Christoph Klein

Hi @fmusiani, do you have a test case and script that you can share that reproduces this behavior?

> the first three distances in the first output element should be different What are you basing this on? Is it possible to share the trajectory and pdb? Without those...

AFAICT `pytest` adoption has outpaced `nose2` and it has a more active community. On the more anecdotal side, everyone I've bumped into over the last few years that researched this...

The Python standard: https://www.python.org/dev/peps/pep-0440/

Finding molecules based on the bond graph is pretty straightforward so we can definitely do that. The main limitation here comes from which metadata is and is not included in...

Could you give a specific piece of code that reproduces this and what specifically the other option would produce?

Libraries are sort of there. Things to think about: - "import all" structure to easily get access to everything without typing out the full import - Functionality to search and...

Hook up with pubchem: https://github.com/mcs07/PubChemPy and CIR https://github.com/mcs07/CIRpy

Trevor had worked on a "visualize the compound hierarchy" feature a while back but I can't find it on his fork: https://github.com/Jonestj1/mbuild In general, it should be very possible to...

Look into adding a tree view to https://github.com/patrickfuller/igraph