[chimera-dev] Re: [Chimera-users] Zones to create inspector list of "contacts"

[Thomas Goddard]

Hi Eric,

  Thanks for telling me of those routines.

  I think I would optimize the close contact pseudobond routine I gave to
Grant by first grouping the atoms by molecule and only comparing pairs in
different molecules.  For more speed I would use the _closepoints module
to limit the atoms from each molecule to only those within the requested
distance range of atoms in all other molecules.  With these improvements
the code would be 3 times longer but finish in less than a second for
anything ribosome size or smaller and a reasonable number of contacts
(< 10000).

	 Tom