[chimera-dev] source of ~10x slowdown in opening of Molecules in lastest chimera

[Greg Couch]

After much digging, it turns out that the slowdown occurs when the
PDBio wrapper returns the new molecules to chimera.  Due to wrappy's
C++/Python reference count caching, the molecule's attributes are
fetched at that time, and one of those attributes, sortedAtoms, takes a
long time to compute (for 4371 atoms it takes 4.1 seconds on socrates,
3.2 on spin and 5.9 on my home P4).  With a timing script, we can see
that sortedAtoms isn't any slower in the lastest chimera, and
sortedAtoms has been an attribute since 2000/05/02, so an optimization
to speed up the initial sorting of atoms seems to have been lost
recently.  So far, I have been unable to find it, so I'm hoping Eric
or Conrad will chime in.

In the mean time, making sortedAtoms a member function instead of an
attribute (which wrappy much prefers anyway) avoids the delay.  Luckily
no .py file in /usr/local/src/chimera calls sortedAtoms, so it is a
fairly safe fix.

	- Greg