On Wednesday, September 24, 2003, at 08:18 AM, Lars Kunert wrote:

I do like to reference chimera-atoms from my extension. I have the problem that chimera reorders the atoms (and probably also the bond entries) of mol2 files. Which of the following workarounds would you suggest:

• resort all my mol2-files -> will only work if the resorting ist

stable

• use a dictionary -> puts some unwellcome functionallity into my

python-wrapper

• refer by name -> mol2-atom names do not have to be unique and will be

slow without a dictionary or is there a way to switch it of???

Hi Lars, As you have discovered, Chimera reorders the atoms into a sequence that is more useful for itself (graph traversal order). However, each atom has a 'serialNumber' field that corresponds to the order in the input file. So, if 'mol' is a Python reference to your molecule, you can get a list of atoms in input order with:

atoms = mol.atoms atoms.sort(lambda a, b: cmp(a.serialNumber, b.serialNumber))

Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu