Update connection members during parameterization #808
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…connection_members from types
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| # for connection in getattr(top2, connection_type): | ||
| # connection_types_mirror[ | ||
| # tuple( | ||
| # top2.get_index(member) | ||
| # for member in sort_connection_members(connection, "atom_type") |
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Do we want to remove these commented out block?
| # for connection in getattr(top1, connection_type): | ||
| # connection_types_original[ | ||
| # tuple( | ||
| # top1.get_index(member) | ||
| # for member in sort_connection_members(connection, "atom_type") |
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #808 +/- ##
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+ Coverage 92.44% 92.45% +0.01%
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Files 66 66
Lines 7024 7036 +12
==========================================
+ Hits 6493 6505 +12
Misses 531 531 ☔ View full report in Codecov by Sentry. |
| # for connection in getattr(top2, connection_type): | ||
| # connection_types_mirror[ | ||
| # tuple( | ||
| # top2.get_index(member) | ||
| # for member in sort_connection_members(connection, "atom_type") |
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Do we want to remove these commented out block?
| The attribute of the site to sort by. Can take "name", "atom_type", | ||
| and "atom_class" as the sorting attribute. |
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Need to add "index" here (with contignent of top is not None)
Add tests and change behavior when applying types, update connection connection_members from types.
This addressed a bug found by @bc118 using NAMD, which write the indices of impropers which must match with the types of the improper types listed.
This is a potentially impactful issue if using improper in GMSO. Anyone doing so should check that the improper atoms in their output files are ordered as expected, with the central atom first, and the last atom last.