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

Jaime Rodríguez-Guerra jaime.rodriguezguerra at uab.cat
Fri Sep 23 02:56:38 PDT 2016

Hi Joe!

You're welcome! Glad to see you got it working. I've reviewed your
code and would want to point out some details that might be helpful to
you in the future, though. These are mostly style-related things, but
those will contribute to a cleaner reading experience!

1. You don't need backslashes if you're inside parenthesis. So, in all
those parse_argument lines, you can safely delete them. Related to
this, you can wrap imports with parenthesis, so that backslashes are
not needed.
2. Tuple unpacking does not need parenthesis in you're dealing with
1D-tuples. Only needed if you are dealing with more than one dimension
(ie, (animal, fruit), sport = [['tiger', 'pear'], 'soccer']
3. Since you are opening files with the "with" context manager, you
don't need to manually close the file later. It's closed automatically
as soon as you leave that with block.
4. Lines 166-170 could be replaced with a (cleaner, but not
necessarily more performant) glob.glob() call. Check it out to see if
it satisfies your requirements.
5. While you are at it, take a look at the PEP8 docs and the Google
Python style guide. You don't need to follow all the rules, but they
are really helpful in bringing consistency to your own style!

That's it! Hope you don't mind these pieces of advice :)


2016-09-23 11:27 GMT+02:00 Healey, Joe <J.R.J.Healey at warwick.ac.uk>:
> 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:
> http://pastebin.com/xJNSWJGq
> Joe Healey
> M.Sc. B.Sc. (Hons)
> PhD Student
> MOAC CDT, Senate House
> University of Warwick
> Coventry
> CV47AL
> Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk
> Jointly working in:
> Waterfield Lab (WMS Microbiology and Infection Unit)
> and the Gibson Lab (Warwick Chemistry)
> Twitter: @JRJHealey  |  Website: MOAC Page
> ________________________________
> 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.
> —Eric
>> 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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