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

Healey, Joe J.R.J.Healey at warwick.ac.uk
Fri Sep 23 02:27:35 PDT 2016

That was exactly what I was after thanks! I figured the object orientation should provide that somewhere but was barking up slightly the wrong tree!

Thank you all for all your help - definitely wouldn't have been able to do it without you!

If it's of any interest, or it helps for any future questions where you might want to refer back to code segments, I've put the more-or-less-finished script in this paste:


Joe Healey

M.Sc. B.Sc. (Hons)
PhD Student
MOAC CDT, Senate House
University of Warwick
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: 22 September 2016 20:54:35
To: Jaime Rodríguez-Guerra
Cc: chimera-users at cgl.ucsf.edu; Healey, Joe
Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers

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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