Adding Single Chain system class #192
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Contributor
StephMcCallum
commented
Feb 28, 2025
•
StephMcCallum
commented
- doc strings
- add to library/systems.py
- make it work for AA atom models and atom indices (different ways to get length of polymer or mbuild compound, spicy.pdist)
- unit tests
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chrisjonesBSU
requested changes
Feb 28, 2025
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #192 +/- ##
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+ Coverage 94.77% 94.90% +0.13%
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Files 26 26
Lines 1970 2023 +53
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+ Hits 1867 1920 +53
Misses 103 103 |
flowermd/library/systems.py
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| class SingleChainSystem(System): | ||
| """Builds a box around a single chain. | ||
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| Calculates the maximum distance of the chain using scipy.spatial.distance.pdist(). |
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We can expand here a little. We should say that the box lengths are chosen so that they are at least as long as the largest particle part distance. We could say that the chain is centered in the volume.
flowermd/library/systems.py
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| Parameters | ||
| ---------- | ||
| See System class. |
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Add a doc string for the buffer parameter.
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