improve performance of is_independent #1037
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daico007
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1037 +/- ##
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Coverage 90.37% 90.37%
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Files 64 64
Lines 9014 9014
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Hits 8146 8146
Misses 868 868 ☔ View full report in Codecov by Sentry. |
CalCraven
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Jun 6, 2022
CalCraven
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This PR adds two methods to a compound, `_recursive_id_molecules` and `group_by_molecules`. These functions let a user reconfigure an mBuild compound using the top down approach of iterating through children. The is_independent() method is checked on each children until False is returned, which identifies when the hierarchy is made of a bonded together "molecule". This will be of use when converting to GMSO `Topology`, the subtop information can be parsed from this reconfigured mBuild compound in order to speed up atomtyping. These methods use the compound.name attribute to group molecules together. With a generic name like "Compound", the top level child will be a single compound. **Note that these tests won't pass until PR mosdef-hub#1037 is merged * Add mbuild.compound.Compound._recursive_id_molecules method * Add mbuild.compound.Compound.group_by_molecules method
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CalCraven
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Jun 6, 2022
This PR adds two methods to a compound, `_recursive_id_molecules` and `group_by_molecules`. These functions let a user reconfigure an mBuild compound using the top down approach of iterating through children. The is_independent() method is checked on each children until False is returned, which identifies when the hierarchy is made of a bonded together "molecule". This will be of use when converting to GMSO `Topology`, the subtop information can be parsed from this reconfigured mBuild compound in order to speed up atomtyping. These methods use the compound.name attribute to group molecules together. With a generic name like "Compound", the top level child will be a single compound. **Note that these tests won't pass until PR mosdef-hub#1037 is merged * Add mbuild.compound.Compound._recursive_id_molecules method * Add mbuild.compound.Compound.group_by_molecules method
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PR Summary:
The current
Compound.is_independent()is not very performant and @CalCraven found out that changing the check fromif neigh not in selfto ifneigh not in self.particles()will significantly speed thing up.PR Checklist