On 12/15/11 10:03 AM, David Lonie wrote:
> On Thu, Dec 15, 2011 at 12:48 PM, David Lonie<lonieda...@gmail.com> wrote:
>> This seems like something that someone may have encountered before, so
>> I figured I'd ask before rolling my own solution/attempting to patch
>> the cml reader/writer.
>
> small update:
> 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.
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.
(I wonder ... would "SMILES-with-coordinates" be an interesting addition to the
SMILES parser? The code is all written.)
Craig
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