxsmarts:qh it fails. (see screenshot attached)
When I try molconvert.bat smarts:qh it succeeds.
When I try molconvert.bat cxsmarts:qs it succeeds.
The error is not restricted to reactions, it also occurs with single molecules.
The error message I get reads: error: 8 java.lang.ArrayIndexOutOfBoundsException: 8 (more detail in the screenshot).
I have also attached two MRV files:
1. the addition reaction of propene with HI, which fails to produce CXSMARTS with the 'qh' flags
2. the addition reaction of propene with I2, which produces output as expected with the 'qh' flags
This seems a bug to me. There is no indication in the documentation that this combination of flags is invalid or nonsensical.
Windows XP SP2