Parameterized Parmed Conversions #721
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…nique potential types
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Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## main #721 +/- ##
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+ Coverage 92.05% 92.09% +0.03%
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Files 66 66
Lines 6370 6350 -20
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- Hits 5864 5848 -16
+ Misses 506 502 -4
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I tested this with two different numbers of atoms: So I think we're looking pretty much good to merge this. |
Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>
Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>
Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>
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The latest commit has addressed the changes to parmed conversion. Required changes due to sorting of GMSO object from ParmEd by topology index:
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… appearance in the topology. Copies of connection types are made, which must be filtered using potential filters to get whatever subset is considered unique.
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| return potential.member_types or potential.member_classes | |||
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| def get_sorted_names(potential): | |||
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Explicit returns mixed with implicit (fall through) returns
gmso/core/views.py
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| """Get identifier for a topology potential based on name or membertype/class.""" | ||
| if isinstance(potential, AtomType): | ||
| return potential.name | ||
| if isinstance(potential, BondType): |
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| if isinstance(potential, BondType): | |
| elif isinstance(potential, BondType): |
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very minor change for consistency
This PR should fix minor issues #716 which didn't account for symmetries in conversions from parmed structures. This checks that the expected number of potentials are found, which were only being checked over simple molecules such as ethane, and as such missing that some connection types were repeated.
Additional tests were done to check for urey bradleys, harmonic and periodic impropers, and periodic propers.