mosdef-hub / foyer

A package for atom-typing as well as applying and disseminating forcefields
https://foyer.mosdef.org
MIT License
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Include bond order in TopologyGraph #461

Open justinGilmer opened 2 years ago

justinGilmer commented 2 years ago

PR Summary:

Foyer currently does not understand bond order in its TopologyGraph representation and in its SMARTS grammar aside from number of connected neighbors [C;X4], for example.

This PR adds bond order as an attribute when adding bonds in the TopologyGraph, accepted options currently are:

"1" : single bonds "2" : double bonds "3" : triple bonds "ar" : aromatic bonds "am" : amide bonds "un": unknown, "du": dummy "nc": not connected

The last 3 bond types ("un", "du", and "nc") are subject to change and may not be here in the final iteration of this PR.

Support has been added when converting parmed structures, openff topologies, as well as GMSO topologies.

PR Checklist


codecov[bot] commented 2 years ago

Codecov Report

Merging #461 (e031e05) into main (882fd32) will decrease coverage by 21.09%. The diff coverage is 31.57%.

:exclamation: Current head e031e05 differs from pull request most recent head dfb9825. Consider uploading reports for the commit dfb9825 to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #461 +/- ## =========================================== - Coverage 69.55% 48.47% -21.09% =========================================== Files 16 17 +1 Lines 1662 1863 +201 =========================================== - Hits 1156 903 -253 - Misses 506 960 +454 ```