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It is not possible to use align_principal_axis with a principal axis #1045

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kain88-de opened this issue Oct 21, 2016 · 0 comments
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It is not possible to use align_principal_axis with a principal axis #1045

kain88-de opened this issue Oct 21, 2016 · 0 comments
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Component-Core defect
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0.16.0

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Expected behaviour

Align with first PA should be possible.

pa = ag.principal_axes()
ag.align_principal_axis(0, pa[0])

Then I have my protein in the principal axis reference frame. Note that it would work if align to different principal axes

Actual behaviour

All values in the position array are set to NaN

Why does this happen

The problem for this specific case is that mda.lib.transformations.rotaxis will return NaN if both vectors are the same. The solution is to catch this before and return a fixed axis like [1, 0, 0].
@kain88-de kain88-de added this to the 0.16.0 milestone Oct 21, 2016
@kain88-de kain88-de self-assigned this Oct 21, 2016
@kain88-de kain88-de mentioned this issue Oct 21, 2016
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@kain88-de kain88-de mentioned this issue Oct 25, 2016
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abiedermann pushed a commit to abiedermann/mdanalysis that referenced this issue Jan 5, 2017
@kain88-de @richardjgowers
PEP8 changes to topologyattrs: Fixes MDAnalysis#1045 (MDAnalysis#1042)
43ef521 
* pep8 changes topologyattrs

* pep8 changes test file

* add license to test
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