I’m doing some work in an extension with conformers, and I’m looking
for a way to serialize the data from my runs. Obviously the best way
to store the conformer data is in an OB supported file format that
already has structure in place for conformers. Can anyone recommend a
format that I could use that supports conformer information?
I thought that cml might do it, but it looks like it won’t…
Obviously the best way to store the conformer data is in an OB
supported file format that
already has structure in place for conformers.
At the moment, there’s no supported OB format which reads in
conformers. The closest might be the undocumented “FIX” format for
smiles, which writes all conformers. You might also try XYZ "movies"
which are basically a list of conformers.
I suspect we may still have a 2.2.4 release, so you could certainly
add conformer support to CML.
Also, remember that you can compile formats into your extension.
Hope that helps – please ask me if you have more questions.
I was planning on just dumping the coords, etc to a resume file, but
I would like to add conformer support to cml. Is there a
specification for cml files somewhere that I should follow? The link
on the OB wiki for the cml specification url leads to a blank page…
Contact the cml-discuss mailing list:
I suspect you’re just supposed to supply multiple coordinate sets.