Improved performance of bond look up #1084
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…nting for flattened compounds
…into fastbonds
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| if self.root.bond_graph: | ||
| connected_subgraph = self.root.bond_graph.connected_components() | ||
| bonds = [] | ||
| molecule_tags = {} |
Check notice
Code scanning / CodeQL
Unused local variable
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…into fastbonds
Codecov ReportBase: 90.54% // Head: 90.58% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## main #1084 +/- ##
==========================================
+ Coverage 90.54% 90.58% +0.03%
==========================================
Files 61 61
Lines 6190 6216 +26
==========================================
+ Hits 5605 5631 +26
Misses 585 585
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…nting for flattened compounds
* Reorder bond, angle, and dihedral in write_lammpsdata * Update ordering charm angles/dihedrals * Bug fix tests * Update bond/angle/dihedral sorting algorithm --------- Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>
updates: - [github.com/pycqa/isort: 5.11.4 → 5.12.0](PyCQA/isort@5.11.4...5.12.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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|
While this works and provides a big improvement, it will be much more beneficial to simply swap out bond_graph for networkx, so I'm going to just remove this. |
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PR Summary:
Related to issue #1082
This code uses the connected_components information in the bond graph to substantially speed up to accessing information on the bonds in Compounds.
PR Checklist