On 12/10/2013 11:47 AM, Geoffrey Hutchison wrote: >> OpenBabel crash more nicely with an error message rather than >> entering an infinite loop… > > Right. Infinite loops are a clear bug, and "crash" certainly is too. > I think what you really mean is that it'll refuse to translate the > CIF because there's nothing in it.
Unfortunately it's not quite that simple. You have to define "nothing" and you should to also error out on mmCIFs that have "too much" in them. :( Long story: CIF may have a chem. comp. section: chemical component (aka ligand or residue) definition, with all the atoms and bonds and R/S & E/Z stereochemistry and a bunch of other goodies. You can make an OBMol from that. It may have an entity/chain section: a chain of linked chem. comps, and for any that aren't the "standard 28" there should be chem. comp section(s) elsewhere in the file. I forget exactly how they model homo-n-mers and other interesting stuff -- but anyway, you could make an OBMol from that. Then there's coordinates: the atom_site section. I believe OpenBabel currently makes OBMols from that. Off the top of my head and I won't vouch for most of this, but 1. Ligand Expo CIFs have only the chem. comp section (unless you ask for coordinates) -- if you treat them as "there's nothing in it", you'd be wrong. 2. Solution NMR structures may not have the coordinates for e.g. terminal residues because they're flapping around and don't produce stable peaks -- but I think the entity/chain section should have the complete residue sequence. So if you're making the molecule from atom_site alone, without looking at the entity, your molecule can be incomplete. 3. Solution NMR structures have multiple models (usually 20 for some reason) -- _atom_site.ndb_model or _atom_site.pdbx_PDB_model_num dep. on the CIF version. So now you have to look at _pdbx_nmr_ensemble.representative_conformer to figure out which set of coordinates to use for building your molecule, and its value may be like "1, 3, 7". Because they had a mix of 3 conformers in the sample. On top of which there are a few tentacles hiding just under the surface when it comes to parsing STAR formats like CIF. Keywords inside values being one. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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