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topologyobjects.Angle does not know about the periodic boundaries nor is this behaviour documented #1938

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matsikora opened this issue Jun 14, 2018 · 1 comment
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topologyobjects.Angle does not know about the periodic boundaries nor is this behaviour documented #1938

matsikora opened this issue Jun 14, 2018 · 1 comment
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@richardjgowers
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Component-Core Component-Docs Component-lib PBC
Milestone
0.19.0

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@matsikora
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Expected behaviour

topologyobjects.Angle.angle (and probably dihedral as well) should have a "box" option to allow for correct calculation of angles when contributing atoms cross periodic boundaries. Analogous to lib.distances.calc_angles().

Actual behaviour

angle function is not aware of PBC and this behaviour is not documented.

Code to reproduce the behaviour

Currently version of MDAnalysis:

0.17.0
@richardjgowers richardjgowers mentioned this issue Jun 14, 2018
Merged
@orbeckst orbeckst added this to the 0.18.x milestone Jun 15, 2018
@orbeckst
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@richardjgowers I assigned to you as you're working on PR #1939 already

richardjgowers added a commit that referenced this issue Jun 16, 2018
@richardjgowers
Added single distance calculations to lib.distances
04cf3eb 
calc_distance, calc_angle and calc_dihedral

Fixes Issue #1262 #1938

redid 180 degree angle test for new function
richardjgowers added a commit that referenced this issue Jun 23, 2018
@richardjgowers
Added single distance calculations to lib.distances
f46f6b8 
calc_distance, calc_angle and calc_dihedral

Fixes Issue #1262 #1938

redid 180 degree angle test for new function
richardjgowers added a commit that referenced this issue Jun 29, 2018
@richardjgowers
Added single distance calculations to lib.distances
b5c2665 
calc_distance, calc_angle and calc_dihedral

Fixes Issue #1262 #1938

redid 180 degree angle test for new function
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@richardjgowers richardjgowers

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Component-Core Component-Docs Component-lib PBC
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0.19.0
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@orbeckst @richardjgowers @matsikora