Topology Biopolymer Refactor Release

Owned by Jeffrey Wagner, created
Jan 05, 2022
1 min read

Driver

@Jeffrey Wagner

Approver

@Matt Thompson

Contributors

Informed

Objective

Bundle our API breaks and behavior changes into a major breaking release in 0.11.0.

Due date

Feb 2022

Key outcomes

  • Make to_interchange public

  • Biopolymers

    • can be loaded

    • have chemical information assigned

    • residue/chain hierarchies are maintained and traversable

  • Topologies no longer contain TopologyMolecules

  • OpenMM units are replaced with OpenFF units/Pint

Status

in progress

 

Problem Statement

Scope

Must have:

  •  

Must have:

  •  

Nice to have:

  •  

Not in scope:

  •  

 

Timeline

27-Dec202103-Jan202210-Jan17-Jan24-Jan31-Jan07-Feb14-Feb21-Feb28-Feb07-Mar14-Mar21-Mar28-Mar04-Apr11-AprTK 0.11.0 and Interchang…
OFFTK
Interchange
Essential to update
Update if possible
Communication

RC packages

Toolkit migration guide

RC packages

Unit migration guide

Evaluator RC

Recharge, QCSubmit, Bespokefit RCs

Evaluator unit update

Update Evaluator (MT)

Fragmenter RC

Update Fragmenter (JW)

Update ForceBalance (MT)

ForceBalance RC

Update Recharge, QCSubmit, BespokeFit (JW)

pAPRika update

OpenMMForceFields update

Amber FF porting update

Alert Perses devs about RC

Alert BioSimSpace about RC

Alert espaloma devs about RC