Log charge assignment

[mattwthompson]

Description

Resolves #1048

Checklist

• [x] Log, for most cases, which atom (with some topology index) got what charge assigned by which method
  • [x] Library charges
  • [x] Preset charges
  • [x] ChargeIncrementHandler
  • [x] AM1-BCC
  • [x] Virtual sites
• [x] Add tests
  • [x] Sage with a ligand in vacuum
  • [x] Sage with a ligand in water/ions
  • Water gets library charges
  • Ions get library charges
  • Non-water solvent gets AM1-BCC
  • Ligands get AM1-BCC
  • [x] Sage with a ligand in non-water solvent
  • Non-water solvent gets AM1-BCC
  • Ligands get AM1-BCC
  • [x] Sage with a ligand in mixed solvent
  • Water gets library charges
  • Ions get library charges
  • Non-water solvent gets AM1-BCC
  • Ligands get AM1-BCC
  • [x] ff14SB with Sage
  • Protein gets library charges
  • Water gets library charges
  • Ions get library charges
  • Non-water solvent gets AM1-BCC
  • Ligands get AM1-BCC
  • [x] ff14SB with Sage and preset charges on Protein A
  • Protein A gets preset charges
  • Other proteins get library charges
  • Water gets library charges
  • Ions get library charges
  • Non-water solvent gets AM1-BCC
  • Ligands get AM1-BCC
  • [x] Sage with ligand and OPC water
  • Water gets library charges
  • Water virtual sites get ??
  • Ions get library charges
  • Non-water solvent gets AM1-BCC
  • Ligands get AM1-BCC
  • [x] Sage with preset charges on ligand A
  • Water gets library charges
  • Ions get library charges
  • Non-water solvent gets AM1-BCC
  • Ligand A gets preset charges
  • Other ligands get AM1-BCC
  • [x] Sage with preset charges on water
  • Water gets preset charges
  • Ions get library charges
  • Non-water solvent gets AM1-BCC
  • Ligands get AM1-BCC
  • [x] Sage with (ligand) virtual site parameters
  • Water gets preset charges
  • Ions get library charges
  • Non-water solvent gets AM1-BCC
  • Ligand heavy atoms get AM1-BCC and charge increments
  • Virtual sites get charge increments
  • [x] AM1-with-custom-BCCs Sage with ligand and ions water
  • Water gets library charges
  • Ions get library charges
  • Ligand gets charge increments
  • [x] Capture specifics of charge method (AM1-BCC, AM1-BCC-ELF10, AM1-BCC via NAGL)
  • [ ] Slightly non-isomorphic molecules with one having preset charges
  • [ ] Preset charges and virtual sites is underspecified and cannot be tested (yet)
  • [ ] Run some test cases with shuffled topologies
  • [x] Report all atom indices, not just unique molecules
• [x] Lint
• [ ] Update docstrings No particular docstring to update, I don't think?
• [x] Add section in user guide
• [x] Update release history

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 90.47619% with 2 lines in your changes missing coverage. Please review.

Project coverage is 93.51%. Comparing base (292faec) to head (a3679db).

Additional details and impacted files

[mattwthompson]

Here's what this looks like for a set of fairly simple cases:

import logging

from openff.toolkit import ForceField, Molecule, Topology

logging.basicConfig(level=logging.INFO)

ff = ForceField("openff-2.0.0.offxml")

water = Molecule.from_smiles("O")
ligand = Molecule.from_smiles("CC")
ligand.assign_partial_charges("am1bcc")

ff.create_interchange(Topology.from_molecules([water, water]))
ff.create_interchange(ligand.to_topology())
ff.create_interchange(ligand.to_topology(), charge_from_molecules=[ligand])

ForceField("opc.offxml").create_openmm_system(Molecule.from_smiles("O").to_topology())

$ python run.py
INFO:openff.toolkit.typing.engines.smirnoff.parameters:Attempting to up-convert vdW section from 0.3 to 0.4
INFO:openff.toolkit.typing.engines.smirnoff.parameters:Successfully up-converted vdW section from 0.3 to 0.4. `method="cutoff"` is now split into `periodic_method="cutoff"` and `nonperiodic_method="no-cutoff"`.
INFO:openff.toolkit.typing.engines.smirnoff.parameters:Attempting to up-convert Electrostatics section from 0.3 to 0.4
INFO:openff.toolkit.typing.engines.smirnoff.parameters:Successfully up-converted Electrostatics section from 0.3 to 0.4. `method="PME"` is now split into `periodic_potential="Ewald3D-ConductingBoundary"`, `nonperiodic_potential="Coulomb"`, and `exception_potential="Coulomb"`.
/Users/mattthompson/micromamba/envs/new-models/lib/python3.11/site-packages/mdtraj/formats/__init__.py:13: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13
  from mdtraj.formats.trr import TRRTrajectoryFile
INFO:openff.interchange.smirnoff._nonbonded:Charge section LibraryCharges applied to (topology) atom index 0
INFO:openff.interchange.smirnoff._nonbonded:Charge section LibraryCharges applied to (topology) atom index 3
INFO:openff.interchange.smirnoff._nonbonded:Charge section LibraryCharges applied to (topology) atom index 1
INFO:openff.interchange.smirnoff._nonbonded:Charge section LibraryCharges applied to (topology) atom index 4
INFO:openff.interchange.smirnoff._nonbonded:Charge section LibraryCharges applied to (topology) atom index 2
INFO:openff.interchange.smirnoff._nonbonded:Charge section LibraryCharges applied to (topology) atom index 5
INFO:openff.interchange.smirnoff._nonbonded:Charge section ToolkitAM1BCC, using charge method am1bccelf10, applied to (topology) atom index 0
INFO:openff.interchange.smirnoff._nonbonded:Charge section ToolkitAM1BCC, using charge method am1bccelf10, applied to (topology) atom index 1
INFO:openff.interchange.smirnoff._nonbonded:Charge section ToolkitAM1BCC, using charge method am1bccelf10, applied to (topology) atom index 2
INFO:openff.interchange.smirnoff._nonbonded:Charge section ToolkitAM1BCC, using charge method am1bccelf10, applied to (topology) atom index 3
INFO:openff.interchange.smirnoff._nonbonded:Charge section ToolkitAM1BCC, using charge method am1bccelf10, applied to (topology) atom index 4
INFO:openff.interchange.smirnoff._nonbonded:Charge section ToolkitAM1BCC, using charge method am1bccelf10, applied to (topology) atom index 5
INFO:openff.interchange.smirnoff._nonbonded:Charge section ToolkitAM1BCC, using charge method am1bccelf10, applied to (topology) atom index 6
INFO:openff.interchange.smirnoff._nonbonded:Charge section ToolkitAM1BCC, using charge method am1bccelf10, applied to (topology) atom index 7
INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 0
INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 1
INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 2
INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 3
INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 4
INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 5
INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 6
INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 7
INFO:openff.interchange.smirnoff._nonbonded:Charge section LibraryCharges applied to (topology) atom index 0
INFO:openff.interchange.smirnoff._nonbonded:Charge section LibraryCharges applied to (topology) atom index 1
INFO:openff.interchange.smirnoff._nonbonded:Charge section LibraryCharges applied to (topology) atom index 2
INFO:openff.interchange.smirnoff._virtual_sites:Charge section VirtualSites applied to virtual site with orientation atoms (0, 1, 2)

[IAlibay]

Sorry only very briefly looking at this, so please ignore me if I'm missing something important.

Report all atom indices, not just unique molecules

This seems like it would be incredibly overwhelming to users, indeed a solvated protein-ligand complex could easily be incomprehensible.

Is there no way to:

1. Condense this to each unique molecule
2. Condense the per atom report of each molecule to just a summary (N atoms got this, N atoms got this, etc...)
3. If necessary, offer a flag for folks to turn on to get a per-atom breakdown?