>> After skimming the spec, It looks like cml doesn't have a way to
>> specify conformers, either. I suppose a separate cml string for each
>> conformer would be the best solution I can think of at this point.
>
> This may sound hokey, but if you want to "roll your own," storing canonical
> SMILES with X/Y/Z coordinates is very easy to do, and very easy to parse.
> It's also very compact and compresses about 10- or 20-to-1 with gzip.
IIRC, this is the "FIX" format, probably created by Open Eye -- I can't find
any reference to it anywhere else.
> prints out the X/Y coordinates in canonical order. The code to do this is
> about 15 lines of C++ in smilesformat.cpp (look for IsOption("x")). You can
> copy the code and just add the Z coordinate and it would do what you want.
> Parsing is pretty simple too because the coordinates are in the same order as
> the atoms. If you're interested, I can send you a function that parses a
> string of X/Y coordinates into an OBMol object - it's about 50 lines of C++
> code and includes a certain amount of error checking. Again, all you'd have
> to change is to add the Z coordinate.
At the moment, I think FIX only supports writing and not reading, but as Craig
said, it's trivial to add.
All the code (for Craig's -xx and the FIX format) is in
src/formats/smilesformat.cpp.
BTW, CML (the format) does allow multiple conformations -- it's basically as
you said, just a catenation of multiple coordinate sets. XYZ format is similar,
albeit without bonds.
-Geoff
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