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mirnylab / nglutils

Utility module for using nglview to visualize stuff
MIT License
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Additional bonds #1

Open SGrosse-Holz opened 5 years ago

SGrosse-Holz commented 5 years ago

When plotting data with bonds shorter than 1 (absolute units), additional bonds are added in. (reported by Johannes, reproduced by me)

SGrosse-Holz commented 5 years ago

This is nglview... probably makes sense when visualizing actual molecules. Managed to reduce the issue a little bit by changing elements to helium (inert, small) and assigning (more or less) unique residue names, but it still happens for monomers that come close.

Added a scale option to xyz2nglview. If there are unwanted bonds, scale up by an appropriate factor.