Irfan Alibay

Type guessing should attempt to go via elements first

3

## Current behaviour The current behaviour, and something we reinforce in #3753 is that type works by attempting to guess elements from atom names. ## Proposed behaviour The proposal here...

Warn about and deprecate element guessing in ITP parser

1

## Behaviour post #3753 In #3753 element guessing is added to the ITP parser in order to partially guess masses. ## Intended behaviour Ideally we want: 1. To make sure...

TOPParser doesn't parse chamber-style parm7 files

7

**Introduction** So this is something that has been brought up in the past in the discussion group (see [this post](https://groups.google.com/forum/#!searchin/mdnalysis-discussion/CTITLE%7Csort:date/mdnalysis-discussion/nJG_ex2e6ZY/AupS3RXZAgAJ) as an example). Some time back, chamber style parm7 got...

Adding support for future OpenFF virtual site releases in AbsoluteAlchemicalFactory

1

Follow-up from #509 and #508 We would like to add support for doing AFE calculations using future releases of OpenFF force fields that will contain virtual sites. This is a...

Very minor thing. The phosaa14SB paper has now been released: https://pubs.acs.org/doi/full/10.1021/acs.jctc.4c00732 It might be good to update the reference accordingly (probably in ~ a month when the volume number etc.....

Add box vector fix to AFE base

2

Checklist * [ ] Added a ``news`` entry ## Developers certificate of origin - [ ] I certify that this contribution is covered by the MIT License [here](https://github.com/OpenFreeEnergy/openfe/blob/main/LICENSE) and the...

[WIP] ABFE protocol

5

Checklist * [ ] Added a ``news`` entry ## Developers certificate of origin - [x] I certify that this contribution is covered by the MIT License [here](https://github.com/OpenFreeEnergy/openfe/blob/main/LICENSE) and the **Developer...

[WIP] Restraints API

22

Checklist * [ ] Added a ``news`` entry ## Developers certificate of origin - [x] I certify that this contribution is covered by the MIT License [here](https://github.com/OpenFreeEnergy/openfe/blob/main/LICENSE) and the **Developer...

Unpin pint / openff-units

2

TODO: - [ ] Update all type hints to use pint.Quantity instead of unit.Quantity ## Developers certificate of origin - [x] I certify that this contribution is covered by the...

NumPy 2.0 support

6

This is the meta issue for OpenFE supporting NumPy 2.0 across its stack. Things which are blocking this: - [ ] OpenMMTools (@mikemhenry ) - [ ] Support for OpenMM...