Hello. A very interesting initiative and rather related to what I am
working in.
I am working in the Crystallography Open Database (COD,
www.crystallography.net), a large collection of openly accessible CIF
files. I have posted a few times messages previously to this list. COD
contains today
A colleague has pointed out to me the likely problem with the
depictions. Mol files can have either 2D or 3D coordinates. I'm
guessing that 3D mol files are not interpreted correctly by the
drawing program you used to view the structures; it must have set the
z coordinate to 0 without any warning.
I think, I've pin-pointed the issue in the source - OBConversion class. The
first and last molecule is set by SetStartAndEnd method. It's being called
only by Convert method, not by Read nor ReadFile, hence the binding dont
use -f and -l. I figure if i't called SetStartAndEnd in Read or ReadFile,
This is very interesting - sounds like you came across the same issues as we
did and came to the same conclusions too.
We're also very interested to hear that you've got smiles for so many of
your structures which would indeed make it straightforward to link
ChemSpider to COD. We'll be in touch!
