On Jan 14, 2019, at 13:36, Andrew Dalke <da...@dalkescientific.com> wrote: > I think the more correct solution is to ensure that OBConversion always > starts with an initial output Index of 1 instead of 0. > > I don't know where that might be done. Could someone provide advice?
I think I've found it. OBConversion() was designed to convert between the input and output using an intermediate "ChemObject". The Convert() function calls a function which gets the ChemObject(), and as a side-effect, increments the Index. Thus, during conversion the Index starts at 1. The WriteString() and WriteFile() methods bypass the Convert() step to write a molecule object directly. These don't call Convert(), so don't pre-increment the Index, leaving it as 0. Many of the formats test for Index == 1 for initialization, like the FPS format, which crashes if the initialization isn't done. I have a patched version which appears to fix the problem (though it may not be the best solution). I've submitted it to https://github.com/openbabel/openbabel/issues/1922 and will work on a pull request based on my patch. Further discussion will be in the issue tracker. Cheers, Andrew da...@dalkescientific.com _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
