On Thu, Dec 15, 2011 at 2:04 PM, Craig A. James <cja...@emolecules.com> wrote:
> 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.
>
> You can store multiple conformers by just appending them to the line with a
> tab separator.
>
> The code is almost there already.
>
> echo "CCO" | babel --gen2D -i smi -o can -xx
>
> 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.
>
> Like I said, it's a bit hokey and certainly not a supported format, but it's
> very effective.
This sounds promising, I'll try it out.
> (I wonder ... would "SMILES-with-coordinates" be an interesting addition to
> the SMILES parser? The code is all written.)
Something like this would be very useful -- a compact,
straightforward, and complete description. I like it.
Thanks,
Dave
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