Christoph Klein

__eq__ function for compound

1

Would be useful for testing

Library ideas

3

- [x] A library of elements with ports attached to them. The default would be to have a ports oriented in the most common orientations. E.g. hydrogen with one port,...

Render hierarchy viewer as IPython widget

2

Just jotting this down but it would be really neat to be able to pull up the interactive hierarchy view within an ipynb

Current and unimplemented SMARTS functionality

1

We currently do not support all of [SMARTS' features](http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html). Here we're keeping track of which portions are supported. Left column denotes current foyer support. See [here](https://github.com/mosdef-hub/foyer/blob/master/foyer/smarts.py#L3) for implemented SMARTS grammar....

Documentation regarding input/output options

1

Current inputs can come from mbuild, parmed or openmm topologies + an xml file. By default `Forcefield.apply()` yields a parmed structure but for users interested in running in OpenMM we...

Re-implement sanity checking on blacklist

1

* generate blacklist graph * check for unconnected graphs * check for graphs without any non-recursive defs

E.g. I have a working gromacs system, how do I get into using this

Basically take this from the docs and turn it into something interactive: https://github.com/mosdef-hub/foyer/blob/master/docs/smarts.md#overriding-atomtypes