cmelab / polybinder

Initialization of thermoplastic polymer systems to simulate thermal welding
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Update Interface and Fused classes, renaname types in pps_opls FF #104

Closed chrisjonesBSU closed 1 year ago

chrisjonesBSU commented 1 year ago

This PR makes some needed changes for the Interface and Fused system classes that are required to work with other changes made recently (e.g. populating charges when creating an Interface system).

This also renames the atom types in the pps_opls.xml file. This change is required to use the no-SMARTS method of applying a foyer Forcefield, where the name and element must be the same as the particle name in the mBuild compound, but with a leading underscore. There were parsing issues with the opls style names that already have an underscore in the name.

codecov[bot] commented 1 year ago

Codecov Report

Merging #104 (2cfb807) into master (28ed7ef) will decrease coverage by 1.05%. The diff coverage is 77.04%.

:exclamation: Current head 2cfb807 differs from pull request most recent head 92bdd8a. Consider uploading reports for the commit 92bdd8a to get more accurate results

Additional details and impacted files [![Impacted file tree graph](https://codecov.io/gh/cmelab/polybinder/pull/104/graphs/tree.svg?width=650&height=150&src=pr&token=8Z9MBA7M16&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab)](https://codecov.io/gh/cmelab/polybinder/pull/104?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab) ```diff @@ Coverage Diff @@ ## master #104 +/- ## ========================================== - Coverage 91.80% 90.75% -1.06% ========================================== Files 7 7 Lines 781 822 +41 ========================================== + Hits 717 746 +29 - Misses 64 76 +12 ``` | [Impacted Files](https://codecov.io/gh/cmelab/polybinder/pull/104?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab) | Coverage Δ | | |---|---|---| | [polybinder/system.py](https://codecov.io/gh/cmelab/polybinder/pull/104?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmelab#diff-cG9seWJpbmRlci9zeXN0ZW0ucHk=) | `92.24% <77.04%> (-2.09%)` | :arrow_down: |