2021 Topology Refactor

Owned by Jeffrey Wagner
Last updated: Feb 23, 2022
1 min read

Requirements resources:

Meeting notes:

API proposal resources:

  • Draft API and tests notebooks:

  • Scratch space for considering data structures that could support needed API https://docs.google.com/presentation/d/1sV4CQ5bORuAKy2q8TUJvaSVf2SI5Dy8HS8b-S7TsVis/edit#slide=id.gd4a1e76e85_2_65

 

Implementations:

 

API specced

Design + corner case tests

Prototyped

Finalized

 

API specced

Design + corner case tests

Prototyped

Finalized

Refactor Topology to have entire molecules

Let a Topology have a single set of coordinates Just treat each molecule’s first conformer as its coords in the Topology

Make substructure dictionary from CCD

Residue perception from SDF

Loading from PDB

Bond order+formal charge perception from PDB

Atom metadata implementation

HierarchyElements and Schemes

TypedAtom + TypedMolecule

merge_molecules

Extract residue as mol

SMARTS matching performance improvements for biopolymers