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MobleyLab / chemper

Repository for Chemical Perception Sampling Tools
MIT License
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Update the way layers are added per issue #56 #58

Closed bannanc closed 5 years ago

bannanc commented 5 years ago

This pull request updates the _add_layers function in cluster_graph and remove_atom in fragment_graph per issue #56.

This also includes support for MDL aromaticity which is required to test chemper with smirnoff99Frosst. (Note the aromaticity model was technically always supported since the user could have externally specified the aromaticity model in their OE or RDK molecule and then made a chemper Mol out of it). However, making an internal method for changing the aromaticity model might make it easier to test chemper with travis down the line.

bannanc commented 5 years ago

Note, the main test/test_ files pass locally, but I haven't tried all the notebooks yet. I am working on checking if this solves all of the can't type molecules like smirnoff99Frosst now.

codecov[bot] commented 5 years ago

Codecov Report

Merging #58 into master will decrease coverage by 3.06%. The diff coverage is 49.61%.

bannanc commented 5 years ago

Per a discussion with @jmaat on Slack, I will merge this. Then I'll add suggestions to issue #55
Specifically, next I'll focus on issue #59 to finish addressing bugs that make it impossible to match smirnoff99Frosst.