Chimera does not use an attribute for "selectedness" because there are actually multiple classes of objects that may be selected. As you discovered, chimera.selection.currentSOMETHING() will return the selected objects of the correct type. To make your code run faster, you should not call chimera.selection.currentAtoms() inside the loop because it gets recomputed unnecessarily. Instead, try something like: selected = frozenset(chimera.selection.currentAtoms()) for a in chimera.openModels.list()[0].atoms: if a in selected: print "this atom is selected" else: print "this one isn't" This should run much faster for two reasons: (a) the selected atoms are not recomputed multiple times, and (b) the "a in ..." test is using a set instead of a list (returned by currentAtoms()) and should be much more efficient. Hope this helps Conrad On 10/11/12 5:19 AM, Jean Didier Pie Marechal wrote:
Sorry,
just to clarify my previous request:
this is a script that does what I want though a selection attribute would be faster I think.
for a in chimera.openModels.list()[0].atoms: if a in chimera.selection.currentAtoms(): print "this atom of the molecule is selected" #to say something else: print "this one isn't"
cheers
Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es www: http://asklipio.qf.uab.es
----- Missatge original ----- De: Jean Didier Pie Marechal <JeanDidier.Marechal@uab.cat> Data: Dijous, Octubre 11, 2012 12:39 pm Assumpte: attribute for selection?
HI,
I want to add attributes to atoms that are selected and those that aren't. I thought that atoms had a selection attribute already defined in chimera (something like a boolean) but I don't find it. I am wrong with that?
best, JD
Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es www: http://asklipio.qf.uab.es
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