Essential features

• Object model and all components can be serialized to (at minimum) dict and JSON

• Object model and all components can be hashed

• Atoms must

  • Have elements

  • Have masses (think “isotopes”)

  • Have a topology indices

  • Be able to store a 4-character atom type name → JW – Can provide a “standardize” method that will cut atom names/types down to 4 characters

• Molecule representations must not require that they can be represented SMILES

• Multi-residue structures can be treated as individual molecules

Essential behaviors

These can either be explicitly part of the API or enabled by downstream code

• Create iterators storing the indices of atoms of any valence term, indexed to the topology

  • i.e. a big list of tuples containing the indices of atoms in each bond - a little ugly at the moment since

• Look up the following based only on an atom’s index

  • What molecule it is a part of

  • What residue (if any) it is a part of

  • What chain (if any) it is a part of

  • What other atoms it is bonded to

Ambiguous behavior/open questions

• When molecules are converted to residues (i.e. in a conversion to Amber files), is that information (that this molecule is a molecule, not a residue) lost forever?

• What information will acceptably be lost in round-trips with

  • OpenMM

  • MDTraj

  • other objects?

  • PDB files

  • other files?

  • For all converters, JW and IP should make tables like those for the Molecule core properties, showing which data is preserved and how fields are converted.

• What assumptions are made about each components?

  • Connectivity within/between molecules and residues?

  • SMILES-ability of molecules (JW: NetworkX graph hash – We will provide at least an atom-order-dependent solution for this)

  • Non-element/isotope/bead “atoms”

Feature wishlist

• Type annotations → JW – Will the return values of atomtyped molecules' inherited methods correctly indicate that they’re atomtypedmolecules, or will their return signature just indicate the base class?

• Atoms can have masses not equal to their element’s mass

• Atoms can have non-physical elements

• Residues know if they include any other bonds to other residues

• Atom type names limited to 4 characters

• Fast generators and membership checks for atoms, bonds, angles, dihedrals, propers, impropers