[MMTK] PartitionedCollection.selectShell

Chris MacRaild c.a.macraild at leeds.ac.uk
Fri Jan 19 17:39:43 UTC 2007


I'm probably missing something basic here, but I'm not getting the
results I expect from PartitionedCollection.selectShell

eg. if I do:

>>> bb = PartitionedCollection(1.0,
...	chain.backbone().atomsWithDefinedPositions())
>>> res = chain[15]
>>> rPos = res.position()

>>> bb.selectShell(rPos, 0.3).atomList()
[]


whereas:

>>> for atom in bb:
...     if universe.distance(rPos, atom.pos) <= 0.3:
...         print atom, universe.distance(rPos, atom.pos)
...
Atom .Glu16.peptide.C 0.278183394332
Atom .Glu16.peptide.C_alpha 0.162686972188
Atom .Glu16.peptide.H 0.2878402478
Atom .Glu16.peptide.H_alpha 0.206802524354
Atom .Glu16.peptide.N 0.250664650392


likewise:

>>> bb = Collection(chain.backbone().atomsWithDefinedPositions())
>>> bb.selectShell(rPos, 0.3).atomList()
[Atom .Glu16.peptide.C, Atom .Glu16.peptide.C_alpha,
Atom .Glu16.peptide.H, Atom .Glu16.peptide.H_alpha,
Atom .Glu16.peptide.N]



Shouldn't these procedures give the same set of atoms?


Thanks,

Chris






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