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Fix 199 #206

Merged
merged 4 commits into from
Jun 24, 2024
Merged

Fix 199 #206

merged 4 commits into from
Jun 24, 2024

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chryswoods
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This pull request fixes issue #199

  • I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
  • I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
  • I confirm that I have permission to release this code under the GPL3 license: [y]

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@lohedges

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This builds on #fix_202, so merging this will merge both. It's a small change, but looks bigger as I had to regenerate the System wrappers (I added the "center" keyword to the C++ class too)

…AtomIdx order.

This works really well, except that it fails when merging submolecules, because the
CGAtomIdx order changes on commit. I need to fix this. I suspect it will be by converting
merged proteins into a single cutgroup?
…m is correct

for its position in the molecule (i.e. is one higher than the AtomIdx of the last
atom in the residue)
…plus legacy.System.System).

Also added "origin" and "zero" as recognised options for constructing vectors, e.g.

```
c = mols.cursor()
c.make_whole(center="origin")
```

will work.
@chryswoods chryswoods added this to the 2024.2.0 milestone Jun 23, 2024
@chryswoods chryswoods linked an issue Jun 23, 2024 that may be closed by this pull request
@lohedges lohedges self-requested a review June 24, 2024 09:05
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Brilliant, many thanks for this. I've retested the example and the kwarg is now working at all levels.

@chryswoods chryswoods merged commit 5783c97 into devel Jun 24, 2024
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@chryswoods chryswoods deleted the fix_199 branch June 24, 2024 09:59
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[BUG] make_whole center kwarg not exposed
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