[Chimera-users] Recursive structure matching and acquisition of descriptive numbers

Eric Pettersen pett at cgl.ucsf.edu
Thu Sep 22 12:54:35 PDT 2016

Thanks Jaime — exactly right.  I realized that the “atoms1, atoms2” in my original example didn’t really give any indication of which atoms were which, which is why in my later examples I changed to "simAtoms, refAtoms”, so it’s actually “atoms2” that are the reference atoms.


> On Sep 22, 2016, at 11:45 AM, Jaime Rodríguez-Guerra <jaime.rodriguezguerra at uab.cat> wrote:
> Hi!
> Since you are getting lists of atoms back, you only need to do some
> attribute access (rather than method calling)!
> Every chimera.Atom object has an attribute called molecule: a
> reference to its parent chimera.Molecule. chimera.Molecule objects
> have an attribute called 'name', but sometimes this is not very
> informative (depends on your input), so you need to resort to the pdb
> filename, stored in the first element of the openedAs tuple.
> In code, this looks like this:
> for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST, [ref, sims],
> defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]):
>    molecule1 = atoms1[0].molecule # any atom from the list will do
>    molecule2 = atoms2[0].molecule
>    print molecule1.name, "\t", molecule2.name, "\t",  rmsd #
> molecule1.openedAs[0] will also work here
> I don't know if atoms1 comes consistently from the reference molecule,
> but I'd guess it does.
> Hope it helps!
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