tag:blogger.com,1999:blog-9015174234871442237.post4208125804154108797..comments2024-03-17T00:33:08.666-07:00Comments on The art of blowing up protein: Guess bond order in Rdkit by number of bound atomsMatteo Ferlahttp://www.blogger.com/profile/04090452288769979595noreply@blogger.comBlogger1125tag:blogger.com,1999:blog-9015174234871442237.post-37295402579477780202021-06-25T16:57:24.853-07:002021-06-25T16:57:24.853-07:00Great blog post. I've been looking at ways to ...Great blog post. I've been looking at ways to determine bond orders+formal charges from coordinates+elements, and how reliable the guesses are. I haven't benchmarked them, but some other implementations I've found are:<br /><br />xyz2mol: https://github.com/jensengroup/xyz2mol/<br />A recent MDAnalysis addition: https://cedric.bouysset.net/blog/2020/07/22/rdkit-converter-part2<br />AmberTools' bondtype program: https://github.com/choderalab/openmoltools/blob/96292f7b603f9f0fcb8ccae06a0adf5a8d7483fd/openmoltools/forcefield_generators.py#L84-L146<br />OpenEye's OEPercieveBondOrders (requires a license): https://docs.eyesopen.com/toolkits/python/oechemtk/OEChemFunctions/OEPerceiveBondOrders.htmlJeff Wagnerhttp://openforcefield.orgnoreply@blogger.com