Fix index issue in make_whole

[jbarnoud]

I missed an error when reviewing @richardjgowers 's #1965. Coordinates of the AtomGroup where indexed with indices relative to the whole system.

[richardjgowers]

@jbarnoud we'll also have to fix that when you supply a reference atom it doesn't check where in the atomgroup this reference atom is from?

[codecov]

Codecov Report

Merging #1986 into develop will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop    #1986   +/-   ##
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  Coverage    88.48%   88.48%           
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  Files          142      142           
  Lines        17202    17202           
  Branches      2635     2635           
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  Hits         15221    15221           
  Misses        1385     1385           
  Partials       596      596

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[jbarnoud]

@richardjgowers I do not think so. The atom that can be given as reference is checked to be part of the AtomGroup. The index is obtained relative to the system with the .index attribute, which is what we want since it is used to get the bonds.

I realize, though, that my fix assumes that the atoms in the atomgroup are sorted.

[jbarnoud]

Superseded by #1987.