Versions Compared

Old Version 35

changes.mady.by.user Karmen Condic-Jurkic

Saved on

compared with

New Version Current

changes.mady.by.user Jeffrey Wagner

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

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

  •  
  •  
  •  
  •