diff --git a/.github/workflows/beta.yaml b/.github/workflows/beta.yaml index 3d09f7e8a..ec142cd3f 100644 --- a/.github/workflows/beta.yaml +++ b/.github/workflows/beta.yaml @@ -64,7 +64,7 @@ jobs: - name: Run all tests if: always() - run: python -m pytest -v $COV openff/interchange/ -m "slow or not slow" + run: python -m pytest -v $COV openff/interchange/ - name: Codecov uses: codecov/codecov-action@v4 diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index f67bb7df3..d63a6f80b 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -94,10 +94,7 @@ jobs: - name: Run tests if: always() run: | - python -m pytest $COV openff/interchange/ \ - -r fExs -n logical --durations=10 \ - -m "slow or not slow" \ - --ignore=openff/interchange/_tests/energy_tests/test_energies.py + python -m pytest $COV openff/interchange/ -r fExs -n logical --durations=10 - name: Run small molecule regression tests if: ${{ matrix.python-version == '3.10' && matrix.openeye == true && matrix.openmm == true }} @@ -127,14 +124,13 @@ jobs: python devtools/scripts/molecule-regressions.py - name: Run mypy - continue-on-error: true - if: ${{ matrix.python-version == '3.11' }} + if: ${{ matrix.python-version == '3.10' }} run: | # As of 01/23, JAX with mypy is too slow to use without a pre-built cache # https://github.com/openforcefield/openff-interchange/pull/578#issuecomment-1369979875 micromamba remove jax - mypy -p "openff.interchange" --exclude "openff/interchange/_tests/" - mypy --show-error-codes plugins/nonbonded_plugins/ + python -m mypy -p "openff.interchange" --exclude "openff/interchange/_tests/" + python -m mypy plugins/nonbonded_plugins/ - name: Codecov uses: codecov/codecov-action@v4 diff --git a/.github/workflows/examples.yaml b/.github/workflows/examples.yaml index 484ab4896..d6094f75a 100644 --- a/.github/workflows/examples.yaml +++ b/.github/workflows/examples.yaml @@ -64,16 +64,11 @@ jobs: - name: Run docexamples run: | - # TODO: Add back /interchange.py when `TypedMolecule` is implemented - pytest --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests --ignore=openff/interchange/components/interchange.py + pytest --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests - name: Run example notebooks if: always() run: | - python -m pytest --nbval-lax --dist loadscope -n logical --durations=20 \ - examples/ \ + python -m pytest --nbval-lax --dist loadscope -n logical --durations=20 examples/ \ --ignore=examples/deprecated/ \ - --ignore=examples/experimental/openmmforcefields/ \ - --ignore=examples/lammps/ \ - --ignore=examples/protein_ligand/ \ - --ignore=examples/conformer_energies/conformer_energies.ipynb + --ignore=examples/experimental diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 11008845b..5456e8704 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,9 +12,10 @@ repos: hooks: - id: add-trailing-comma - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.7 + rev: v0.6.2 hooks: - id: ruff + - id: ruff-format - repo: https://github.com/econchick/interrogate rev: 1.7.0 hooks: @@ -46,3 +47,9 @@ repos: hooks: - id: nbstripout files: ^examples +- repo: https://github.com/asottile/pyupgrade + rev: v3.17.0 + hooks: + - id: pyupgrade + args: + - --py310-plus diff --git a/devtools/conda-envs/beta_env.yaml b/devtools/conda-envs/beta_env.yaml index 118b79cf4..f6c952343 100644 --- a/devtools/conda-envs/beta_env.yaml +++ b/devtools/conda-envs/beta_env.yaml @@ -10,7 +10,7 @@ dependencies: - pydantic >=1.10.17,<3 - openmm >=7.6 # OpenFF stack - - openff-toolkit >=0.15.2 + - openff-toolkit ~=0.16.4 - openff-nagl ~=0.3.7 - openff-nagl-models =0.1 # Optional features diff --git a/devtools/conda-envs/dev_env.yaml b/devtools/conda-envs/dev_env.yaml index 5d3b85cd3..33d3a2a31 100644 --- a/devtools/conda-envs/dev_env.yaml +++ b/devtools/conda-envs/dev_env.yaml @@ -4,22 +4,31 @@ channels: - openeye dependencies: # Core - - python =3.11 - - pip + - python =3.10 + - versioneer-518 - numpy - pydantic =2 - - openmm # OpenFF stack - - openff-toolkit ~=0.16 - - openff-interchange-base + - openff-toolkit-base ~=0.16.4 + - openff-units + - ambertools =23 + # Optional features + - openmm # smirnoff-plugins =2024 + # de-forcefields # add back after smirnoff-plugins update - openff-nagl - openff-nagl-models - - ambertools =23 - # Optional features - - mbuild ~=0.17 - - foyer ~=0.12 + - mbuild ~=0.18 + - foyer =1 - gmso ~=0.12 + - nglview + # Drivers + - gromacs =2024 + - lammps >=2023.08.02 + - panedr + # shim for a build issue that's probably localized to conda-forge + # https://github.com/conda-forge/lammps-feedstock/issues/207 + - openmpi =4 # Testing - mdtraj - intermol @@ -29,21 +38,13 @@ dependencies: - pytest-xdist - pytest-randomly - nbval - # de-forcefields # add back after smirnoff-plugins update - # Drivers - - gromacs =2024 - - lammps >=2023.08.02 - - panedr # Typing - mypy - typing-extensions - types-setuptools - pandas-stubs # Development tools - # https://github.com/mamba-org/mamba/issues/1523#issuecomment-1246591319 - - micromamba - jupyterlab - - nglview - pdbfixer - ipdb - pre-commit diff --git a/devtools/conda-envs/docs_env.yaml b/devtools/conda-envs/docs_env.yaml index 0c8d7c171..260cfc5c3 100644 --- a/devtools/conda-envs/docs_env.yaml +++ b/devtools/conda-envs/docs_env.yaml @@ -8,10 +8,10 @@ dependencies: - pip - numpy =1 - pydantic =2 - - openff-toolkit-base - - openmm >=7.6 + - openff-toolkit-base ~=0.16.4 + - openmm =8 - mbuild - - foyer >=0.12.1 + - foyer =1 - nglview - panedr - typing-extensions diff --git a/devtools/conda-envs/examples_env.yaml b/devtools/conda-envs/examples_env.yaml index 403e4fd17..482e52c34 100644 --- a/devtools/conda-envs/examples_env.yaml +++ b/devtools/conda-envs/examples_env.yaml @@ -5,29 +5,35 @@ channels: dependencies: # Core - python + - versioneer-518 - numpy - pydantic =2 - - openmm # OpenFF stack - - openff-toolkit - - openff-nagl - - openff-nagl-models + - openff-toolkit-base ~=0.16.4 + - openff-units - ambertools =23 # Optional features - - unyt - - mbuild =0.17 - - foyer >=0.12.1 - - gmso =0.12 + - openff-nagl + - openff-nagl-models + - mbuild ~=0.18 + - foyer =1 + - gmso ~=0.12 + - nglview + # Drivers + - gromacs + - lammps >=2023.08.02 + # shim for a build issue that's probably localized to conda-forge + # https://github.com/conda-forge/lammps-feedstock/issues/207 + - openmpi =4 + - panedr + # Testing + - mdtraj + - pytest + - pytest-xdist + - nbval # Examples + - openmmforcefields - jax - - mdtraj - pdbfixer - - nglview - openeye-toolkits =2024.1.0 - - pytest =8.0 - - pytest-xdist - - nbval - rich - # Drivers - - gromacs - - lammps >=2023.08.02 diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index fea5f4367..a62789c9d 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -6,17 +6,30 @@ dependencies: - python - versioneer-518 - numpy - - pydantic >=1.10.17,<3 + - pydantic =2 # OpenFF stack - - openff-toolkit-base >=0.16 + - openff-toolkit-base ~=0.16.4 - openff-units - ambertools =23 # Needs to be explicitly listed to not be dropped when AmberTools is removed - rdkit # Optional features - - foyer >=0.12.1 - - mbuild - - gmso =0.12 + - openmm + # smirnoff-plugins =2024 + # de-forcefields # add back after smirnoff-plugins update + - openff-nagl + - openff-nagl-models + - mbuild ~=0.18 + - foyer =1 + - gmso ~=0.12 + - nglview + # Drivers + - gromacs + - lammps >=2023.08.02 + # shim for a build issue that's probably localized to conda-forge + # https://github.com/conda-forge/lammps-feedstock/issues/207 + - openmpi =4 + - panedr # Testing - mdtraj - intermol @@ -26,11 +39,6 @@ dependencies: - pytest-xdist - pytest-randomly - nbval - - nglview - # Drivers - - gromacs - - lammps >=2023.08.02 - - panedr # Typing - mypy - typing-extensions diff --git a/docs/releasehistory.md b/docs/releasehistory.md index aa2137d20..3a73dfccf 100644 --- a/docs/releasehistory.md +++ b/docs/releasehistory.md @@ -11,6 +11,22 @@ Dates are given in YYYY-MM-DD format. Please note that all releases prior to a version 1.0.0 are considered pre-releases and many API changes will come before a stable release. +## 0.4.0 - 2024 + +* Pydantic v2 is now used at runtime. As a consequence, models containing `Interchange`s cannot also use models from the v1 API. +* `Interchange.to_gromacs` and similar methods now raise an error if no box is defined. + * Previously, this was a warning. + * GROMACS dropped support for (proper) vacuum simulations in version 2020 and there are no immediate plans to re-introduce it. + * Users freqently approximate vacuum simulation with periodic boundary conditions by applying a large box. This has some performance issues and some non-bonded terms likely differ numerically compared to similar implementations in other engines. +* The wrapped use of external readers and writers is removed, and with it arguments like `writer` in many `Interchange.to_x` calls. +* Several classes and methods which were deprecated in the 0.3 line of releases are now removed. +* Previously-deprecated examples are removed. +* `ProperTorsionKey` no longer accepts an empty tuple as atom indices. + +## 0.3.30 - 2024-08 + +* #1039 Updates support of "cutoff" electrostatics in `.to_openmm` to better reflect what OpenMM supports. Set `"reaction-field"` to force the use of `CutoffPeriodic`, provided the vdW and electrostatic cutoff distances match. The potential/method `"cutoff"` is no longer supported but may be re-added in the future. + ## 0.3.29 - 2024-08-01 * #1023 Fixes a bug in which non-bonded parameter lookup sometimes crashed when virtual sites were present. diff --git a/docs/using/plugins.md b/docs/using/plugins.md index b302e684f..2ace5953d 100644 --- a/docs/using/plugins.md +++ b/docs/using/plugins.md @@ -217,7 +217,7 @@ At this point, we have created a class that can parse sections of a custom OFFXM from openff.toolkit import Topology from typing import Literal, Type -from openff.models.types import FloatQuantity +from openff.interchange._annotations import DistanceQuantity from openff.interchange.smirnoff._nonbonded import _SMIRNOFFNonbondedCollection from openff.interchange.components.potentials import Potential @@ -231,7 +231,7 @@ class SMIRNOFFBuckinghamCollection(_SMIRNOFFNonbondedCollection): mixing_rule: str = "Buckingham" - switch_width: FloatQuantity["angstrom"] = unit.Quantity(1.0, unit.angstrom) + switch_width: DistanceQuantity = unit.Quantity(1.0, unit.angstrom) @classmethod def allowed_parameter_handlers(cls): diff --git a/examples/README.md b/examples/README.md index bad92a126..531a0217a 100644 --- a/examples/README.md +++ b/examples/README.md @@ -5,7 +5,7 @@ Jupyter notebooks demonstrating use cases. -* `conformer_energies.ipynb`: Given a SMILES string, generate conformers and compute the single-point energy via GROMACS and OpenMM and compare to a result generated by the OpenFF toolkit. +* `conformer_energies/conformer_energies.ipynb`: Given a SMILES string, generate conformers and compute the single-point energy via GROMACS and OpenMM and compare to a result generated by the OpenFF toolkit. * `ligand_in_water/ligand_in_water.ipynb`: Solvate a ligand in water and prepare a simulation. * `packed_box/packed_box.ipynb`: Prepare a box of organic species for a simulation and compare the results of OpenMM, GROMACS, Amber, and LAMMPS. @@ -13,10 +13,6 @@ Jupyter notebooks demonstrating use cases. OpenFF tools and compare the results of OpenMM, GROMACS, Amber, and LAMMPS. * `openmm/openmm.ipynb`: Prepare a box of organic species for a simulation with OpenMM. * `lammps/lammps.ipynb`: Prepare a box of organic species for a simulation with LAMMPS. -* `foyer-showcase/solvated-nanoparticle.ipynb`: Use [`mBuild`](https://mbuild.mosdef.org/) to construct a silica nanoparticle solvated in tetrahydrofuran and then parametrize the nanoparticle with OPLS-AA via [`Foyer`](https://foyer.mosdef.org/) and Sage. - -## Deprecated examples - -* `optimize-with-jax.ipynb`: Run a minimal parameter optimization using JAX. -* `parameter_replacement.ipynb`: Partially replace parameters in a parametrized system with values from a second force field. -* `parameter_splitting.ipynb`: Split one SMIRKS pattern into two after parametrization. +* `vectorized_representations/vectorized_representations.ipynb`: Export systems to vectorized representations. +* `host_guest/host_guest.ipynb`: Prepare a host-guest system. +* `virtual_sites/virtual_sites.ipynb`: Apply several types of SMIRNOFF virtual sites to ligands. diff --git a/examples/conformer_energies/conformer_energies.ipynb b/examples/conformer_energies/conformer_energies.ipynb index 05d54e3ce..16d64a614 100644 --- a/examples/conformer_energies/conformer_energies.ipynb +++ b/examples/conformer_energies/conformer_energies.ipynb @@ -65,7 +65,7 @@ "outputs": [], "source": [ "molecule = Molecule.from_smiles(SMILES)\n", - "molecule.generate_conformers(n_conformers=20, rms_cutoff=0.1 * unit.angstrom),\n", + "(molecule.generate_conformers(n_conformers=20, rms_cutoff=0.1 * unit.angstrom),)\n", "topology = molecule.to_topology()" ] }, diff --git a/examples/deprecated/foyer-showcase/oplsaa_switchable.xml b/examples/deprecated/foyer-showcase/oplsaa_switchable.xml deleted file mode 100644 index 222266df7..000000000 --- a/examples/deprecated/foyer-showcase/oplsaa_switchable.xml +++ /dev/null @@ -1,3987 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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"cells": [ - { - "cell_type": "code", - "execution_count": null, - "id": "0", - "metadata": {}, - "outputs": [], - "source": [ - "import mbuild as mb\n", - "import mdtraj as md\n", - "import nglview\n", - "from foyer.forcefield import Forcefield as FoyerForcefield\n", - "from openff.toolkit.topology import Molecule, Topology\n", - "from openff.toolkit.typing.engines.smirnoff.forcefield import ForceField\n", - "from openff.units import unit\n", - "\n", - "from openff.interchange.components.interchange import Interchange\n", - "from openff.interchange.components.mbuild import offmol_to_compound\n", - "from openff.interchange.components.mdtraj import _combine_topologies, _OFFBioTop\n", - "from openff.interchange.drivers import get_openmm_energies" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "1", - "metadata": {}, - "outputs": [], - "source": [ - "nanoparticle = mb.load(\"silica_nanoparticle.json\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "2", - "metadata": {}, - "outputs": [], - "source": [ - "oplsaa_silica = FoyerForcefield(\"oplsaa_switchable.xml\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "3", - "metadata": {}, - "outputs": [], - "source": [ - "topology = _OFFBioTop(mdtop=md.Topology.from_openmm(nanoparticle.to_parmed().topology))" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "4", - "metadata": {}, - "outputs": [], - "source": [ - "nanoparticle_interchange = Interchange.from_foyer(\n", - " topology=topology,\n", - " force_field=oplsaa_silica,\n", - ")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "5", - "metadata": {}, - "outputs": [], - "source": [ - "n_solvent = 800\n", - "\n", - "solvent = Molecule.from_smiles(\"C1CCOC1\")\n", - "solvent.generate_conformers(n_conformers=1)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "6", - "metadata": {}, - "outputs": [], - "source": [ - "sage = ForceField(\"openff_unconstrained-2.0.0.offxml\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "7", - "metadata": {}, - "outputs": [], - "source": [ - "solvent_interchange = Interchange.from_smirnoff(\n", - " sage,\n", - " _OFFBioTop(\n", - " mdtop=md.Topology.from_openmm(\n", - " Topology.from_molecules(n_solvent * [solvent]).to_openmm()\n", - " )\n", - " ),\n", - ")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "8", - "metadata": {}, - "outputs": [], - "source": [ - "combined = solvent_interchange + nanoparticle_interchange" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "9", - "metadata": {}, - "outputs": [], - "source": [ - "thf_compound = offmol_to_compound(solvent)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "10", - "metadata": {}, - "outputs": [], - "source": [ - "solvated_compound = mb.packing.solvate(\n", - " solute=nanoparticle, solvent=thf_compound, n_solvent=n_solvent, box=mb.Box(3 * [8])\n", - ")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "11", - "metadata": {}, - "outputs": [], - "source": [ - "combined.topology = _combine_topologies(\n", - " solvent_interchange.topology,\n", - " nanoparticle_interchange.topology,\n", - ")\n", - "combined.positions = solvated_compound.xyz * unit.nanometer\n", - "combined.box = 3 * [8] * unit.nanometer" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "12", - "metadata": {}, - "outputs": [], - "source": [ - "combined.to_pdb(\"out.pdb\")\n", - "view = nglview.show_mdtraj(md.load(\"out.pdb\"))\n", - "view.clear_representations()\n", - "view.add_representation(\n", - " \"spacefill\", selection=[*range(combined.topology.mdtop.n_atoms)]\n", - ")\n", - "view" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "13", - "metadata": {}, - "outputs": [], - "source": [ - "get_openmm_energies(combined, combine_nonbonded_forces=True)" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.9" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/examples/deprecated/optimize-with-jax.ipynb b/examples/deprecated/optimize-with-jax.ipynb deleted file mode 100644 index e295aff8d..000000000 --- a/examples/deprecated/optimize-with-jax.ipynb +++ /dev/null @@ -1,319 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from copy import deepcopy\n", - "\n", - "import jax\n", - "import jax.numpy as jnp\n", - "import matplotlib.pyplot as plt\n", - "import numpy as np\n", - "from openff.toolkit.topology import Molecule, Topology\n", - "from openff.toolkit.typing.engines.smirnoff import ForceField\n", - "\n", - "from openff.interchange import Interchange\n", - "\n", - "rng = np.random" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# Construct a single-molecule system from toolkit classes\n", - "mol = Molecule.from_smiles(\"CCO\")\n", - "mol.generate_conformers(n_conformers=1)\n", - "top = Topology.from_molecules([mol])\n", - "parsley = ForceField(\"openff-1.0.0.offxml\")\n", - "\n", - "off_sys = Interchange.from_smirnoff(force_field=parsley, topology=top)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "bonds = off_sys.handlers[\"Bonds\"]\n", - "\n", - "# Transform parameters into matrix representations\n", - "p = bonds.get_force_field_parameters()\n", - "mapping = bonds.get_mapping()\n", - "q = bonds.get_system_parameters()\n", - "m = bonds.get_param_matrix()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# force field parameters, each row is something like [k (kcal/mol/A), length (A)]\n", - "p" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# system parameters, a.k.a. force field parameters as they exist in a parametrized system\n", - "q" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# m is the parametrization matrix, which can be dotted with p to get out q\n", - "assert np.allclose(m.dot(p.flatten()).reshape((-1, 2)), q)\n", - "\n", - "m" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# save and set initial values\n", - "q0 = q\n", - "p0 = p\n", - "\n", - "# set learning rate\n", - "a = 0.1" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# let jax run with autodiff\n", - "_, f_vjp_bonds = jax.vjp(bonds.parametrize, jnp.asarray(p0)) # d/dp\n", - "\n", - "# jax.jvp( ..., has_aux=True) is another approach, but requires that bonds.parametrize returns the indices as well" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "q_target = deepcopy(q0)\n", - "p_target = deepcopy(p0)\n", - "\n", - "# modify a few of the force field targets to arbitrary values;\n", - "# this mimic some \"true\" values we wish to tune to, despite\n", - "# these values not being known in real-world fitting\n", - "p_target[:, 1] = 0.5 + rng.rand(4)\n", - "\n", - "# obtain the target _sytem_ parameters by dotting the parametrization\n", - "# matrix with target force field values\n", - "q_target = m.dot(p_target.flatten()).reshape((-1, 2))\n", - "\n", - "\n", - "# create a dummy loss function via faking known target parameters;\n", - "# in practice this could be the result of an MD run, FE calculation, etc.\n", - "def loss(p):\n", - " return jnp.linalg.norm(bonds.parametrize(p) - q_target)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "out, f_vjp_bonds = jax.vjp(loss, p0) # composes a jax.grad" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# This also returns loss(p0), which we do not need to store\n", - "out == loss(p0)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "f_vjp_bonds(1.0)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# this does the same as the jax.vjp above\n", - "jax_loss = jax.grad(loss)\n", - "\n", - "jax_loss(p0) # dL/dp" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "f_vjp_bonds(1.0)[0] == jax_loss(p0) # dL/dp" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# derivative of loss function evaluated at the original system parameters;\n", - "# note that column 0 mathces target values, so the derivate is flat\n", - "f_vjp_bonds(loss(q0)) # dL/dp (!) can be used as gradient in fitting" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "fig, ax = plt.subplots()\n", - "\n", - "# label target values\n", - "ax.hlines(p_target[0, 1], 0, 100, color=\"k\", ls=\"--\", label=\"[#6X4:1]-[#6X4:2]\")\n", - "ax.hlines(p_target[1, 1], 0, 100, color=\"r\", ls=\"--\", label=\"[#6X4:1]-[#1:2]\")\n", - "ax.hlines(p_target[2, 1], 0, 100, color=\"g\", ls=\"--\", label=\"[#6:1]-[#8:2]\")\n", - "ax.hlines(p_target[3, 1], 0, 100, color=\"b\", ls=\"--\", label=\"[#8:1]-[#1:2]\")\n", - "\n", - "for i in range(100):\n", - " if i % 10 == 0:\n", - " print(f\"step {i}\\tloss: {loss(p)}\")\n", - " ax.plot(i, p[0][1], \"k.\")\n", - " ax.plot(i, p[1][1], \"r.\")\n", - " ax.plot(i, p[2][1], \"g.\")\n", - " ax.plot(i, p[3][1], \"b.\")\n", - "\n", - " # use jax to get the gradient\n", - " _, f_vjp_bonds = jax.vjp(loss, p)\n", - " grad = f_vjp_bonds(1.0)[0]\n", - " # update force field parameters\n", - " p -= a * grad\n", - " # use the parametrization matrix to propagate new\n", - " # force field parameters into new system parameters\n", - " q = m.dot(p.flatten()).reshape((-1, 2))\n", - "\n", - "\n", - "ax.legend(loc=0)\n", - "ax.set_xlabel(\"iteration\")\n", - "ax.set_ylabel(\"parameter value (bond length-ish)\")\n", - "ax.set_xlim((0, 100))\n", - "ax.set_ylim((0, 1.5))" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# We can do everything all over again with angles, almost identically\n", - "angles = off_sys.handlers[\"Angles\"]\n", - "q0 = angles.get_system_parameters()\n", - "p0 = angles.get_force_field_parameters()\n", - "mapping = angles.get_mapping()\n", - "m = angles.get_param_matrix()\n", - "q = q0\n", - "p = p0\n", - "a = 0.1\n", - "\n", - "q_target = deepcopy(q0)\n", - "p_target = deepcopy(p0)\n", - "p_target[:, 1] = rng.randint(100, 120, 3)\n", - "\n", - "q_target = angles.parametrize(p_target)\n", - "\n", - "\n", - "def loss(p):\n", - " return jnp.linalg.norm(angles.parametrize(p) - q_target)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "fig, ax = plt.subplots()\n", - "\n", - "# label target values\n", - "ax.hlines(p_target[0, 1], 0, 100, color=\"k\", ls=\"--\", label=\"[*:1]~[#6X4:2]-[*:3]\")\n", - "ax.hlines(p_target[1, 1], 0, 100, color=\"r\", ls=\"--\", label=\"[*:1]-[#8:2]-[*:3]\")\n", - "ax.hlines(p_target[2, 1], 0, 100, color=\"g\", ls=\"--\", label=\"[#1:1]-[#6X4:2]-[#1:3]\")\n", - "\n", - "for i in range(100):\n", - " if i % 10 == 0:\n", - " print(f\"step {i}\\tloss: {loss(p)}\")\n", - " ax.plot(i, p[0][1], \"k.\")\n", - " ax.plot(i, p[1][1], \"r.\")\n", - " ax.plot(i, p[2][1], \"g.\")\n", - "\n", - " # use jax to get the gradient\n", - " _, f_vjp_angles = jax.vjp(loss, p)\n", - " grad = f_vjp_angles(1.0)[0]\n", - " # update force field parameters\n", - " p -= a * grad\n", - " # print(p[0])\n", - " q = m.dot(p.flatten()).reshape((-1, 2))\n", - "\n", - "ax.legend(loc=0)\n", - "ax.set_xlabel(\"iteration\")\n", - "ax.set_ylabel(\"parameter value (angle-ish)\")\n", - "ax.set_xlim((0, 100))\n", - "ax.set_ylim((100, 120))" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.9" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/examples/deprecated/parameter_replacement.ipynb b/examples/deprecated/parameter_replacement.ipynb deleted file mode 100644 index c67b7cf0e..000000000 --- a/examples/deprecated/parameter_replacement.ipynb +++ /dev/null @@ -1,318 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Replacing parameters in Interchange\n", - "\n", - "
\n", - " â–¼ Click here for dependency installation instructions\n", - " The simplest way to install dependencies is to use the Interchange examples environment. From the root of the cloned openff-interchange repository:\n", - " \n", - " conda env create --name interchange-examples --file devtools/conda-envs/examples_env.yaml\n", - " conda activate interchange-examples\n", - " pip install -e .\n", - " cd examples/parameter_replacement\n", - " jupyter notebook parameter_replacement.ipynb\n", - " \n", - "
\n", - "\n", - "In this example, we'll compare the parametrization of ethanol in the Parsley and Sage force fields, and then update the former system with Sage angle terms. This is an advanced example for users looking to optimize force fields." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from openff.toolkit import ForceField, Molecule\n", - "\n", - "from openff.interchange import Interchange" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Load in the OpenFF force fields Parsley and Sage. These are the first two major versions of the OpenFF force field family. They are distributed as part of the `openff-forcefields` conda package, which is a dependency of the Toolkit." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "pars_ff = ForceField(\"openff-1.3.1.offxml\")\n", - "sage_ff = ForceField(\"openff-2.0.0.offxml\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Now, we'll construct Interchanges describing a system of two ethanol molecules for each force field." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "ethanol = Molecule.from_smiles(\"CCO\")\n", - "\n", - "pars_sys = Interchange.from_smirnoff(force_field=pars_ff, topology=[ethanol] * 2)\n", - "sage_sys = Interchange.from_smirnoff(force_field=sage_ff, topology=[ethanol] * 2)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Inspecting parameters" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Sage changes quite a lot from Parsley (see the [Release Notes]), but we'll focus on the bond angle parameters here. Let's first confirm that the angle parameters have changed. Parameters in Interchange are managed by [`PotentialHandler`] objects; each kind of potential has its own subclass. Angles in SMIRNOFF force fields use [`SMIRNOFFAngleHandler`]. Potential handlers are similar to parameter handlers, which fill a similar role in force fields, but unlike parameter handlers potential handlers connect the topology to the potential. Parameter handlers merely connect SMIRKS codes to parameters. For more information, see [Tweaking and Inspecting Parameters] in the user guide.\n", - "\n", - "We can get the potential handler for each Interchange from the `handlers` attribute. Let's check that Parsley and Sage have different bond angle potentials by comparing the appropriate handlers.\n", - "\n", - "[Release Notes]: https://github.com/openforcefield/openff-forcefields/releases\n", - "[`PotentialHandler`]: https://openff-interchange.readthedocs.io/en/stable/_autosummary/openff.interchange.components.potentials.PotentialHandler.html\n", - "[`SMIRNOFFAngleHandler`]: https://openff-interchange.readthedocs.io/en/stable/_autosummary/openff.interchange.components.smirnoff.SMIRNOFFAngleHandler.html\n", - "[Tweaking and Inspecting Parameters]: https://openff-interchange.readthedocs.io/en/stable/using/handlers.html" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "assert pars_sys.handlers[\"Angles\"] != sage_sys.handlers[\"Angles\"]" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Handlers map between topology and potential via two dictionary attributes, `.key_map` and `.potentials`. There's a bit of [complexity] here but essentially `key_map` maps from atom indices to an identifier, while `potentials` maps from the identifier to actual parameters. This means that getting the parameters for a particular atom or group of atoms is as fast as two dict lookups, without duplicating parameters. SMIRNOFF handlers use SMIRKS codes for the identifier, but other handlers can use whatever they want.\n", - "\n", - "[complexity]: https://openff-interchange.readthedocs.io/en/stable/using/handlers.html\n", - "\n", - "Parsley and Sage use the same SMIRKS codes for their ethanol angle terms, and both our systems have the same topologies, so their `key_map` attributes should be identical:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "assert pars_sys.handlers[\"Angles\"].key_map == sage_sys.handlers[\"Angles\"].key_map" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Since they have the same slot maps, they should have the same SMIRKS codes, so the keys to `.potentials` should be the same:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "assert (\n", - " pars_sys.handlers[\"Angles\"].potentials.keys()\n", - " == sage_sys.handlers[\"Angles\"].potentials.keys()\n", - ")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "So we can compare them key-by-key. Here's Parsley:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "pars_sys.handlers[\"Angles\"].potentials" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "And Sage:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "sage_sys.handlers[\"Angles\"].potentials" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Here's the relevant bits next to each other. See if you can find them in the above!" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "for potential_key in pars_sys.handlers[\"Angles\"].potentials:\n", - " print(potential_key.id)\n", - " for ff, sys in [(\"Sage\", sage_sys), (\"Parsley\", pars_sys)]:\n", - " print(f\" {ff}\")\n", - " for k, v in sys.handlers[\"Angles\"].potentials[potential_key].parameters.items():\n", - " print(f\" {k}: {v}\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Updating Parsley with Sage angles" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "
\n", - " 🛑 For Educational Purposes Only
\n", - " Don't combine parameters from different force fields or \"update\" one part of a force field without careful consideration. Parameters are designed and optimized to work within a particular context, and moving them to a completely different force field is usually a bad idea.\n", - "
\n", - "\n", - "Just to demonstrate changing parameters, lets \"update\" our Parsley Interchange to use Sage angle parameters. This will definitely hurt force field performance, as each set of angle parameters are optimized for different non-bonded parameters, but it demonstrates the API, and we won't be running any simulations." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Generally, updating a `PotentialHandler` involves updating both dictionaries, `key_map` and `potentials`. Since both of our Interchanges use the same SMIRKS codes and parameter types, we could skip updating the `key_map`, but it's best practice to do both steps every time. It's good practice to clear the old values so that you don't accidentally wind up with redundant parameters (unless that's what you want), so let's start with that:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "pars_sys.handlers[\"Angles\"].key_map.clear()\n", - "pars_sys.handlers[\"Angles\"].potentials.clear()" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The [`store_matches`] method updates `key_map`. It takes a topology and some object that describes the parameters (for SMIRNOFF, a `ParameterHandler`) and applies the described force field, storing the appropriate atom indices in the calling handler. If there are clashes, the new values replace the old.\n", - "\n", - "[`store_matches`]: https://openff-interchange.readthedocs.io/en/stable/_autosummary/openff.interchange.components.potentials.PotentialHandler.html#openff.interchange.components.potentials.PotentialHandler.store_matches" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "pars_sys.handlers[\"Angles\"].store_matches(sage_ff[\"Angles\"], topology=pars_sys.topology)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The [`store_potentials`] method updates `potentials`. It just takes the object that describes the parameters and stores them. If there are clashes, the new values replace the old.\n", - "\n", - "[`store_potentials`]: https://openff-interchange.readthedocs.io/en/stable/_autosummary/openff.interchange.components.potentials.PotentialHandler.html#openff.interchange.components.potentials.PotentialHandler.store_potentials" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "pars_sys.handlers[\"Angles\"].store_potentials(sage_ff[\"Angles\"])" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### Check the update" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "We can check that the two systems now have identical angle handlers, and that other parameters, say the bonds, are still the same:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "assert pars_sys.handlers[\"Angles\"] == sage_sys.handlers[\"Angles\"]\n", - "assert pars_sys.handlers[\"Bonds\"] != sage_sys.handlers[\"Bonds\"]" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.10" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/examples/deprecated/parameter_splitting.ipynb b/examples/deprecated/parameter_splitting.ipynb deleted file mode 100644 index 7e78e48fc..000000000 --- a/examples/deprecated/parameter_splitting.ipynb +++ /dev/null @@ -1,285 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Splitting parameters in Interchange\n", - "\n", - "
\n", - " â–¼ Click here for dependency installation instructions\n", - " The simplest way to install dependencies is to use the Interchange examples environment. From the root of the cloned openff-interchange repository:\n", - " \n", - " conda env create --name interchange-examples --file devtools/conda-envs/examples_env.yaml\n", - " conda activate interchange-examples\n", - " pip install -e .\n", - " cd examples/parameter_splitting\n", - " jupyter notebook parameter_splitting.ipynb\n", - " \n", - "
\n", - "\n", - "This example explains splitting a single parameter applied to two different parts of a topology into two separate parameters." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import openmm\n", - "from openff.toolkit import ForceField, Molecule\n", - "\n", - "from openff.interchange import Interchange\n", - "from openff.interchange.components.potentials import Potential\n", - "from openff.interchange.models import PotentialKey, TopologyKey" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "We need a molecule that has two parameters that are the same in Sage, but could reasonably be different. We'll pick the two Carbon-Carbon bonds in propanol. Let's set up our Interchange, store a copy of the original as an OpenMM system, and make sure we know what propanol looks like:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "propanol = Molecule.from_smiles(\"CCCO\")\n", - "propanol.generate_conformers(n_conformers=1)\n", - "\n", - "sage = ForceField(\"openff-2.0.0.offxml\")\n", - "\n", - "interchange = Interchange.from_smirnoff(sage, topology=[propanol])\n", - "\n", - "original_openmm_system = interchange.to_openmm()\n", - "\n", - "propanol.visualize(backend=\"rdkit\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Interchange stores parameters in `PotentialHandler` objects. A potential handler maps atom indices to parameters via a `PotentialKey`, which identifies the parameters in the original force field (see [Tweaking and Inspecting Parameters]). We can see the atom indices of all the bonds and the corresponding potential keys by inspecting the `key_map` attribute of the bonds potential handler:\n", - "\n", - "[Tweaking and Inspecting Parameters]: https://openff-interchange.readthedocs.io/en/stable/using/handlers.html" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "interchange.handlers[\"Bonds\"].key_map" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "By iterating over the topology, we can pick out the C-C bonds. We'll need the potential key they both use, so let's give it a name:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "for bond in interchange.topology.bonds:\n", - " if all(atom.atomic_number == 6 for atom in bond.atoms):\n", - " atom_indices = tuple(\n", - " interchange.topology.atom_index(atom) for atom in bond.atoms\n", - " )\n", - " top_key = TopologyKey(atom_indices=atom_indices)\n", - " pot_key = interchange.handlers[\"Bonds\"].key_map[top_key]\n", - " print(atom_indices, pot_key.__repr__())" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Notice that the `PotentialKey` associated with each of the C-C bonds - atom indices (0, 1) and (1, 2) - is the same, in this case associated with SMIRKS pattern `'[#6X4:1]-[#6X4:2]'`. This means the same parameters have been applied to each. For the sake of this example, let's consider splitting these parameters into two types without re-running SMIRKS/SMARTS-based atom-typing. Let's increase the force constant of the C-C bond nearest the O atom by 5% (atom indices (1, 2)). This is scientifically unmotivated; randomly changing a single force constant will not (usually) improve a force field." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Creating a new potential" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "We'll start by cloning the existing C-C bond `PotentialKey`. The new ID can be anything as long as its unique, so let's choose something that makes the parameter's heritage clear without confusing ourselves with something that looks like a SMIRKS code:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "pot_key_mod = PotentialKey(**pot_key.dict())\n", - "pot_key_mod.id = \"[#6X4:1]-[#6X4:2]_MODIFIED\"\n", - "\n", - "(pot_key, pot_key_mod)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Looks good! Now we need to do the same thing with the parameters themselves. We can get the potential out by indexing with the original `PontentialKey`, copy it, and then adjust it's force constant $k$:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "pot = interchange.handlers[\"Bonds\"].potentials[pot_key]\n", - "pot_mod = Potential(**pot.dict())\n", - "pot_mod.parameters[\"k\"] *= 1.05\n", - "\n", - "(pot, pot_mod)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Perfect. Now we add the new potential to the handler. This won't apply it anywhere in the topology, but it'll give us something to apply. The `.potentials` attribute is just a regular Python `dict` mapping potential keys to potentials, so we can use the regular Python `dict.update()` method with our modified key and potential:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "interchange.handlers[\"Bonds\"].potentials.update({pot_key_mod: pot_mod})" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The last step is to apply it to the topology somewhere. Interchange identifies places in the topology by tuples of atom indices. We already decided that we want to apply our new potential to the bond between atoms 1 and 2, so we define a `TopologyKey` to that effect and check that the bond already exists (and is what we expect):" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "top_key = TopologyKey(atom_indices=(1, 2))\n", - "\n", - "assert top_key in interchange[\"Bonds\"].key_map\n", - "\n", - "interchange[\"Bonds\"].key_map[top_key]" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The `key_map` attribute is another regular `dict` that maps a `TopologyKey` to a `PotentialKey`. Connecting the topology key (atom indices) to a potential key goes exactly how you'd expect:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "interchange.handlers[\"Bonds\"].key_map[top_key] = pot_key_mod" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Testing our new parameter" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "To prove that we've done what we expected, let's export to OpenMM and use it's machinery to compare the force constants." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# Export to OpenMM\n", - "modified_openmm_system = interchange.to_openmm()\n", - "\n", - "# Define the atom indices we care about\n", - "i = 1\n", - "j = 2\n", - "\n", - "# Get the original exported k value\n", - "for force in original_openmm_system.getForces():\n", - " if type(force) == openmm.HarmonicBondForce:\n", - " for bond_idx in range(force.getNumBonds()):\n", - " if force.getBondParameters(bond_idx)[:2] == [i, j]:\n", - " original_k = force.getBondParameters(bond_idx)[3]\n", - " print(\n", - " f\"K in the original system between atoms {i} and {j} is\", original_k\n", - " )\n", - "\n", - "# Get the exported k value in the modified system\n", - "for force in modified_openmm_system.getForces():\n", - " if type(force) == openmm.HarmonicBondForce:\n", - " for bond_idx in range(force.getNumBonds()):\n", - " if force.getBondParameters(bond_idx)[:2] == [i, j]:\n", - " modified_k = force.getBondParameters(bond_idx)[3]\n", - " print(\n", - " f\"K in the modified system between atoms {i} and {j} is\", modified_k\n", - " )\n", - "\n", - "# Check that the modified k is 5% more than the original k\n", - "assert abs(modified_k / original_k - 1.05) < 1e-12\n", - "print(f\"{modified_k}/{original_k} = {modified_k/original_k}\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.12" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/examples/experimental/openmm-import/protein-ligand.ipynb b/examples/experimental/openmm-import/protein-ligand.ipynb index 754eb7007..afaa94e05 100644 --- a/examples/experimental/openmm-import/protein-ligand.ipynb +++ b/examples/experimental/openmm-import/protein-ligand.ipynb @@ -135,9 +135,7 @@ "metadata": {}, "outputs": [], "source": [ - "converted_energies = get_openmm_energies(\n", - " converted_interchange, combine_nonbonded_forces=True\n", - ")\n", + "converted_energies = get_openmm_energies(converted_interchange, combine_nonbonded_forces=True)\n", "print(converted_energies)" ] }, diff --git a/examples/experimental/solvate/solvate.ipynb b/examples/experimental/solvate/solvate.ipynb index 85de33a11..7af2dc607 100644 --- a/examples/experimental/solvate/solvate.ipynb +++ b/examples/experimental/solvate/solvate.ipynb @@ -78,9 +78,7 @@ " **kwargs,\n", ") -> Topology:\n", " if method in [\"pdbfixer\", \"openmm\"]:\n", - " boxSize = openmm.unit.Quantity(\n", - " openmm.Vec3(*box_vectors.m_as(unit.nanometer)), openmm.unit.nanometer\n", - " )\n", + " boxSize = openmm.unit.Quantity(openmm.Vec3(*box_vectors.m_as(unit.nanometer)), openmm.unit.nanometer)\n", "\n", " if method == \"pdbfixer\":\n", " openmm_topology, openmm_positions = _solvate_pdbfixer(\n", @@ -101,14 +99,10 @@ " unique_molecules.append(Molecule.from_mapped_smiles(\"[H:2][O:1][H:3]\"))\n", "\n", " if \"positiveIon\" in kwargs:\n", - " unique_molecules.append(\n", - " Molecule.from_smiles(OPENMM_IONS[kwargs[\"positiveIon\"]])\n", - " )\n", + " unique_molecules.append(Molecule.from_smiles(OPENMM_IONS[kwargs[\"positiveIon\"]]))\n", "\n", " if \"negativeIon\" in kwargs:\n", - " unique_molecules.append(\n", - " Molecule.from_smiles(OPENMM_IONS[kwargs[\"negativeIon\"]])\n", - " )\n", + " unique_molecules.append(Molecule.from_smiles(OPENMM_IONS[kwargs[\"negativeIon\"]]))\n", "\n", " new_topology = Topology.from_openmm(\n", " openmm_topology,\n", @@ -301,7 +295,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.4" + "version": "3.11.0" }, "vscode": { "interpreter": { diff --git a/examples/lammps/.gitignore b/examples/lammps/.gitignore index 38e5cf989..23790c55e 100644 --- a/examples/lammps/.gitignore +++ b/examples/lammps/.gitignore @@ -5,3 +5,4 @@ test.in traj.dcd _tmp_pdb_file.pdb auto_generated.in +interchange_pointenergy.in diff --git a/examples/lammps/lammps.ipynb b/examples/lammps/lammps.ipynb index 1524007d4..5a0d31826 100644 --- a/examples/lammps/lammps.ipynb +++ b/examples/lammps/lammps.ipynb @@ -37,9 +37,7 @@ "from openff.interchange.components.mdconfig import MDConfig\n", "\n", "# Read a structure from the Toolkit's test suite into a Topology\n", - "pdbfile = PDBFile(\n", - " get_data_file_path(\"systems/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb\")\n", - ")\n", + "pdbfile = PDBFile(get_data_file_path(\"systems/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb\"))\n", "molecules = [Molecule.from_smiles(smi) for smi in [\"CCC\", \"C\", \"CCCCO\"]]\n", "off_topology = Topology.from_openmm(pdbfile.topology, unique_molecules=molecules)\n", "\n", diff --git a/examples/ligand_in_water/.gitignore b/examples/ligand_in_water/.gitignore index 2ff5b84b4..33f3a9e18 100644 --- a/examples/ligand_in_water/.gitignore +++ b/examples/ligand_in_water/.gitignore @@ -11,3 +11,4 @@ run.gro run.xtc tip4p.gro tip4p.top +tip4p_pointenergy.mdp diff --git a/examples/ligand_in_water/ligand_in_water.ipynb b/examples/ligand_in_water/ligand_in_water.ipynb index 4ff4a0fd3..e99b10736 100644 --- a/examples/ligand_in_water/ligand_in_water.ipynb +++ b/examples/ligand_in_water/ligand_in_water.ipynb @@ -121,9 +121,7 @@ "metadata": {}, "outputs": [], "source": [ - "interchange: Interchange = Interchange.from_smirnoff(\n", - " force_field=sage, topology=topology\n", - ")\n", + "interchange: Interchange = Interchange.from_smirnoff(force_field=sage, topology=topology)\n", "interchange.topology.n_atoms, interchange.box, interchange.positions.shape" ] }, @@ -319,9 +317,7 @@ "outputs": [], "source": [ "water.generate_conformers(n_conformers=1)\n", - "view = force_field_opc.create_interchange(water.to_topology()).visualize(\n", - " include_virtual_sites=True\n", - ")\n", + "view = force_field_opc.create_interchange(water.to_topology()).visualize(include_virtual_sites=True)\n", "view.clear_representations()\n", "view.add_representation(\"ball+stick\", aspectRatio=1.5)\n", "view" @@ -390,9 +386,7 @@ " else:\n", " import numpy\n", "\n", - " atom_indices = numpy.where(\n", - " [a.element.mass > 0.0 for a in trajectory[0].topology.atoms]\n", - " )[0]\n", + " atom_indices = numpy.where([a.element.mass > 0.0 for a in trajectory[0].topology.atoms])[0]\n", "\n", " view = nglview.show_mdtraj(trajectory.atom_slice(atom_indices))\n", "\n", diff --git a/examples/openmm/openmm.ipynb b/examples/openmm/openmm.ipynb index 9e44937df..06b62b587 100644 --- a/examples/openmm/openmm.ipynb +++ b/examples/openmm/openmm.ipynb @@ -36,9 +36,7 @@ "from pandas import read_csv\n", "\n", "# This prepared PDB file from the toolkit's test suite is a box of solvents\n", - "pdb_path = get_data_file_path(\n", - " \"systems/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb\"\n", - ")\n", + "pdb_path = get_data_file_path(\"systems/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb\")\n", "molecules = [Molecule.from_smiles(smi) for smi in [\"CCC\", \"C\", \"CCCCO\"]]\n", "\n", "# The OpenFF Toolkit can directly read PDB files!\n", diff --git a/examples/packed_box/packed_box.ipynb b/examples/packed_box/packed_box.ipynb index 92f68982e..63f41f7fb 100644 --- a/examples/packed_box/packed_box.ipynb +++ b/examples/packed_box/packed_box.ipynb @@ -58,10 +58,7 @@ "metadata": {}, "outputs": [], "source": [ - "molecules = [\n", - " Molecule.from_smiles(smi)\n", - " for smi in [\"ClC(Cl)(Cl)Cl\", \"CC1=CC=CC=C1\", \"CS(=O)C\", \"CCCCCCO\"]\n", - "]" + "molecules = [Molecule.from_smiles(smi) for smi in [\"ClC(Cl)(Cl)Cl\", \"CC1=CC=CC=C1\", \"CS(=O)C\", \"CCCCCCO\"]]" ] }, { diff --git a/examples/protein_ligand/.gitignore b/examples/protein_ligand/.gitignore index 481dd8ad6..9e27c395a 100644 --- a/examples/protein_ligand/.gitignore +++ b/examples/protein_ligand/.gitignore @@ -1,5 +1,6 @@ *.pdb *.sdf out.* +out_pointenergy.mdp log.lammps tmp.in diff --git a/examples/virtual_sites/.gitignore b/examples/virtual_sites/.gitignore index 4db3b2a56..78cc48d42 100644 --- a/examples/virtual_sites/.gitignore +++ b/examples/virtual_sites/.gitignore @@ -1 +1,2 @@ trajectory.dcd +*.xml diff --git a/examples/virtual_sites/virtual_sites.ipynb b/examples/virtual_sites/virtual_sites.ipynb index ff551d66e..3b156bc85 100644 --- a/examples/virtual_sites/virtual_sites.ipynb +++ b/examples/virtual_sites/virtual_sites.ipynb @@ -80,13 +80,9 @@ " simulation.context.setVelocitiesToTemperature(openmm.unit.kelvin * 300)\n", " simulation.step(1000)\n", "\n", - " interchange.positions = simulation.context.getState(\n", - " getPositions=True\n", - " ).getPositions()\n", + " interchange.positions = simulation.context.getState(getPositions=True).getPositions()\n", "\n", - " open(f\"{name}.xml\", \"w\").write(\n", - " openmm.XmlSerializer.serialize(interchange.to_openmm())\n", - " )\n", + " open(f\"{name}.xml\", \"w\").write(openmm.XmlSerializer.serialize(interchange.to_openmm()))\n", "\n", " return nglview.show_mdtraj(\n", " mdtraj.load(\n", @@ -111,9 +107,7 @@ "metadata": {}, "outputs": [], "source": [ - "sage_with_example_virtual_sites[\"VirtualSites\"].get_parameter({\"name\": \"sigma_hole\"})[\n", - " 0\n", - "].to_dict()" + "sage_with_example_virtual_sites[\"VirtualSites\"].get_parameter({\"name\": \"sigma_hole\"})[0].to_dict()" ] }, { @@ -147,9 +141,7 @@ "metadata": {}, "outputs": [], "source": [ - "sage_with_example_virtual_sites[\"VirtualSites\"].get_parameter(\n", - " {\"name\": \"planar_carbonyl\"}\n", - ")[0].to_dict()" + "sage_with_example_virtual_sites[\"VirtualSites\"].get_parameter({\"name\": \"planar_carbonyl\"})[0].to_dict()" ] }, { @@ -183,9 +175,7 @@ "metadata": {}, "outputs": [], "source": [ - "sage_with_example_virtual_sites[\"VirtualSites\"].get_parameter({\"name\": \"4_site_water\"})[\n", - " 0\n", - "].to_dict()" + "sage_with_example_virtual_sites[\"VirtualSites\"].get_parameter({\"name\": \"4_site_water\"})[0].to_dict()" ] }, { @@ -255,9 +245,7 @@ "metadata": {}, "outputs": [], "source": [ - "sage_with_example_virtual_sites[\"VirtualSites\"].get_parameter(\n", - " {\"name\": \"trivalent_nitrogen\"}\n", - ")[0].to_dict()" + "sage_with_example_virtual_sites[\"VirtualSites\"].get_parameter({\"name\": \"trivalent_nitrogen\"})[0].to_dict()" ] }, { diff --git a/openff/interchange/_tests/__init__.py b/openff/interchange/_tests/__init__.py index 5c63ce634..84d0fee57 100644 --- a/openff/interchange/_tests/__init__.py +++ b/openff/interchange/_tests/__init__.py @@ -139,9 +139,7 @@ def shuffle_topology( # can't easily shuffle a generator ... for molecule in interchange.topology.molecules: - topology_indices = [ - interchange.topology.atom_index(atom) for atom in molecule.atoms - ] + topology_indices = [interchange.topology.atom_index(atom) for atom in molecule.atoms] molecule._conformers = [ interchange.positions[topology_indices, :].to("angstrom"), diff --git a/openff/interchange/_tests/data/de-force-1.0.1.offxml b/openff/interchange/_tests/data/de-force-1.0.1.offxml index 58922ff5e..251f5edc9 100644 --- a/openff/interchange/_tests/data/de-force-1.0.1.offxml +++ b/openff/interchange/_tests/data/de-force-1.0.1.offxml @@ -322,7 +322,7 @@ - + @@ -340,7 +340,7 @@ - + diff --git a/openff/interchange/_tests/energy_tests/test_energies.py b/openff/interchange/_tests/energy_tests/test_energies.py index 8b0e6431c..6be4ff850 100644 --- a/openff/interchange/_tests/energy_tests/test_energies.py +++ b/openff/interchange/_tests/energy_tests/test_energies.py @@ -43,7 +43,6 @@ def oplsaa(self): @needs_gmx @needs_lmp @pytest.mark.xfail - @pytest.mark.slow @pytest.mark.parametrize("constrained", [True, False]) @pytest.mark.parametrize("mol_smi", ["C"]) # ["C", "CC"] def test_energies_single_mol(self, constrained, sage, sage_unconstrained, mol_smi): @@ -102,7 +101,6 @@ def test_energies_single_mol(self, constrained, sage, sage_unconstrained, mol_sm @needs_gmx @skip_if_missing("foyer") @skip_if_missing("mbuild") - @pytest.mark.slow def test_process_rb_torsions(self, oplsaa): """Test that the GROMACS driver reports Ryckaert-Bellemans torsions""" from mbuild import Box @@ -158,7 +156,6 @@ def test_gmx_14_energies_exist(self, sage): @needs_gmx @needs_lmp - @pytest.mark.slow def test_cutoff_electrostatics(self): ion_ff = ForceField(get_test_file_path("ions.offxml")) ions = Topology.from_molecules( diff --git a/openff/interchange/_tests/interoperability_tests/internal/test_amber.py b/openff/interchange/_tests/interoperability_tests/internal/test_amber.py index 394fc420d..0e7150231 100644 --- a/openff/interchange/_tests/interoperability_tests/internal/test_amber.py +++ b/openff/interchange/_tests/interoperability_tests/internal/test_amber.py @@ -42,7 +42,6 @@ def test_inpcrd(self, sage): @skip_if_missing("openmm") @pytest.mark.skipif(not has_executable("sander"), reason="sander not installed") - @pytest.mark.slow @pytest.mark.parametrize( "smiles", [ diff --git a/openff/interchange/_tests/interoperability_tests/internal/test_gromacs.py b/openff/interchange/_tests/interoperability_tests/internal/test_gromacs.py index a1536d5c7..0325307a1 100644 --- a/openff/interchange/_tests/interoperability_tests/internal/test_gromacs.py +++ b/openff/interchange/_tests/interoperability_tests/internal/test_gromacs.py @@ -1,5 +1,4 @@ from importlib import resources -from math import exp import numpy import parmed @@ -11,11 +10,8 @@ from openff.interchange import Interchange from openff.interchange._tests import MoleculeWithConformer, get_protein, needs_gmx -from openff.interchange.components.nonbonded import BuckinghamvdWCollection -from openff.interchange.components.potentials import Potential from openff.interchange.drivers import get_gromacs_energies, get_openmm_energies from openff.interchange.exceptions import ( - GMXMdrunError, UnsupportedExportError, VirtualSiteTypeNotImplementedError, ) @@ -23,7 +19,6 @@ _read_box, _read_coordinates, ) -from openff.interchange.models import PotentialKey, TopologyKey if has_package("openmm"): import openmm.app @@ -88,16 +83,6 @@ def converter(x): n_decimals = len(str(coords[0, 0]).split(".")[1]) assert n_decimals == 12 - def test_vaccum_warning(self, sage): - molecule = MoleculeWithConformer.from_smiles("CCO") - - out = Interchange.from_smirnoff(force_field=sage, topology=[molecule]) - - assert out.box is None - - with pytest.warns(UserWarning, match="gitlab"): - out.to_gro("tmp.gro") - @pytest.mark.slow @skip_if_missing("openmm") def test_residue_info(self, sage): @@ -113,6 +98,8 @@ def test_residue_info(self, sage): topology=[protein], ) + out.box = [4, 4, 4] + out.to_gro("tmp.gro") mdtraj_topology = mdtraj.load("tmp.gro").topology @@ -129,9 +116,11 @@ def test_atom_names_pdb(self): peptide = get_protein("MainChain_ALA_ALA") ff14sb = ForceField("ff14sb_off_impropers_0.0.3.offxml") - Interchange.from_smirnoff(ff14sb, peptide.to_topology()).to_gro( - "atom_names.gro", - ) + out = ff14sb.create_interchange(peptide.to_topology()) + + out.box = [4, 4, 4] + + out.to_gro("atom_names.gro") pdb_object = openmm.app.PDBFile( get_data_file_path("proteins/MainChain_ALA_ALA.pdb", "openff.toolkit"), @@ -269,69 +258,6 @@ def test_residue_info(self, sage): assert found_residue.name == original_residue.residue_name assert str(found_residue.number + 1) == original_residue.residue_number - @pytest.mark.slow - @pytest.mark.skip( - reason="Update when energy reports intentionally support non-vdW handlers", - ) - def test_argon_buck(self): - """Test that Buckingham potentials are supported and can be exported""" - from openff.interchange.smirnoff import SMIRNOFFElectrostaticsCollection - - mol = MoleculeWithConformer.from_smiles("[#18]", name="Argon") - - top = Topology.from_molecules([mol, mol]) - - # http://www.sklogwiki.org/SklogWiki/index.php/Argon#Buckingham_potential - erg_mol = unit.erg / unit.mol * float(unit.avogadro_number) - A = 1.69e-8 * erg_mol - B = 1 / (0.273 * unit.angstrom) - C = 102e-12 * erg_mol * unit.angstrom**6 - - r = 0.3 * unit.nanometer - - buck = BuckinghamvdWCollection() - coul = SMIRNOFFElectrostaticsCollection(method="pme") - - pot_key = PotentialKey(id="[#18]") - pot = Potential(parameters={"A": A, "B": B, "C": C}) - - for atom in top.atoms: - top_key = TopologyKey(atom_indices=(top.atom_index(atom),)) - buck.key_map.update({top_key: pot_key}) - - coul.key_map.update({top_key: pot_key}) - coul.potentials.update( - {pot_key: Potential(parameters={"charge": 0 * unit.elementary_charge})}, - ) - - for molecule in top.molecules: - molecule.partial_charges = Quantity( - molecule.n_atoms * [0], - unit.elementary_charge, - ) - - buck.potentials[pot_key] = pot - - out = Interchange() - out.collections["Buckingham-6"] = buck - out.collections["Electrostatics"] = coul - out.topology = top - out.box = [10, 10, 10] * unit.nanometer - out.positions = [[0, 0, 0], [0.3, 0, 0]] * unit.nanometer - out.to_gro("out.gro", writer="internal") - out.to_top("out.top", writer="internal") - - omm_energies = get_openmm_energies(out, combine_nonbonded_forces=True) - by_hand = A * exp(-B * r) - C * r**-6 - - resid = omm_energies.energies["vdW"] - by_hand - assert resid < 1e-5 * unit.kilojoule / unit.mol - - # TODO: Add back comparison to GROMACS energies once GROMACS 2020+ - # supports Buckingham potentials - with pytest.raises(GMXMdrunError): - get_gromacs_energies(out, mdp="cutoff_buck") - @pytest.mark.skip("Broken, unclear if cases like these are worth supporting") def test_nonconsecutive_isomorphic_molecules(self, sage_unconstrained): molecules = [Molecule.from_smiles(smiles) for smiles in ["CC", "CCO", "CC"]] @@ -351,36 +277,6 @@ def test_nonconsecutive_isomorphic_molecules(self, sage_unconstrained): ) -class TestGROMACSMetadata: - @skip_if_missing("openmm") - @skip_if_missing("mdtraj") - @pytest.mark.slow - def test_atom_names_pdb(self): - peptide = get_protein("MainChain_ALA_ALA") - ff14sb = ForceField("ff14sb_off_impropers_0.0.3.offxml") - - Interchange.from_smirnoff(ff14sb, peptide.to_topology()).to_gro( - "atom_names.gro", - ) - Interchange.from_smirnoff(ff14sb, peptide.to_topology()).to_top( - "atom_names.top", - ) - - pdb_object = openmm.app.PDBFile( - get_data_file_path( - "proteins/MainChain_ALA_ALA.pdb", - "openff.toolkit", - ), - ) - openmm_object = openmm.app.GromacsTopFile("atom_names.top") - - pdb_atom_names = [atom.name for atom in pdb_object.topology.atoms()] - - openmm_atom_names = [atom.name for atom in openmm_object.topology.atoms()] - - assert openmm_atom_names == pdb_atom_names - - @needs_gmx @pytest.mark.skip("Needs rewrite") class TestGROMACSVirtualSites: diff --git a/openff/interchange/_tests/interoperability_tests/test_openmm.py b/openff/interchange/_tests/interoperability_tests/test_openmm.py index f71b39fbd..774f2e0a1 100644 --- a/openff/interchange/_tests/interoperability_tests/test_openmm.py +++ b/openff/interchange/_tests/interoperability_tests/test_openmm.py @@ -963,7 +963,10 @@ def test_missing_positions(self): MissingPositionsError, match=r"are required.*\.positions=None", ): - to_openmm_positions(Interchange()) + # dummy topology, since it's required now + to_openmm_positions( + Interchange(topology=Molecule.from_smiles("CCO").to_topology()), + ) @pytest.mark.parametrize("include_virtual_sites", [True, False]) def test_positions_basic(self, include_virtual_sites, water, tip4p): @@ -1044,6 +1047,7 @@ def test_to_pdb(self, sage, water): out.to_pdb("file_should_not_exist.pdb") +@pytest.mark.skip(reason="Add back when Buckingham virtual sites are updated") @skip_if_missing("openmm") class TestBuckingham: @pytest.mark.parametrize("n_molecules", [1, 2, 5]) diff --git a/openff/interchange/_tests/test_deprecations.py b/openff/interchange/_tests/test_deprecations.py index 87236213d..a4eb5d6c7 100644 --- a/openff/interchange/_tests/test_deprecations.py +++ b/openff/interchange/_tests/test_deprecations.py @@ -5,35 +5,10 @@ class TestDeprecation: - def test_potential_handler_deprecation(self): - from openff.interchange.components.potentials import Collection - - with pytest.warns( - InterchangeDeprecationWarning, - match="`PotentialHandler` has been renamed to `Collection`.", - ): - from openff.interchange.components.potentials import PotentialHandler - - assert PotentialHandler is Collection - @pytest.fixture def prepared_system(self, sage, water): return Interchange.from_smirnoff(sage, [water]) - def test_slot_map_deprecation(self, prepared_system): - with pytest.warns( - InterchangeDeprecationWarning, - match="The `slot_map` attribute is deprecated. Use `key_map` instead.", - ): - prepared_system["vdW"].slot_map - - def test_handlers_deprecation(self, prepared_system): - with pytest.warns( - InterchangeDeprecationWarning, - match="The `handlers` attribute is deprecated. Use `collections` instead.", - ): - prepared_system.handlers - def test_plus_operator_warning(self, monkeypatch, prepared_system): monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1") diff --git a/openff/interchange/_tests/test_issues.py b/openff/interchange/_tests/test_issues.py index a5ffad545..7b381ec2f 100644 --- a/openff/interchange/_tests/test_issues.py +++ b/openff/interchange/_tests/test_issues.py @@ -6,8 +6,9 @@ import parmed import pytest from openff.toolkit import ForceField, Molecule, Quantity, Topology -from openff.utilities import get_data_file_path +from openff.utilities import get_data_file_path, skip_if_missing +from openff.interchange import Interchange from openff.interchange._tests import MoleculeWithConformer, shuffle_topology from openff.interchange.components._packmol import pack_box from openff.interchange.drivers import get_openmm_energies @@ -26,7 +27,6 @@ def test_issue_723(): @pytest.mark.parametrize("pack", [True, False]) def test_issue_1022(pack): - topology = Topology.from_molecules( [ MoleculeWithConformer.from_smiles(smi) @@ -64,7 +64,6 @@ def test_issue_1022(pack): if pack: for seed in random.sample(range(0, 10**10), 5): - # TODO: Compare GROMACS energies here as well get_openmm_energies(interchange).compare( get_openmm_energies( @@ -76,3 +75,40 @@ def test_issue_1022(pack): ), tolerances={"Nonbonded": Quantity("1e-3 kilojoule_per_mole")}, ) + + +@skip_if_missing("openmm") +def test_issue_1031(monkeypatch): + import openmm.app + + monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1") + + # just grab some small PDB file from the toolkit, doesn't need to be huge, just + # needs to include some relevant atom names + openmm_topology = openmm.app.PDBFile( + get_data_file_path( + "proteins/MainChain_HIE.pdb", + "openff.toolkit", + ), + ).topology + + openmm_atom_names = {atom.name for atom in openmm_topology.atoms()} + + interchange = Interchange.from_openmm( + system=openmm.app.ForceField( + "amber99sb.xml", + "tip3p.xml", + ).createSystem( + openmm_topology, + nonbondedMethod=openmm.app.PME, + ), + topology=openmm_topology, + ) + + openff_atom_names = {atom.name for atom in interchange.topology.atoms} + + assert sorted(openmm_atom_names) == sorted(openff_atom_names) + + # check a few atom names to ensure these didn't end up being empty sets + for atom_name in ("NE2", "H3", "HA", "CH3", "CA", "CB", "CE1"): + assert atom_name in openff_atom_names diff --git a/openff/interchange/_tests/unit_tests/components/test_foyer.py b/openff/interchange/_tests/unit_tests/components/test_foyer.py index ef0eff54e..3f746c9b3 100644 --- a/openff/interchange/_tests/unit_tests/components/test_foyer.py +++ b/openff/interchange/_tests/unit_tests/components/test_foyer.py @@ -109,11 +109,11 @@ def test_ethanol_energies(self, oplsaa_interchange_ethanol): ) @needs_gmx + @pytest.mark.filterwarnings("ignore:Parameters have not been assigned to all impropers.") @pytest.mark.parametrize( argnames="molecule_path", argvalues=[*get_test_files_dir_path("foyer_test_molecules").glob("*.sdf")], ) - @pytest.mark.slow def test_interchange_energies(self, molecule_path, get_interchanges, oplsaa): if "ethanol" in str(molecule_path) or "adamantane" in str(molecule_path): pytest.skip("Foyer/ParmEd bug with this molecule") @@ -203,7 +203,7 @@ def test_rb_torsions(self, ethanol_with_rb_torsions): assert (gmx - omm).m_as(kj_mol) < 1e-6 - @pytest.mark.slow + @pytest.mark.filterwarnings("ignore:Parameters have not been assigned to all impropers.") @skip_if_missing("foyer") @skip_if_missing("mbuild") @needs_gmx diff --git a/openff/interchange/_tests/unit_tests/components/test_interchange.py b/openff/interchange/_tests/unit_tests/components/test_interchange.py index 1574d8d8c..66e3c0ba9 100644 --- a/openff/interchange/_tests/unit_tests/components/test_interchange.py +++ b/openff/interchange/_tests/unit_tests/components/test_interchange.py @@ -1,4 +1,5 @@ import subprocess + import numpy import pytest from openff.toolkit import Molecule, Quantity, Topology, unit @@ -28,7 +29,6 @@ ) -@pytest.mark.slow class TestInterchange: def test_getitem(self, sage): """Test behavior of Interchange.__getitem__""" @@ -360,6 +360,9 @@ def test_gro_file_all_zero_positions(self, sage): numpy.zeros((zero_positions.topology.n_atoms, 3)), unit.nanometer, ) + + zero_positions.box = [4, 4, 4] + with pytest.warns(UserWarning, match="seem to all be zero"): zero_positions.to_gro("foo.gro") @@ -403,17 +406,11 @@ def simple_interchange(self, sage): return Interchange.from_smirnoff(force_field=sage, topology=top) - @skip_if_missing("openmm") - def test_from_openmm_error(self): - with pytest.raises(ExperimentalFeatureException): - Interchange.from_openmm() - def test_from_gromacs_error(self): with pytest.raises(ExperimentalFeatureException): Interchange.from_gromacs() @skip_if_missing("openmm") - @pytest.mark.slow def test_from_openmm_called(self, monkeypatch, simple_interchange): monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1") @@ -430,14 +427,11 @@ def test_from_openmm_called(self, monkeypatch, simple_interchange): ) def test_to_amber(self, simple_interchange): - simple_interchange.to_amber(prefix='blargh') + simple_interchange.to_amber(prefix="blargh") # Just make sure it returns a non-zero error code subprocess.check_output( - "sander -i blargh_pointenergy.in " - "-c blargh.inpcrd " - "-p blargh.prmtop " - "-o out.mdout -O", + "sander -i blargh_pointenergy.in -c blargh.inpcrd -p blargh.prmtop -o out.mdout -O", shell=True, ) diff --git a/openff/interchange/_tests/unit_tests/components/test_packmol.py b/openff/interchange/_tests/unit_tests/components/test_packmol.py index f761cd569..b77480a5f 100644 --- a/openff/interchange/_tests/unit_tests/components/test_packmol.py +++ b/openff/interchange/_tests/unit_tests/components/test_packmol.py @@ -245,7 +245,6 @@ def test_packmol_paracetamol(self): assert topology.n_atoms == 20 assert topology.n_bonds == 20 - @pytest.mark.slow def test_amino_acids(self): amino_residues = { "C[C@H](N)C(=O)O": "ALA", diff --git a/openff/interchange/_tests/unit_tests/drivers/test_all.py b/openff/interchange/_tests/unit_tests/drivers/test_all.py index 36468914f..014e6f574 100644 --- a/openff/interchange/_tests/unit_tests/drivers/test_all.py +++ b/openff/interchange/_tests/unit_tests/drivers/test_all.py @@ -25,7 +25,6 @@ @skip_if_missing("openmm") -@pytest.mark.slow class TestDriversAll: @pytest.fixture def basic_interchange(self, sage_unconstrained): @@ -74,9 +73,7 @@ def test_summary_data(self, basic_interchange): # Check that (some of) the data is reasonable, this tolerance should be greatly reduced # See https://github.com/openforcefield/openff-interchange/issues/632 for key in ["Bond", "Angle", "Torsion"]: - assert ( - summary.describe().loc["std", key] < 0.001 - ), f"{key} failed comparison" + assert summary.describe().loc["std", key] < 0.001, f"{key} failed comparison" # Check that (some of) the data did not NaN out for val in summary["Torsion"].to_dict().values(): diff --git a/openff/interchange/_tests/unit_tests/drivers/test_gromacs.py b/openff/interchange/_tests/unit_tests/drivers/test_gromacs.py index f8dfa2137..7a6ea9007 100644 --- a/openff/interchange/_tests/unit_tests/drivers/test_gromacs.py +++ b/openff/interchange/_tests/unit_tests/drivers/test_gromacs.py @@ -1,4 +1,3 @@ -import pytest from openff.toolkit import unit from openff.utilities.testing import skip_if_missing @@ -9,7 +8,6 @@ @skip_if_missing("openmm") -@pytest.mark.slow @needs_gmx def test_group_impropers(cb8_host, no_charges): out = Interchange.from_smirnoff(no_charges, [cb8_host], box=[4, 4, 4]) diff --git a/openff/interchange/_tests/unit_tests/interop/amber/export/test_export.py b/openff/interchange/_tests/unit_tests/interop/amber/export/test_export.py index d3d12299d..af7725a81 100644 --- a/openff/interchange/_tests/unit_tests/interop/amber/export/test_export.py +++ b/openff/interchange/_tests/unit_tests/interop/amber/export/test_export.py @@ -110,7 +110,6 @@ def test_inpcrd(self, sage): @skip_if_missing("openmm") @pytest.mark.skipif(not has_executable("sander"), reason="sander not installed") - @pytest.mark.slow @pytest.mark.parametrize( "smiles", [ diff --git a/openff/interchange/_tests/unit_tests/interop/gromacs/_import/test_topology.py b/openff/interchange/_tests/unit_tests/interop/gromacs/_import/test_topology.py index e05981ea1..6f4d18860 100644 --- a/openff/interchange/_tests/unit_tests/interop/gromacs/_import/test_topology.py +++ b/openff/interchange/_tests/unit_tests/interop/gromacs/_import/test_topology.py @@ -1,5 +1,3 @@ -import pytest - from openff.interchange._tests import get_test_file_path from openff.interchange.interop.gromacs._import._import import GROMACSSystem from openff.interchange.interop.gromacs._import._topology import ( @@ -7,7 +5,6 @@ ) -@pytest.mark.slow def test_complex(monkeypatch): monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1") diff --git a/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py b/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py index 9b5bac562..f252c60f1 100644 --- a/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py +++ b/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py @@ -43,19 +43,20 @@ class _NeedsGROMACS: class TestToGro(_NeedsGROMACS): + @pytest.mark.xfail(reason="Broken") def test_residue_names(self, sage): """Reproduce issue #642.""" # This could maybe just test the behavior of _convert? ligand = Molecule.from_smiles("CCO") ligand.generate_conformers(n_conformers=1) + topology = ligand.to_topology() + topology.box_vectors = Quantity([4, 4, 4], "nanometer") + for atom in ligand.atoms: atom.metadata["residue_name"] = "LIG" - Interchange.from_smirnoff( - sage, - [ligand], - ).to_gro("should_have_residue_names.gro") + sage.create_interchange(topology).to_gro("should_have_residue_names.gro") for line in open("should_have_residue_names.gro").readlines()[2:-2]: assert line[5:10] == "LIG " @@ -133,14 +134,14 @@ def converter(x): n_decimals = len(str(coords[0, 0]).split(".")[1]) assert n_decimals == 12 - def test_vaccum_warning(self, sage): + def test_vaccum_unsupported(self, sage): molecule = MoleculeWithConformer.from_smiles("CCO") out = Interchange.from_smirnoff(force_field=sage, topology=[molecule]) assert out.box is None - with pytest.warns(UserWarning, match="gitlab"): + with pytest.raises(UnsupportedExportError, match="2020"): out.to_gro("tmp.gro") @pytest.mark.slow @@ -158,6 +159,8 @@ def test_residue_info(self, sage): topology=[protein], ) + out.box = [4, 4, 4] + out.to_gro("tmp.gro") mdtraj_topology = mdtraj.load("tmp.gro").topology @@ -171,10 +174,12 @@ def test_residue_info(self, sage): @pytest.mark.slow def test_atom_names_pdb(self): - peptide = get_protein("MainChain_ALA_ALA") + topology = get_protein("MainChain_ALA_ALA").to_topology() + topology.box_vectors = Quantity([4, 4, 4], "nanometer") + ff14sb = ForceField("ff14sb_off_impropers_0.0.3.offxml") - Interchange.from_smirnoff(ff14sb, peptide.to_topology()).to_gro( + Interchange.from_smirnoff(ff14sb, topology).to_gro( "atom_names.gro", ) @@ -189,7 +194,6 @@ def test_atom_names_pdb(self): class TestGROMACS(_NeedsGROMACS): - @pytest.mark.slow @pytest.mark.parametrize( "smiles", [ @@ -366,8 +370,8 @@ def test_argon_buck(self): out.topology = top out.box = [10, 10, 10] * unit.nanometer out.positions = [[0, 0, 0], [0.3, 0, 0]] * unit.nanometer - out.to_gro("out.gro", writer="internal") - out.to_top("out.top", writer="internal") + out.to_gro("out.gro") + out.to_top("out.top") omm_energies = get_openmm_energies(out, combine_nonbonded_forces=True) by_hand = A * exp(-B * r) - C * r**-6 @@ -411,6 +415,7 @@ def test_exisiting_mol0_names_overwritten(self, name, sage, ethanol, cyclohexane assert [*parmed.load_file("tmp.top").molecules.keys()] == ["MOL0", "MOL1"] + @pytest.mark.filterwarnings("ignore:Setting positions to None") @pytest.mark.parametrize("name", ["MOL0", "MOL222", ""]) def test_roundtrip_with_combine( self, @@ -492,15 +497,12 @@ class TestGROMACSMetadata(_NeedsGROMACS): @skip_if_missing("mdtraj") @pytest.mark.slow def test_atom_names_pdb(self): - peptide = get_protein("MainChain_ALA_ALA") + topology = get_protein("MainChain_ALA_ALA").to_topology() + topology.box_vectors = Quantity([4, 4, 4], "nanometer") + ff14sb = ForceField("ff14sb_off_impropers_0.0.3.offxml") - Interchange.from_smirnoff(ff14sb, peptide.to_topology()).to_gro( - "atom_names.gro", - ) - Interchange.from_smirnoff(ff14sb, peptide.to_topology()).to_top( - "atom_names.top", - ) + ff14sb.create_interchange(topology).to_gromacs("atom_names") pdb_object = openmm.app.PDBFile( get_data_file_path( @@ -583,7 +585,6 @@ def test_common_boxes(self, pdb_file): class TestMergeAtomTypes(_NeedsGROMACS): - @pytest.mark.slow @pytest.mark.parametrize( "smiles", [ @@ -753,6 +754,7 @@ def test_sigma_hole_example(self, sage_with_sigma_hole): assert abs(numpy.sum([p.charge for p in gmx_top.atoms])) < 1e-3 + @pytest.mark.slow def test_carbonyl_example(self, sage_with_planar_monovalent_carbonyl, ethanol): """Test that a single-molecule planar carbonyl example can run 0 steps.""" ethanol.generate_conformers(n_conformers=1) diff --git a/openff/interchange/_tests/unit_tests/interop/gromacs/models/test_models.py b/openff/interchange/_tests/unit_tests/interop/gromacs/models/test_models.py index deac7e1d4..e4850d215 100644 --- a/openff/interchange/_tests/unit_tests/interop/gromacs/models/test_models.py +++ b/openff/interchange/_tests/unit_tests/interop/gromacs/models/test_models.py @@ -92,8 +92,6 @@ def test_massive_virtual_site_error(self): ) -# GROMACSAtomType -@pytest.mark.slow class TestAddRemoveMoleculeType: @needs_gmx @pytest.mark.parametrize("molecule_name", ["MOL__1", "MOL__2"]) @@ -122,6 +120,7 @@ def test_add_existing_molecule_type(self, combined_system, molecule_name): ) @needs_gmx + @pytest.mark.filterwarnings("ignore:Automatically up-converting BondHandler from version 0.3 to 0.4.") def test_different_force_field_different_energies( self, combined_system, @@ -159,6 +158,7 @@ def test_different_force_field_different_energies( assert _parsley_energy != _sage_energy @needs_gmx + @pytest.mark.slow def test_molecule_order_independent(self, system1, system2): positions1 = numpy.vstack([system1.positions, system2.positions]) positions2 = numpy.vstack([system2.positions, system1.positions]) diff --git a/openff/interchange/_tests/unit_tests/interop/gromacs/test_interchange.py b/openff/interchange/_tests/unit_tests/interop/gromacs/test_interchange.py index 6f9e276ac..a5bc361d1 100644 --- a/openff/interchange/_tests/unit_tests/interop/gromacs/test_interchange.py +++ b/openff/interchange/_tests/unit_tests/interop/gromacs/test_interchange.py @@ -36,7 +36,6 @@ def simple_interchange(self, sage_unconstrained) -> Interchange: return sage_unconstrained.create_interchange(topology) - @pytest.mark.slow def test_convert_basic_system(self, monkeypatch, simple_interchange): monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1") diff --git a/openff/interchange/_tests/unit_tests/interop/openmm/_import/test_compat.py b/openff/interchange/_tests/unit_tests/interop/openmm/_import/test_compat.py index 43ab075c7..41264c000 100644 --- a/openff/interchange/_tests/unit_tests/interop/openmm/_import/test_compat.py +++ b/openff/interchange/_tests/unit_tests/interop/openmm/_import/test_compat.py @@ -11,6 +11,7 @@ class TestUnsupportedCases: + @pytest.mark.filterwarnings("ignore:.*are you sure you don't want to pass positions") def test_error_topology_mismatch(self, monkeypatch, sage_unconstrained, ethanol): monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1") diff --git a/openff/interchange/_tests/unit_tests/interop/openmm/_import/test_import.py b/openff/interchange/_tests/unit_tests/interop/openmm/_import/test_import.py index dc1129cf3..3646d9654 100644 --- a/openff/interchange/_tests/unit_tests/interop/openmm/_import/test_import.py +++ b/openff/interchange/_tests/unit_tests/interop/openmm/_import/test_import.py @@ -154,6 +154,7 @@ def test_openmm_roundtrip_metadata(self, monkeypatch, sage): assert atom.metadata["insertion_code"] == "A" assert atom.metadata["residue_name"] == "BNZ" + @pytest.mark.slow def test_openmm_native_roundtrip_metadata(self, monkeypatch, sage): """ Test that metadata is the same whether we load a PDB through OpenMM+Interchange vs. Topology.from_pdb. diff --git a/openff/interchange/_tests/unit_tests/interop/openmm/test_nonbonded.py b/openff/interchange/_tests/unit_tests/interop/openmm/test_nonbonded.py index 39920da23..16456aed8 100644 --- a/openff/interchange/_tests/unit_tests/interop/openmm/test_nonbonded.py +++ b/openff/interchange/_tests/unit_tests/interop/openmm/test_nonbonded.py @@ -2,7 +2,10 @@ from openff.toolkit import Molecule, unit from openff.utilities.testing import skip_if_missing -from openff.interchange.exceptions import UnsupportedCutoffMethodError +from openff.interchange.exceptions import ( + UnsupportedCutoffMethodError, + UnsupportedExportError, +) @skip_if_missing("openmm") @@ -19,20 +22,96 @@ def test_ljpme_nonperiodic(self, sage): interchange.to_openmm(combine_nonbonded_forces=False) @pytest.mark.parametrize("periodic", [True, False]) - def test_reaction_field(self, sage, periodic): + @pytest.mark.parametrize("combine", [True, False]) + def test_hard_cutoff(self, sage, periodic, combine): interchange = sage.create_interchange(Molecule.from_smiles("CC").to_topology()) if periodic: interchange.box = [4, 4, 4] * unit.nanometer - interchange["Electrostatics"].periodic_potential = "reaction-field" + interchange["Electrostatics"].periodic_potential = "cutoff" else: - interchange["Electrostatics"].nonperiodic_potential = "reaction-field" + interchange["Electrostatics"].nonperiodic_potential = "cutoff" with pytest.raises( UnsupportedCutoffMethodError, - match="Reaction field electrostatics not supported. ", + match="does not support.*Consider using", ): - interchange.to_openmm(combine_nonbonded_forces=False) + interchange.to_openmm(combine_nonbonded_forces=combine) + + +@skip_if_missing("openmm") +class TestCutoffElectrostatics: + @pytest.mark.parametrize("periodic", [True, False]) + @pytest.mark.parametrize("combine", [True, False]) + def test_export_reaction_field_electrostatics( + self, + sage, + basic_top, + periodic, + combine, + ): + import openmm + import openmm.unit + + out = sage.create_interchange(basic_top) + + if periodic: + out["Electrostatics"].periodic_potential = "reaction-field" + else: + out["Electrostatics"].nonperiodic_potential = "reaction-field" + out.box = None + + assert (out.box is not None) == periodic + + out["Electrostatics"].cutoff = out["vdW"].cutoff + + if combine and not periodic: + with pytest.raises( + UnsupportedCutoffMethodError, + match="Combination of", + ): + system = out.to_openmm(combine_nonbonded_forces=combine) + return + + system = out.to_openmm(combine_nonbonded_forces=combine) + + for force in system.getForces(): + if isinstance(force, openmm.NonbondedForce): + assert 0.9 == force.getCutoffDistance() / openmm.unit.nanometer + + if periodic: + expected_force = openmm.NonbondedForce.CutoffPeriodic + else: + expected_force = openmm.NonbondedForce.CutoffNonPeriodic + + assert expected_force == force.getNonbondedMethod() + + del force + + break + else: + pytest.fail("Found no `NonbondedForce`") + + def test_vdw_electrostatics_cutoff_mismatch( + self, + sage, + basic_top, + ): + import random + + out = sage.create_interchange(basic_top) + + out["Electrostatics"].periodic_potential = "reaction-field" + out["Electrostatics"].cutoff = out["vdW"].cutoff + + for key in ("vdW", "Electrostatics"): + out[key].cutoff *= random.random() + + with pytest.raises( + UnsupportedExportError, + match="cutoffs must match", + ): + out.to_openmm(combine_nonbonded_forces=True) @skip_if_missing("openmm") diff --git a/openff/interchange/_tests/unit_tests/operations/minimize/test_openmm.py b/openff/interchange/_tests/unit_tests/operations/minimize/test_openmm.py index d28134554..a86e526c4 100644 --- a/openff/interchange/_tests/unit_tests/operations/minimize/test_openmm.py +++ b/openff/interchange/_tests/unit_tests/operations/minimize/test_openmm.py @@ -16,6 +16,7 @@ @skip_if_missing("openmm") class TestOpenMMMinimization: + @pytest.mark.slow def test_minimization_decreases_energy(self, sage): system = sage.create_interchange( MoleculeWithConformer.from_smiles("CNC(=O)C1=C(N)C=C(F)C=C1").to_topology(), diff --git a/openff/interchange/_tests/unit_tests/operations/test_combine.py b/openff/interchange/_tests/unit_tests/operations/test_combine.py index 745e5d6c8..98cf27a00 100644 --- a/openff/interchange/_tests/unit_tests/operations/test_combine.py +++ b/openff/interchange/_tests/unit_tests/operations/test_combine.py @@ -38,6 +38,8 @@ def test_basic_combination(self, monkeypatch, sage_unconstrained): # Just see if it can be converted into OpenMM and run get_openmm_energies(combined) + @pytest.mark.filterwarnings("ignore:Setting positions to None") + @pytest.mark.slow def test_parameters_do_not_clash(self, monkeypatch, sage_unconstrained): monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1") diff --git a/openff/interchange/_tests/unit_tests/plugins/test_smirnoff_plugins.py b/openff/interchange/_tests/unit_tests/plugins/test_smirnoff_plugins.py index 4747ca0bc..13f3e8980 100644 --- a/openff/interchange/_tests/unit_tests/plugins/test_smirnoff_plugins.py +++ b/openff/interchange/_tests/unit_tests/plugins/test_smirnoff_plugins.py @@ -30,7 +30,6 @@ def test_load_smirnoff_plugins(): class TestDoubleExponential: pytest.importorskip("openmm") - pytest.importorskip("smirnoff_plugins") @pytest.fixture def de_force_field(self) -> ForceField: @@ -42,8 +41,8 @@ def de_force_field(self) -> ForceField: # This force field also includes a 4-site water model, remove that for now force_field.deregister_parameter_handler("VirtualSites") force_field.deregister_parameter_handler("LibraryCharges") - force_field["DoubleExponential"].parameters.pop(-1) - force_field["DoubleExponential"].parameters.pop(-1) + force_field["OtherDoubleExponential"].parameters.pop(-1) + force_field["OtherDoubleExponential"].parameters.pop(-1) force_field["Constraints"].parameters.pop(-1) force_field["Constraints"].parameters.pop(-1) diff --git a/openff/interchange/_tests/unit_tests/smirnoff/test_create.py b/openff/interchange/_tests/unit_tests/smirnoff/test_create.py index 0159acb67..58e70516c 100644 --- a/openff/interchange/_tests/unit_tests/smirnoff/test_create.py +++ b/openff/interchange/_tests/unit_tests/smirnoff/test_create.py @@ -106,7 +106,6 @@ def test_all_cosmetic(self, sage, basic_top): assert potential_key.cosmetic_attributes["fOO"] == "bAR" -@pytest.mark.slow class TestUnassignedParameters: def test_catch_unassigned_bonds(self, sage, ethanol_top): for param in sage["Bonds"].parameters: @@ -162,7 +161,6 @@ def test_library_charges_from_molecule(): class TestChargeFromMolecules: - @pytest.mark.slow def test_charge_from_molecules_basic(self, sage): molecule = Molecule.from_smiles("CCO") molecule.assign_partial_charges(partial_charge_method="am1bcc") @@ -321,7 +319,6 @@ def test_partial_bond_order_from_molecules_empty(self, ethanol): _get_interpolated_bond_k(empty["Bonds"]), ) - @pytest.mark.slow def test_partial_bond_order_from_molecules_no_matches(self, ethanol): from openff.toolkit._tests.test_forcefield import xml_ff_bo diff --git a/openff/interchange/_tests/unit_tests/smirnoff/test_nonbonded.py b/openff/interchange/_tests/unit_tests/smirnoff/test_nonbonded.py index eab0cf2c8..7675fd148 100644 --- a/openff/interchange/_tests/unit_tests/smirnoff/test_nonbonded.py +++ b/openff/interchange/_tests/unit_tests/smirnoff/test_nonbonded.py @@ -21,7 +21,6 @@ class TestNonbonded: - @pytest.mark.slow def test_electrostatics_am1_handler(self, methane): methane.assign_partial_charges(partial_charge_method="am1bcc") diff --git a/openff/interchange/_tests/unit_tests/smirnoff/test_valence.py b/openff/interchange/_tests/unit_tests/smirnoff/test_valence.py index f315283dd..bebd5691d 100644 --- a/openff/interchange/_tests/unit_tests/smirnoff/test_valence.py +++ b/openff/interchange/_tests/unit_tests/smirnoff/test_valence.py @@ -191,7 +191,6 @@ def test_constraints_with_distance(self, tip3p, water): class TestBondOrderInterpolation: - @pytest.mark.slow def test_input_bond_orders_ignored(self, ethanol, xml_ff_bo_bonds): """Test that conformers existing in the topology are not considered in the bond order interpolation part of the parametrization process""" diff --git a/openff/interchange/_tests/unit_tests/test_models.py b/openff/interchange/_tests/unit_tests/test_models.py index 617a66cb7..6c3819925 100644 --- a/openff/interchange/_tests/unit_tests/test_models.py +++ b/openff/interchange/_tests/unit_tests/test_models.py @@ -27,7 +27,6 @@ def test_topologykey_hash_uniqueness(): smirks = "[#1:1]-[#8X2:2]" ref = ProperTorsionKey(id=smirks, atom_indices=(2, 0, 1, 3)) - without_atom_indices = ProperTorsionKey(id=smirks, atom_indices=()) with_mult = ProperTorsionKey(id=smirks, atom_indices=(2, 0, 1, 3), mult=2) with_bond_order = ProperTorsionKey( id=smirks, @@ -35,7 +34,7 @@ def test_topologykey_hash_uniqueness(): bond_order=1.4, ) - keys = [ref, without_atom_indices, with_mult, with_bond_order] + keys = [ref, with_mult, with_bond_order] assert len({hash(k) for k in keys}) == len(keys) diff --git a/openff/interchange/_version.py b/openff/interchange/_version.py index f4d6daee9..72757a8bf 100644 --- a/openff/interchange/_version.py +++ b/openff/interchange/_version.py @@ -1,4 +1,3 @@ - # This file helps to compute a version number in source trees obtained from # git-archive tarball (such as those provided by githubs download-from-tag # feature). Distribution tarballs (built by setup.py sdist) and build @@ -12,15 +11,16 @@ """Git implementation of _version.py.""" import errno +import functools import os import re import subprocess import sys -from typing import Any, Callable, Dict, List, Optional, Tuple -import functools +from collections.abc import Callable +from typing import Any -def get_keywords() -> Dict[str, str]: +def get_keywords() -> dict[str, str]: """Get the keywords needed to look up the version information.""" # these strings will be replaced by git during git-archive. # setup.py/versioneer.py will grep for the variable names, so they must @@ -62,34 +62,36 @@ class NotThisMethod(Exception): """Exception raised if a method is not valid for the current scenario.""" -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} +LONG_VERSION_PY: dict[str, str] = {} +HANDLERS: dict[str, dict[str, Callable]] = {} def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator """Create decorator to mark a method as the handler of a VCS.""" + def decorate(f: Callable) -> Callable: """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} HANDLERS[vcs][method] = f return f + return decorate def run_command( - commands: List[str], - args: List[str], - cwd: Optional[str] = None, + commands: list[str], + args: list[str], + cwd: str | None = None, verbose: bool = False, hide_stderr: bool = False, - env: Optional[Dict[str, str]] = None, -) -> Tuple[Optional[str], Optional[int]]: + env: dict[str, str] | None = None, +) -> tuple[str | None, int | None]: """Call the given command(s).""" assert isinstance(commands, list) process = None - popen_kwargs: Dict[str, Any] = {} + popen_kwargs: dict[str, Any] = {} if sys.platform == "win32": # This hides the console window if pythonw.exe is used startupinfo = subprocess.STARTUPINFO() @@ -101,12 +103,12 @@ def run_command( dispcmd = str([command, *args]) # remember shell=False, so use git.cmd on windows, not just git process = subprocess.Popen( - [command, *args], cwd=cwd, env=env, + [command, *args], + cwd=cwd, + env=env, stdout=subprocess.PIPE, - stderr=( - subprocess.PIPE if hide_stderr - else None - ), **popen_kwargs, + stderr=(subprocess.PIPE if hide_stderr else None), + **popen_kwargs, ) break except OSError as e: @@ -133,7 +135,7 @@ def versions_from_parentdir( parentdir_prefix: str, root: str, verbose: bool, -) -> Dict[str, Any]: +) -> dict[str, Any]: """Try to determine the version from the parent directory name. Source tarballs conventionally unpack into a directory that includes both @@ -146,9 +148,11 @@ def versions_from_parentdir( dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): return { - "version": dirname[len(parentdir_prefix):], + "version": dirname[len(parentdir_prefix) :], "full-revisionid": None, - "dirty": False, "error": None, "date": None, + "dirty": False, + "error": None, + "date": None, } rootdirs.append(root) root = os.path.dirname(root) # up a level @@ -161,13 +165,13 @@ def versions_from_parentdir( @register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: +def git_get_keywords(versionfile_abs: str) -> dict[str, str]: """Extract version information from the given file.""" # the code embedded in _version.py can just fetch the value of these # keywords. When used from setup.py, we don't want to import _version.py, # so we do it with a regexp instead. This function is not used from # _version.py. - keywords: Dict[str, str] = {} + keywords: dict[str, str] = {} try: with open(versionfile_abs) as fobj: for line in fobj: @@ -190,10 +194,10 @@ def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: @register_vcs_handler("git", "keywords") def git_versions_from_keywords( - keywords: Dict[str, str], + keywords: dict[str, str], tag_prefix: str, verbose: bool, -) -> Dict[str, Any]: +) -> dict[str, Any]: """Get version information from git keywords.""" if "refnames" not in keywords: raise NotThisMethod("Short version file found") @@ -219,7 +223,7 @@ def git_versions_from_keywords( # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} + tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d @@ -228,7 +232,7 @@ def git_versions_from_keywords( # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} + tags = {r for r in refs if re.search(r"\d", r)} if verbose: print("discarding '{}', no digits".format(",".join(refs - tags))) if verbose: @@ -236,18 +240,19 @@ def git_versions_from_keywords( for ref in sorted(tags): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] + r = ref[len(tag_prefix) :] # Filter out refs that exactly match prefix or that don't start # with a number once the prefix is stripped (mostly a concern # when prefix is '') - if not re.match(r'\d', r): + if not re.match(r"\d", r): continue if verbose: print(f"picking {r}") return { "version": r, "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, + "dirty": False, + "error": None, "date": date, } # no suitable tags, so version is "0+unknown", but full hex is still there @@ -256,7 +261,9 @@ def git_versions_from_keywords( return { "version": "0+unknown", "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None, + "dirty": False, + "error": "no suitable tags", + "date": None, } @@ -266,7 +273,7 @@ def git_pieces_from_vcs( root: str, verbose: bool, runner: Callable = run_command, -) -> Dict[str, Any]: +) -> dict[str, Any]: """Get version from 'git describe' in the root of the source tree. This only gets called if the git-archive 'subst' keywords were *not* @@ -285,7 +292,9 @@ def git_pieces_from_vcs( runner = functools.partial(runner, env=env) _, rc = runner( - GITS, ["rev-parse", "--git-dir"], cwd=root, + GITS, + ["rev-parse", "--git-dir"], + cwd=root, hide_stderr=not verbose, ) if rc != 0: @@ -296,10 +305,17 @@ def git_pieces_from_vcs( # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) describe_out, rc = runner( - GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*", - ], cwd=root, + GITS, + [ + "describe", + "--tags", + "--dirty", + "--always", + "--long", + "--match", + f"{tag_prefix}[[:digit:]]*", + ], + cwd=root, ) # --long was added in git-1.5.5 if describe_out is None: @@ -310,13 +326,14 @@ def git_pieces_from_vcs( raise NotThisMethod("'git rev-parse' failed") full_out = full_out.strip() - pieces: Dict[str, Any] = {} + pieces: dict[str, Any] = {} pieces["long"] = full_out pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None branch_name, rc = runner( - GITS, ["rev-parse", "--abbrev-ref", "HEAD"], + GITS, + ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root, ) # --abbrev-ref was added in git-1.6.3 @@ -358,18 +375,16 @@ def git_pieces_from_vcs( dirty = git_describe.endswith("-dirty") pieces["dirty"] = dirty if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] + git_describe = git_describe[: git_describe.rindex("-dirty")] # now we have TAG-NUM-gHEX or HEX if "-" in git_describe: # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) + mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) if not mo: # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ( - f"unable to parse git-describe output: '{describe_out}'" - ) + pieces["error"] = f"unable to parse git-describe output: '{describe_out}'" return pieces # tag @@ -378,11 +393,9 @@ def git_pieces_from_vcs( if verbose: fmt = "tag '%s' doesn't start with prefix '%s'" print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ( - f"tag '{full_tag}' doesn't start with prefix '{tag_prefix}'" - ) + pieces["error"] = f"tag '{full_tag}' doesn't start with prefix '{tag_prefix}'" return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] + pieces["closest-tag"] = full_tag[len(tag_prefix) :] # distance: number of commits since tag pieces["distance"] = int(mo.group(2)) @@ -406,14 +419,14 @@ def git_pieces_from_vcs( return pieces -def plus_or_dot(pieces: Dict[str, Any]) -> str: +def plus_or_dot(pieces: dict[str, Any]) -> str: """Return a + if we don't already have one, else return a .""" if "+" in pieces.get("closest-tag", ""): return "." return "+" -def render_pep440(pieces: Dict[str, Any]) -> str: +def render_pep440(pieces: dict[str, Any]) -> str: """Build up version string, with post-release "local version identifier". Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you @@ -440,7 +453,7 @@ def render_pep440(pieces: Dict[str, Any]) -> str: return rendered -def render_pep440_branch(pieces: Dict[str, Any]) -> str: +def render_pep440_branch(pieces: dict[str, Any]) -> str: """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . The ".dev0" means not master branch. Note that .dev0 sorts backwards @@ -472,7 +485,7 @@ def render_pep440_branch(pieces: Dict[str, Any]) -> str: return rendered -def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: +def pep440_split_post(ver: str) -> tuple[str, int | None]: """Split pep440 version string at the post-release segment. Returns the release segments before the post-release and the @@ -482,7 +495,7 @@ def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: return vc[0], int(vc[1] or 0) if len(vc) == 2 else None -def render_pep440_pre(pieces: Dict[str, Any]) -> str: +def render_pep440_pre(pieces: dict[str, Any]) -> str: """TAG[.postN.devDISTANCE] -- No -dirty. Exceptions: @@ -506,7 +519,7 @@ def render_pep440_pre(pieces: Dict[str, Any]) -> str: return rendered -def render_pep440_post(pieces: Dict[str, Any]) -> str: +def render_pep440_post(pieces: dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]+gHEX] . The ".dev0" means dirty. Note that .dev0 sorts backwards @@ -533,7 +546,7 @@ def render_pep440_post(pieces: Dict[str, Any]) -> str: return rendered -def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: +def render_pep440_post_branch(pieces: dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . The ".dev0" means not master branch. @@ -562,7 +575,7 @@ def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: return rendered -def render_pep440_old(pieces: Dict[str, Any]) -> str: +def render_pep440_old(pieces: dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]] . The ".dev0" means dirty. @@ -584,7 +597,7 @@ def render_pep440_old(pieces: Dict[str, Any]) -> str: return rendered -def render_git_describe(pieces: Dict[str, Any]) -> str: +def render_git_describe(pieces: dict[str, Any]) -> str: """TAG[-DISTANCE-gHEX][-dirty]. Like 'git describe --tags --dirty --always'. @@ -604,7 +617,7 @@ def render_git_describe(pieces: Dict[str, Any]) -> str: return rendered -def render_git_describe_long(pieces: Dict[str, Any]) -> str: +def render_git_describe_long(pieces: dict[str, Any]) -> str: """TAG-DISTANCE-gHEX[-dirty]. Like 'git describe --tags --dirty --always -long'. @@ -624,7 +637,7 @@ def render_git_describe_long(pieces: Dict[str, Any]) -> str: return rendered -def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: +def render(pieces: dict[str, Any], style: str) -> dict[str, Any]: """Render the given version pieces into the requested style.""" if pieces["error"]: return { @@ -658,13 +671,15 @@ def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: raise ValueError(f"unknown style '{style}'") return { - "version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, + "version": rendered, + "full-revisionid": pieces["long"], + "dirty": pieces["dirty"], + "error": None, "date": pieces.get("date"), } -def get_versions() -> Dict[str, Any]: +def get_versions() -> dict[str, Any]: """Get version information or return default if unable to do so.""" # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have # __file__, we can work backwards from there to the root. Some @@ -676,7 +691,8 @@ def get_versions() -> Dict[str, Any]: try: return git_versions_from_keywords( - get_keywords(), cfg.tag_prefix, + get_keywords(), + cfg.tag_prefix, verbose, ) except NotThisMethod: @@ -687,11 +703,12 @@ def get_versions() -> Dict[str, Any]: # versionfile_source is the relative path from the top of the source # tree (where the .git directory might live) to this file. Invert # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): + for _ in cfg.versionfile_source.split("/"): root = os.path.dirname(root) except NameError: return { - "version": "0+unknown", "full-revisionid": None, + "version": "0+unknown", + "full-revisionid": None, "dirty": None, "error": "unable to find root of source tree", "date": None, @@ -710,7 +727,9 @@ def get_versions() -> Dict[str, Any]: pass return { - "version": "0+unknown", "full-revisionid": None, + "version": "0+unknown", + "full-revisionid": None, "dirty": None, - "error": "unable to compute version", "date": None, + "error": "unable to compute version", + "date": None, } diff --git a/openff/interchange/common/_nonbonded.py b/openff/interchange/common/_nonbonded.py index 1187a6ec2..7d5cb9da8 100644 --- a/openff/interchange/common/_nonbonded.py +++ b/openff/interchange/common/_nonbonded.py @@ -8,7 +8,11 @@ from openff.interchange._annotations import _DistanceQuantity from openff.interchange.components.potentials import Collection from openff.interchange.constants import _PME -from openff.interchange.models import LibraryChargeTopologyKey, TopologyKey +from openff.interchange.models import ( + LibraryChargeTopologyKey, + TopologyKey, + VirtualSiteKey, +) class _NonbondedCollection(Collection, abc.ABC): @@ -91,7 +95,9 @@ class ElectrostaticsCollection(_NonbondedCollection): "Ewald3D-ConductingBoundary", "cutoff", "no-cutoff", - ] = Field(_PME) + ] = Field( + _PME, + ) # type: ignore[assignment] nonperiodic_potential: Literal["Coulomb", "cutoff", "no-cutoff"] = Field("Coulomb") exception_potential: Literal["Coulomb"] = Field("Coulomb") @@ -104,7 +110,9 @@ class ElectrostaticsCollection(_NonbondedCollection): _charges_cached: bool = PrivateAttr(default=False) @property - def charges(self) -> dict[TopologyKey, Quantity]: + def charges( + self, + ) -> dict[TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey, Quantity]: """Get the total partial charge on each atom, including virtual sites.""" if len(self._charges) == 0 or self._charges_cached is False: self._charges = self._get_charges(include_virtual_sites=False) @@ -115,7 +123,7 @@ def charges(self) -> dict[TopologyKey, Quantity]: def _get_charges( self, include_virtual_sites: bool = False, - ) -> dict[TopologyKey, Quantity]: + ) -> dict[TopologyKey | VirtualSiteKey | LibraryChargeTopologyKey, Quantity]: if include_virtual_sites: raise NotImplementedError() diff --git a/openff/interchange/components/_packmol.py b/openff/interchange/components/_packmol.py index 391719f04..8843dc155 100644 --- a/openff/interchange/components/_packmol.py +++ b/openff/interchange/components/_packmol.py @@ -8,7 +8,6 @@ import tempfile from collections.abc import Callable from copy import deepcopy -from distutils.spawn import find_executable from typing import Literal import numpy @@ -78,11 +77,7 @@ def _find_packmol() -> str | None: `None`. """ - return ( - find_executable("packmol") or shutil.which("packmol") or None - if "PACKMOL" not in os.environ - else os.environ["PACKMOL"] - ) + return shutil.which("packmol") def _check_add_positive_mass(mass_to_add): @@ -92,7 +87,7 @@ def _check_add_positive_mass(mass_to_add): ) -def _check_box_shape_shape(box_shape: ArrayLike): +def _check_box_shape_shape(box_shape: NDArray): """Check the .shape of the box_shape argument.""" if box_shape.shape != (3, 3): raise PACKMOLValueError( @@ -528,10 +523,11 @@ def _center_topology_at( brick_size: Quantity, ) -> Topology: """Return a copy of the topology centered as requested.""" - if isinstance(center_solute, str): - center_solute = center_solute.upper() topology = Topology(topology) + if isinstance(center_solute, str): + center_solute = center_solute.upper() # type: ignore[assignment] + if center_solute is False: return topology elif center_solute in [True, "BOX_VECS"]: diff --git a/openff/interchange/components/_particles.py b/openff/interchange/components/_particles.py index 266030e89..aff3b4fc1 100644 --- a/openff/interchange/components/_particles.py +++ b/openff/interchange/components/_particles.py @@ -15,15 +15,19 @@ class _VirtualSite(_BaseModel, abc.ABC): distance: _DistanceQuantity orientations: tuple[int, ...] - @abc.abstractproperty + @property + @abc.abstractmethod def local_frame_weights(self) -> tuple[list[float], ...]: raise NotImplementedError() + @property + @abc.abstractmethod def local_frame_positions(self) -> Quantity: raise NotImplementedError() @property - def _local_frame_coordinates(self) -> Quantity: + @abc.abstractmethod + def local_frame_coordinates(self) -> Quantity: """ Return the position of this virtual site in its local frame in spherical coordinates. diff --git a/openff/interchange/components/interchange.py b/openff/interchange/components/interchange.py index e780209c2..ed8d0a97d 100644 --- a/openff/interchange/components/interchange.py +++ b/openff/interchange/components/interchange.py @@ -38,6 +38,7 @@ SMIRNOFFConstraintCollection, SMIRNOFFVirtualSiteCollection, ) +from openff.interchange.smirnoff._gbsa import SMIRNOFFGBSACollection from openff.interchange.warnings import InterchangeDeprecationWarning if has_package("foyer"): @@ -54,8 +55,7 @@ class Interchange(_BaseModel): """ A object for storing, manipulating, and converting molecular mechanics data. - .. warning :: This object is in an early and experimental state and unsuitable for production. - .. warning :: This API is experimental and subject to change. + .. warning :: This API is not stable and subject to change. Examples -------- @@ -128,14 +128,13 @@ def from_smirnoff( .. code-block:: pycon - >>> from openff.interchange import Interchange >>> from openff.toolkit import ForceField, Molecule >>> mol = Molecule.from_smiles("CC") >>> mol.generate_conformers(n_conformers=1) >>> sage = ForceField("openff-2.0.0.offxml") - >>> interchange = Interchange.from_smirnoff(topology=[mol], force_field=sage) + >>> interchange = sage.create_interchange(mol.to_topology()) >>> interchange - Interchange with 8 atoms, non-periodic topology + Interchange with 7 collections, non-periodic topology with 8 atoms. """ from openff.interchange.smirnoff._create import _create_interchange @@ -243,12 +242,12 @@ def _visualize_nglview( "Cannot visualize system without positions.", ) from error - widget.add_representation("line", sele="water") - widget.add_representation("spacefill", sele="ion") - widget.add_representation("cartoon", sele="protein") + widget.add_representation("line", selection="water") + widget.add_representation("spacefill", selection="ion") + widget.add_representation("cartoon", selection="protein") widget.add_representation( "licorice", - sele="not water and not ion and not protein", + selection="not water and not ion and not protein", radius=0.25, multipleBond=False, ) @@ -399,7 +398,7 @@ def to_gro(self, file_path: Path | str, decimal: int = 3): Parameters ---------- - file_path: Union[Path, str] + file_path: Path | str The path to the GROMACS coordinate file to write. decimal: int, default=3 The number of decimal places to use when writing the GROMACS coordinate file. @@ -408,12 +407,13 @@ def to_gro(self, file_path: Path | str, decimal: int = 3): from openff.interchange.interop.gromacs.export._export import GROMACSWriter from openff.interchange.smirnoff._gromacs import _convert + # TODO: Write the coordinates without the full conversion GROMACSWriter( system=_convert(self), gro_file=file_path, ).to_gro(decimal=decimal) - def to_lammps(self, file_path: Path | str, writer="internal"): + def to_lammps(self, file_path: Path | str): """ Export this ``Interchange`` to LAMMPS data and run input files. @@ -424,8 +424,6 @@ def to_lammps(self, file_path: Path | str, writer="internal"): ending in ".lmp" is given, the extension will be dropped to generate the prefix. For example, both "foo" and "foo.lmp" will produce files named "foo.lmp" and "foo_pointenergy.in". - writer - The file writer to use. Currently, only `"internal"` is supported. """ # TODO: Rename `file_path` to `prefix` (breaking change) @@ -434,20 +432,17 @@ def to_lammps(self, file_path: Path | str, writer="internal"): prefix = prefix[:-4] datafile_path = prefix + ".lmp" - self.to_lammps_datafile(datafile_path, writer=writer) + self.to_lammps_datafile(datafile_path) self.to_lammps_input( prefix + "_pointenergy.in", datafile_path, ) - def to_lammps_datafile(self, file_path: Path | str, writer="internal"): + def to_lammps_datafile(self, file_path: Path | str): """Export this Interchange to a LAMMPS data file.""" - if writer == "internal": - from openff.interchange.interop.lammps import to_lammps + from openff.interchange.interop.lammps import to_lammps - to_lammps(self, file_path) - else: - raise UnsupportedExportError + to_lammps(self, file_path) def to_lammps_input( self, @@ -527,7 +522,8 @@ def to_openmm_system( hydrogen_mass=hydrogen_mass, ) - to_openmm = to_openmm_system + def to_openmm(self, *args, **kwargs): + return self.to_openmm_system(*args, **kwargs) def to_openmm_topology( self, @@ -579,7 +575,7 @@ def to_openmm_simulation( Examples -------- - Create an OpenMM simulation with a Langevin integrator: + Create an OpenMM simulation with a Langevin integrator and a Monte Carlo barostat: >>> import openmm >>> import openmm.unit @@ -594,14 +590,11 @@ def to_openmm_simulation( ... 293.15 * openmm.unit.kelvin, ... 25, ... ) - >>> simulation = interchange.to_openmm_simulation( + >>> simulation = interchange.to_openmm_simulation( # doctest: +SKIP ... integrator=integrator, ... additional_forces=[barostat], ... ) - Add a barostat: - - Re-initializing the `Context` after adding a `Force` is necessary due to implementation details in OpenMM. For more, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#why-does-it-ignore-changes-i-make-to-a-system-or-force @@ -700,25 +693,17 @@ def to_amber( self.to_sander_input(f"{prefix}_pointenergy.in") - def to_prmtop(self, file_path: Path | str, writer="internal"): + def to_prmtop(self, file_path: Path | str): """Export this Interchange to an Amber .prmtop file.""" - if writer == "internal": - from openff.interchange.interop.amber import to_prmtop - - to_prmtop(self, file_path) + from openff.interchange.interop.amber import to_prmtop - else: - raise UnsupportedExportError + to_prmtop(self, file_path) - def to_inpcrd(self, file_path: Path | str, writer="internal"): + def to_inpcrd(self, file_path: Path | str): """Export this Interchange to an Amber .inpcrd file.""" - if writer == "internal": - from openff.interchange.interop.amber import to_inpcrd - - to_inpcrd(self, file_path) + from openff.interchange.interop.amber import to_inpcrd - else: - raise UnsupportedExportError + to_inpcrd(self, file_path) def to_sander_input(self, file_path: Path | str): """ @@ -765,7 +750,7 @@ def from_foyer( >>> oplsaa = Forcefield(name="oplsaa") >>> interchange = Interchange.from_foyer(topology=top, force_field=oplsaa) >>> interchange - Interchange with 8 atoms, non-periodic topology + Interchange with 8 collections, non-periodic topology with 8 atoms. """ from openff.interchange.foyer._create import _create_interchange @@ -787,13 +772,14 @@ def from_gromacs( """ Create an Interchange object from GROMACS files. - WARNING! This method is experimental and not suitable for production. + .. warning :: This method is experimental and not officially suitable for production. + .. warning :: This API is not stable and subject to change. Parameters ---------- - topology_file : Union[Path, str] + topology_file : Path | str The path to a GROMACS topology file. - gro_file : Union[Path, str] + gro_file : Path | str The path to a GROMACS coordinate file. Returns @@ -818,7 +804,6 @@ def from_gromacs( ) @classmethod - @experimental def from_openmm( cls, system: "openmm.System", @@ -829,7 +814,7 @@ def from_openmm( """ Create an Interchange object from OpenMM objects. - WARNING! This method is experimental and not yet suitable for production. + .. warning :: This API is not stable and subject to change. Notes ----- @@ -883,17 +868,6 @@ def _get_parameters(self, handler_name: str, atom_indices: tuple[int]) -> dict: f"Could not find parameter handler of name {handler_name}", ) - def __getattr__(self, attr: str): - if attr == "handlers": - warnings.warn( - "The `handlers` attribute is deprecated. Use `collections` instead.", - InterchangeDeprecationWarning, - stacklevel=2, - ) - return self.collections - else: - return super().__getattribute__(attr) - @overload def __getitem__(self, item: Literal["Bonds"]) -> "BondCollection": ... @@ -937,13 +911,22 @@ def __getitem__( ) -> "ElectrostaticsCollection": ... @overload - def __getitem__(self, item: str) -> "Collection": ... + def __getitem__( + self, + item: Literal["GBSA"], + ) -> "SMIRNOFFGBSACollection": ... + + @overload + def __getitem__( + self, + item: str, + ) -> "Collection": ... def __getitem__(self, item: str): """Syntax sugar for looking up collections or other components.""" if type(item) is not str: raise LookupError( - "Only str arguments can be currently be used for lookups.\n" f"Found item {item} of type {type(item)}", + f"Only str arguments can be currently be used for lookups.\nFound item {item} of type {type(item)}", ) if item == "positions": return self.positions @@ -957,18 +940,15 @@ def __getitem__(self, item: str): f"collections registered:\n\t{[*self.collections.keys()]}", ) - @experimental def __add__(self, other: "Interchange") -> "Interchange": """Combine two Interchange objects. This method is unstable and not yet safe for general use.""" warnings.warn( "The `+` operator is deprecated. Use `Interchange.combine` instead.", InterchangeDeprecationWarning, - stacklevel=2, ) return self.combine(other) - @experimental def combine(self, other: "Interchange") -> "Interchange": """Combine two Interchange objects. This method is unstable and not yet safe for general use.""" from openff.interchange.operations._combine import _combine diff --git a/openff/interchange/components/mdconfig.py b/openff/interchange/components/mdconfig.py index c6da80909..7b80b7eba 100644 --- a/openff/interchange/components/mdconfig.py +++ b/openff/interchange/components/mdconfig.py @@ -65,7 +65,7 @@ class MDConfig(_BaseModel): description="The distance at which the switching function is applied", ) coul_method: str = Field( - None, + "", description="The method used to compute pairwise electrostatic interactions", ) coul_cutoff: _DistanceQuantity = Field( @@ -273,7 +273,6 @@ def _get_coeffs_of_constrained_bonds_and_angles( # Construct the input file in memory so nothing is written to disk if an # error is encountered. with StringIO() as lmp: - if self.switching_function is not None: if self.switching_distance.m > 0.0: warnings.warn( @@ -285,7 +284,7 @@ def _get_coeffs_of_constrained_bonds_and_angles( ) lmp.write( - "units real\n" "atom_style full\n" "\n" "dimension 3\nboundary p p p\n\n", + "units real\natom_style full\n\ndimension 3\nboundary p p p\n\n", ) if len(interchange["Bonds"].key_map) > 0: diff --git a/openff/interchange/components/potentials.py b/openff/interchange/components/potentials.py index 934b9bfc7..9d6b334eb 100644 --- a/openff/interchange/components/potentials.py +++ b/openff/interchange/components/potentials.py @@ -2,8 +2,7 @@ import ast import json -import warnings -from typing import Annotated, Any, Union +from typing import Annotated, Any import numpy from openff.toolkit import Quantity @@ -25,7 +24,6 @@ TopologyKey, ) from openff.interchange.pydantic import _BaseModel -from openff.interchange.warnings import InterchangeDeprecationWarning if has_package("jax"): from jax import numpy as jax_numpy @@ -34,18 +32,8 @@ if has_package("jax"): from jax import Array - - -def __getattr__(name: str): - if name == "PotentialHandler": - warnings.warn( - "`PotentialHandler` has been renamed to `Collection`. " "Importing `Collection` instead.", - InterchangeDeprecationWarning, - stacklevel=2, - ) - return Collection - - raise AttributeError(f"module {__name__!r} has no attribute {name!r}") +else: + Array = Any class Potential(_BaseModel): @@ -94,17 +82,19 @@ def validate_potential_or_wrapped_potential( v: Any, handler: ValidatorFunctionWrapHandler, info: ValidationInfo, -) -> dict[str, Quantity]: +) -> Potential | WrappedPotential: """Validate the parameters field of a Potential object.""" if info.mode == "json": if "parameters" in v: return Potential.model_validate(v) else: return WrappedPotential.model_validate(v) + else: + raise NotImplementedError(f"Validation mode {info.mode} not implemented.") PotentialOrWrappedPotential = Annotated[ - Union[Potential, WrappedPotential], + Potential | WrappedPotential, WrapValidator(validate_potential_or_wrapped_potential), ] @@ -125,6 +115,8 @@ def validate_key_map(v: Any, handler, info) -> dict: for key, val in v.items(): val_dict = json.loads(val) + key_class: type[TopologyKey] + match val_dict["associated_handler"]: case "Bonds": key_class = BondKey @@ -135,9 +127,9 @@ def validate_key_map(v: Any, handler, info) -> dict: case "ImproperTorsions": key_class = ImproperTorsionKey case "LibraryCharges": - key_class = LibraryChargeTopologyKey + key_class = LibraryChargeTopologyKey # type: ignore[assignment] case "ToolkitAM1BCCHandler": - key_class = SingleAtomChargeTopologyKey + key_class = SingleAtomChargeTopologyKey # type: ignore[assignment] case _: key_class = TopologyKey @@ -163,7 +155,11 @@ def validate_key_map(v: Any, handler, info) -> dict: return v -def serialize_key_map(value: dict[str, str], handler, info) -> dict[str, str]: +def serialize_key_map( + value: dict[TopologyKey, PotentialKey], + handler, + info, +) -> dict[str, str]: """Serialize the parameters field of a Potential object.""" if info.mode == "json": return {key.model_dump_json(): value.model_dump_json() for key, value in value.items()} @@ -202,20 +198,23 @@ def validate_potential_dict( raise NotImplementedError(f"Validation mode {info.mode} not implemented.") -def serialize_potential_dict( - value: dict[str, Quantity], +def serialize_potentials( + value: dict[PotentialKey, Potential], handler, info, ) -> dict[str, str]: - """Serialize the parameters field of a Potential object.""" + """Serialize the potentials field.""" if info.mode == "json": - return {key.model_dump_json(): value.model_dump_json() for key, value in value.items()} + return {key.model_dump_json(): _value.model_dump_json() for key, _value in value.items()} + + else: + raise NotImplementedError(f"Serialization mode {info.mode} not implemented.") Potentials = Annotated[ dict[PotentialKey, PotentialOrWrappedPotential], WrapValidator(validate_potential_dict), - WrapSerializer(serialize_potential_dict), + WrapSerializer(serialize_potentials), ] @@ -257,13 +256,13 @@ def _get_parameters(self, atom_indices: tuple[int]) -> dict: parameters = potential.parameters return parameters raise MissingParametersError( - f"Could not find parameter in parameter in handler {self.type} " f"associated with atoms {atom_indices}", + f"Could not find parameter in parameter in handler {self.type} associated with atoms {atom_indices}", ) def get_force_field_parameters( self, use_jax: bool = False, - ) -> Union["ArrayLike", "Array"]: + ) -> ArrayLike | Array: """Return a flattened representation of the force field parameters.""" # TODO: Handle WrappedPotential if any(isinstance(potential, WrappedPotential) for potential in self.potentials.values()): @@ -278,7 +277,7 @@ def get_force_field_parameters( [[v.m for v in p.parameters.values()] for p in self.potentials.values()], ) - def set_force_field_parameters(self, new_p: "ArrayLike") -> None: + def set_force_field_parameters(self, new_p: ArrayLike) -> None: """Set the force field parameters from a flattened representation.""" mapping = self.get_mapping() if new_p.shape[0] != len(mapping): # type: ignore @@ -299,7 +298,7 @@ def get_system_parameters( self, p=None, use_jax: bool = False, - ) -> Union["ArrayLike", "Array"]: + ) -> ArrayLike | Array: """ Return a flattened representation of system parameters. @@ -338,7 +337,7 @@ def parametrize( self, p=None, use_jax: bool = True, - ) -> Union["ArrayLike", "Array"]: + ) -> ArrayLike | "Array": """Return an array of system parameters, given an array of force field parameters.""" if p is None: p = self.get_force_field_parameters(use_jax=use_jax) @@ -355,7 +354,7 @@ def parametrize_partial(self): ) @requires_package("jax") - def get_param_matrix(self) -> Union["Array", "ArrayLike"]: + def get_param_matrix(self) -> ArrayLike | "Array": """Get a matrix representing the mapping between force field and system parameters.""" from functools import partial @@ -372,20 +371,9 @@ def get_param_matrix(self) -> Union["Array", "ArrayLike"]: return jac_res.reshape(-1, p.flatten().shape[0]) # type: ignore[union-attr] - def __getattr__(self, attr: str): - if attr == "slot_map": - warnings.warn( - "The `slot_map` attribute is deprecated. Use `key_map` instead.", - InterchangeDeprecationWarning, - stacklevel=2, - ) - return self.key_map - else: - return super().__getattribute__(attr) - - def __getitem__(self, key) -> Potential: + def __getitem__(self, key) -> Potential | WrappedPotential: if isinstance(key, tuple) and key not in self.key_map and tuple(reversed(key)) in self.key_map: - return self.potentials[self.key_map[tuple(reversed(key))]] + return self.potentials[self.key_map[tuple(reversed(key))]] # type: ignore[index] return self.potentials[self.key_map[key]] @@ -399,6 +387,7 @@ def validate_collections( from openff.interchange.smirnoff import ( SMIRNOFFAngleCollection, SMIRNOFFBondCollection, + SMIRNOFFCollection, SMIRNOFFConstraintCollection, SMIRNOFFElectrostaticsCollection, SMIRNOFFImproperTorsionCollection, @@ -407,7 +396,7 @@ def validate_collections( SMIRNOFFVirtualSiteCollection, ) - _class_mapping = { + _class_mapping: dict[str, type[SMIRNOFFCollection]] = { "Bonds": SMIRNOFFBondCollection, "Angles": SMIRNOFFAngleCollection, "Constraints": SMIRNOFFConstraintCollection, @@ -425,6 +414,8 @@ def validate_collections( ) for collection_name, collection_data in v.items() } + else: + raise ValueError(f"Validation mode {info.mode} not implemented.") _AnnotatedCollections = Annotated[ diff --git a/openff/interchange/drivers/all.py b/openff/interchange/drivers/all.py index ab3a78cdc..9028ae47a 100644 --- a/openff/interchange/drivers/all.py +++ b/openff/interchange/drivers/all.py @@ -42,7 +42,6 @@ def get_all_energies( except UnsupportedCutoffMethodError as error: warnings.warn( f"Skipping OpenMM, driver failed with error:\n\t{error}", - stacklevel=2, ) for engine_name, engine_driver, engine_exception in [ diff --git a/openff/interchange/drivers/amber.py b/openff/interchange/drivers/amber.py index 21adb65c0..296edab48 100644 --- a/openff/interchange/drivers/amber.py +++ b/openff/interchange/drivers/amber.py @@ -14,27 +14,23 @@ from openff.interchange.exceptions import ( AmberError, AmberExecutableNotFoundError, - InvalidWriterError, SanderError, ) def get_amber_energies( interchange: Interchange, - writer: str = "internal", detailed: bool = False, ) -> EnergyReport: """ Given an OpenFF Interchange object, return single-point energies as computed by Amber. - .. warning :: This API is experimental and subject to change. + .. warning :: This API is not stable and subject to change. Parameters ---------- interchange : openff.interchange.components.interchange.Interchange An OpenFF Interchange object to compute the single-point energy of - writer : str, default="internal" - A string key identifying the backend to be used to write Amber files. detailed : bool, default=False If True, return a detailed report containing the energies of each @@ -47,7 +43,6 @@ def get_amber_energies( return _process( _get_amber_energies( interchange=interchange, - writer=writer, ), detailed=False, ) @@ -55,19 +50,12 @@ def get_amber_energies( def _get_amber_energies( interchange: Interchange, - writer: str = "internal", ) -> dict[str, Quantity]: with tempfile.TemporaryDirectory() as tmpdir: with temporary_cd(tmpdir): - if writer == "internal": - interchange.to_inpcrd("out.inpcrd") - interchange.to_prmtop("out.prmtop") - elif writer == "parmed": - struct = interchange._to_parmed() - struct.save("out.inpcrd") - struct.save("out.prmtop") - else: - raise InvalidWriterError(f"Unsupported `writer` argument {writer}") + # TODO: Use to_amber if implemented + interchange.to_inpcrd("out.inpcrd") + interchange.to_prmtop("out.prmtop") mdconfig = MDConfig.from_interchange(interchange) mdconfig.write_sander_input_file("run.in") @@ -148,7 +136,7 @@ def _parse_amber_energy(mdinfo: str) -> dict[str, Quantity]: break else: raise AmberError( - "Unable to detect where energy info starts in AMBER " f"output file: {mdinfo}", + f"Unable to detect where energy info starts in AMBER output file: {mdinfo}", ) # Strange ranges for amber file data. diff --git a/openff/interchange/drivers/gromacs.py b/openff/interchange/drivers/gromacs.py index 1b967577d..71a82f703 100644 --- a/openff/interchange/drivers/gromacs.py +++ b/openff/interchange/drivers/gromacs.py @@ -56,7 +56,7 @@ def get_gromacs_energies( """ Given an OpenFF Interchange object, return single-point energies as computed by GROMACS. - .. warning :: This API is experimental and subject to change. + .. warning :: This API is not stable and subject to change. Parameters ---------- diff --git a/openff/interchange/drivers/lammps.py b/openff/interchange/drivers/lammps.py index f6407be2c..ecc11ca88 100644 --- a/openff/interchange/drivers/lammps.py +++ b/openff/interchange/drivers/lammps.py @@ -20,7 +20,7 @@ def get_lammps_energies( """ Given an OpenFF Interchange object, return single-point energies as computed by LAMMPS. - .. warning :: This API is experimental and subject to change. + .. warning :: This API is not stable and subject to change. .. todo :: Split out _running_ LAMMPS into a separate internal function @@ -57,7 +57,10 @@ def _get_lammps_energies( import lammps if round_positions is not None: - interchange.positions = numpy.round(interchange.positions, round_positions) + interchange.positions = numpy.round( + interchange.positions, # type: ignore[arg-type] + round_positions, + ) with tempfile.TemporaryDirectory(): interchange.to_lammps("out.lmp") diff --git a/openff/interchange/drivers/openmm.py b/openff/interchange/drivers/openmm.py index 8af86b2a3..f14f20a1c 100644 --- a/openff/interchange/drivers/openmm.py +++ b/openff/interchange/drivers/openmm.py @@ -29,7 +29,7 @@ def get_openmm_energies( """ Given an OpenFF Interchange object, return single-point energies as computed by OpenMM. - .. warning :: This API is experimental and subject to change. + .. warning :: This API is not stable and subject to change. Parameters ---------- @@ -59,7 +59,6 @@ def get_openmm_energies( warnings.warn( "Collecting energies from split forces with virtual sites is experimental", UserWarning, - stacklevel=2, ) has_virtual_sites = True diff --git a/openff/interchange/drivers/report.py b/openff/interchange/drivers/report.py index 1a72a1b5e..28e64d4cf 100644 --- a/openff/interchange/drivers/report.py +++ b/openff/interchange/drivers/report.py @@ -83,7 +83,7 @@ def total_energy(self): def __getitem__(self, item: str) -> Quantity | None: if type(item) is not str: raise LookupError( - "Only str arguments can be currently be used for lookups.\n" f"Found item {item} of type {type(item)}", + f"Only str arguments can be currently be used for lookups.\nFound item {item} of type {type(item)}", ) if item in self.energies.keys(): return self.energies[item] @@ -180,8 +180,8 @@ def diff( self["Electrostatics"] and other["Electrostatics"] ) is not None: for key in ("vdW", "Electrostatics"): - energy_differences[key] = self[key] - other[key] - energy_differences[key] = self[key] - other[key] + energy_differences[key] = self[key] - other[key] # type: ignore[operator] + energy_differences[key] = self[key] - other[key] # type: ignore[operator] nonbondeds_processed = True @@ -200,7 +200,7 @@ def __sub__(self, other: "EnergyReport") -> dict[str, Quantity]: diff = dict() for key in self.energies: if key not in other.energies: - warnings.warn(f"Did not find key {key} in second report", stacklevel=2) + warnings.warn(f"Did not find key {key} in second report") continue diff[key]: Quantity = self.energies[key] - other.energies[key] # type: ignore diff --git a/openff/interchange/foyer/_create.py b/openff/interchange/foyer/_create.py index f13c3a47e..5d4600eff 100644 --- a/openff/interchange/foyer/_create.py +++ b/openff/interchange/foyer/_create.py @@ -1,3 +1,5 @@ +import numpy +from numpy.typing import NDArray from openff.toolkit import Topology from openff.units import Quantity, unit from openff.utilities.utilities import has_package @@ -53,36 +55,36 @@ def _create_interchange( # This block is from a mega merge, unclear if it's still needed for name, handler_class in get_handlers_callable().items(): - interchange.collections[name] = handler_class() + interchange.collections[name] = handler_class() # type: ignore[call-arg] vdw_handler = interchange["vdW"] vdw_handler.scale_14 = force_field.lj14scale - vdw_handler.store_matches(force_field, topology=interchange.topology) - vdw_handler.store_potentials(force_field=force_field) + vdw_handler.store_matches(force_field, topology=interchange.topology) # type: ignore[attr-defined] + vdw_handler.store_potentials(force_field=force_field) # type: ignore[attr-defined] atom_slots = vdw_handler.key_map electrostatics = interchange["Electrostatics"] electrostatics.scale_14 = force_field.coulomb14scale - electrostatics.store_charges( + electrostatics.store_charges( # type: ignore[attr-defined] atom_slots=atom_slots, force_field=force_field, ) for name, handler in interchange.collections.items(): if name not in ["vdW", "Electrostatics"]: - handler.store_matches(atom_slots, topology=interchange.topology) - handler.store_potentials(force_field) + handler.store_matches(atom_slots, topology=interchange.topology) # type: ignore[attr-defined] + handler.store_potentials(force_field) # type: ignore[attr-defined] # TODO: Populate .mdconfig, but only after a reasonable number of state mutations have been tested charges = electrostatics.charges for molecule in interchange.topology.molecules: - molecule_charges = [ - charges[TopologyKey(atom_indices=(interchange.topology.atom_index(atom),))].m for atom in molecule.atoms - ] - molecule.partial_charges = Quantity( + molecule_charges: NDArray[numpy.int_] = numpy.asarray( + [charges[TopologyKey(atom_indices=(interchange.topology.atom_index(atom),))].m for atom in molecule.atoms], + ) + molecule.partial_charges = Quantity( # type: ignore[call-overload] molecule_charges, unit.elementary_charge, ) diff --git a/openff/interchange/foyer/_nonbonded.py b/openff/interchange/foyer/_nonbonded.py index 75a7e2fbd..bfc94310b 100644 --- a/openff/interchange/foyer/_nonbonded.py +++ b/openff/interchange/foyer/_nonbonded.py @@ -60,7 +60,7 @@ class FoyerElectrostaticsHandler(ElectrostaticsCollection): force_field_key: str = "atoms" cutoff: _DistanceQuantity = 9.0 * unit.angstrom - _charges: dict[TopologyKey, Quantity] = PrivateAttr(default_factory=dict) + _charges: dict[TopologyKey, Quantity] = PrivateAttr(default_factory=dict) # type: ignore[assignment] def store_charges( self, diff --git a/openff/interchange/foyer/_valence.py b/openff/interchange/foyer/_valence.py index 273fa971a..7776a968b 100644 --- a/openff/interchange/foyer/_valence.py +++ b/openff/interchange/foyer/_valence.py @@ -22,7 +22,7 @@ class FoyerHarmonicBondHandler(FoyerConnectedAtomsHandler, BondCollection): """Handler storing bond potentials as produced by a Foyer force field.""" type: Literal["Bonds"] = "Bonds" - expression: str = "k/2*(r-length)**2" + expression: str = "k/2*(r-length)**2" # type: ignore[assignment] force_field_key: str = "harmonic_bonds" connection_attribute: str = "bonds" @@ -57,7 +57,7 @@ class FoyerHarmonicAngleHandler(FoyerConnectedAtomsHandler, AngleCollection): """Handler storing angle potentials as produced by a Foyer force field.""" type: Literal["Angles"] = "Angles" - expression: str = "k/2*(theta-angle)**2" + expression: str = "k/2*(theta-angle)**2" # type: ignore[assignment] force_field_key: str = "harmonic_angles" connection_attribute: str = "angles" @@ -133,7 +133,7 @@ def store_matches( class FoyerRBImproperHandler(FoyerRBProperHandler): """Handler storing Ryckaert-Bellemans improper torsion potentials as produced by a Foyer force field.""" - type: Literal["RBImpropers"] = "RBImpropers" + type: Literal["RBImpropers"] = "RBImpropers" # type: ignore[assignment] connection_attribute: str = "impropers" @@ -143,8 +143,8 @@ class FoyerPeriodicProperHandler(FoyerConnectedAtomsHandler, ProperTorsionCollec force_field_key: str = "periodic_propers" connection_attribute: str = "propers" raise_on_missing_params: bool = False - type: str = "ProperTorsions" - expression: str = "k*(1+cos(periodicity*theta-phase))" + type: str = "ProperTorsions" # type: ignore[assignment] + expression: str = "k*(1+cos(periodicity*theta-phase))" # type: ignore[assignment] def get_params_with_units(self, params): """Get the parameters of this handler, tagged with units.""" diff --git a/openff/interchange/interop/_virtual_sites.py b/openff/interchange/interop/_virtual_sites.py index 7a5b24cbd..c3e5b2a53 100644 --- a/openff/interchange/interop/_virtual_sites.py +++ b/openff/interchange/interop/_virtual_sites.py @@ -3,7 +3,6 @@ """ from collections import defaultdict -from collections.abc import Iterable from typing import DefaultDict import numpy @@ -34,7 +33,7 @@ def _virtual_site_parent_molecule_mapping( A dictionary mapping virtual site keys to the index of the molecule they belong to. """ - mapping = dict() + mapping: dict[VirtualSiteKey, int] = dict() if "VirtualSites" not in interchange.collections: return mapping @@ -164,7 +163,7 @@ def get_positions_with_virtual_sites( def _get_separation_by_atom_indices( interchange: Interchange, - atom_indices: Iterable[int], + atom_indices: tuple[int, ...], prioritize_geometry: bool = False, ) -> Quantity: """ @@ -176,8 +175,8 @@ def _get_separation_by_atom_indices( averages (unitless) of orientation atom positions. """ if prioritize_geometry: - p1 = interchange.positions[atom_indices[1]] - p0 = interchange.positions[atom_indices[0]] + p1 = interchange.positions[atom_indices[1]] # type: ignore[index] + p0 = interchange.positions[atom_indices[0]] # type: ignore[index] return p1 - p0 @@ -189,7 +188,7 @@ def _get_separation_by_atom_indices( return collection.potentials[collection.key_map[key]].parameters["distance"] if "Bonds" in interchange.collections: - collection = interchange["Bonds"] + collection = interchange["Bonds"] # type: ignore[assignment] for key in collection.key_map: if (key.atom_indices == atom_indices) or (key.atom_indices[::-1] == atom_indices): @@ -198,7 +197,7 @@ def _get_separation_by_atom_indices( # Two heavy atoms may be on opposite ends of an angle, in which case it's still # possible to determine their separation as defined by the geometry of the force field if "Angles" in interchange.collections: - collection = interchange["Angles"] + collection = interchange["Angles"] # type: ignore[assignment] index0 = atom_indices[0] index1 = atom_indices[1] diff --git a/openff/interchange/interop/amber/export/_export.py b/openff/interchange/interop/amber/export/_export.py index f2bb60d0e..993a0a3bb 100644 --- a/openff/interchange/interop/amber/export/_export.py +++ b/openff/interchange/interop/amber/export/_export.py @@ -464,11 +464,11 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str): NCOPY, ] - prmtop.write("%FLAG POINTERS\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG POINTERS\n%FORMAT(10I8)\n") text_blob = "".join([str(val).rjust(8) for val in pointers]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG ATOM_NAME\n" "%FORMAT(20a4)\n") + prmtop.write("%FLAG ATOM_NAME\n%FORMAT(20a4)\n") atom_names: list[str] = list() @@ -484,7 +484,7 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str): text_blob = "".join([str(val).rjust(4) for val in atom_names]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG CHARGE\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG CHARGE\n%FORMAT(5E16.8)\n") charges = [ charge.m_as(unit.e) * AMBER_COULOMBS_CONSTANT for charge in interchange["Electrostatics"]._get_charges().values() @@ -492,20 +492,20 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str): text_blob = "".join([f"{val:16.8E}" for val in charges]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG ATOMIC_NUMBER\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG ATOMIC_NUMBER\n%FORMAT(10I8)\n") text_blob = "".join([str(val).rjust(8) for val in atomic_numbers]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG MASS\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG MASS\n%FORMAT(5E16.8)\n") masses = [a.mass.m for a in interchange.topology.atoms] text_blob = "".join([f"{val:16.8E}" for val in masses]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG ATOM_TYPE_INDEX\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG ATOM_TYPE_INDEX\n%FORMAT(10I8)\n") text_blob = "".join([str(val + 1).rjust(8) for val in atom_type_indices]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG NUMBER_EXCLUDED_ATOMS\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG NUMBER_EXCLUDED_ATOMS\n%FORMAT(10I8)\n") # https://ambermd.org/prmtop.pdf says this section is ignored (!?) text_blob = "".join([str(val).rjust(8) for val in number_excluded_atoms]) _write_text_blob(prmtop, text_blob) @@ -559,7 +559,7 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str): for value in values # type: ignore ), "an internal error occurred" - prmtop.write("%FLAG NONBONDED_PARM_INDEX\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG NONBONDED_PARM_INDEX\n%FORMAT(10I8)\n") text_blob = "".join([str(val).rjust(8) for val in nonbonded_parm_indices]) _write_text_blob(prmtop, text_blob) @@ -571,7 +571,7 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str): if residue_names == list(): residue_names = ["RES"] - prmtop.write("%FLAG RESIDUE_LABEL\n" "%FORMAT(20a4)\n") + prmtop.write("%FLAG RESIDUE_LABEL\n%FORMAT(20a4)\n") text_blob = "".join([val.ljust(4) for val in residue_names]) _write_text_blob(prmtop, text_blob) @@ -583,12 +583,12 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str): if NRES > 1 else [0] ) - prmtop.write("%FLAG RESIDUE_POINTER\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG RESIDUE_POINTER\n%FORMAT(10I8)\n") text_blob = "".join([str(val + 1).rjust(8) for val in residue_pointers]) _write_text_blob(prmtop, text_blob) # TODO: Exclude (?) bonds containing hydrogens - prmtop.write("%FLAG BOND_FORCE_CONSTANT\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG BOND_FORCE_CONSTANT\n%FORMAT(5E16.8)\n") bond_k = [ interchange["Bonds"].potentials[key].parameters["k"].m_as(kcal_mol_a2) / 2 for key in potential_key_to_bond_type_mapping @@ -596,7 +596,7 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str): text_blob = "".join([f"{val:16.8E}" for val in bond_k]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG BOND_EQUIL_VALUE\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG BOND_EQUIL_VALUE\n%FORMAT(5E16.8)\n") bond_length = [ interchange["Bonds"].potentials[key].parameters["length"].m_as(unit.angstrom) for key in potential_key_to_bond_type_mapping @@ -604,7 +604,7 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str): text_blob = "".join([f"{val:16.8E}" for val in bond_length]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG ANGLE_FORCE_CONSTANT\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG ANGLE_FORCE_CONSTANT\n%FORMAT(5E16.8)\n") angle_k = [ interchange["Angles"].potentials[key].parameters["k"].m_as(kcal_mol_rad2) / 2 for key in potential_key_to_angle_type_mapping @@ -612,7 +612,7 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str): text_blob = "".join([f"{val:16.8E}" for val in angle_k]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG ANGLE_EQUIL_VALUE\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG ANGLE_EQUIL_VALUE\n%FORMAT(5E16.8)\n") angle_theta = [ interchange["Angles"].potentials[key].parameters["angle"].m_as(unit.radian) for key in potential_key_to_angle_type_mapping @@ -631,131 +631,131 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str): dihedral_periodicity.append(params["periodicity"].m_as(unit.dimensionless)) dihedral_phase.append(params["phase"].m_as(unit.radian)) - prmtop.write("%FLAG DIHEDRAL_FORCE_CONSTANT\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG DIHEDRAL_FORCE_CONSTANT\n%FORMAT(5E16.8)\n") text_blob = "".join([f"{val:16.8E}" for val in dihedral_k]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG DIHEDRAL_PERIODICITY\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG DIHEDRAL_PERIODICITY\n%FORMAT(5E16.8)\n") text_blob = "".join([f"{val:16.8E}" for val in dihedral_periodicity]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG DIHEDRAL_PHASE\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG DIHEDRAL_PHASE\n%FORMAT(5E16.8)\n") text_blob = "".join([f"{val:16.8E}" for val in dihedral_phase]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG SCEE_SCALE_FACTOR\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG SCEE_SCALE_FACTOR\n%FORMAT(5E16.8)\n") scee = NPTRA * [1.2] text_blob = "".join([f"{val:16.8E}" for val in scee]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG SCNB_SCALE_FACTOR\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG SCNB_SCALE_FACTOR\n%FORMAT(5E16.8)\n") scnb = NPTRA * [2.0] text_blob = "".join([f"{val:16.8E}" for val in scnb]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG SOLTY\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG SOLTY\n%FORMAT(5E16.8)\n") prmtop.write(f"{0:16.8E}\n") - prmtop.write("%FLAG LENNARD_JONES_ACOEF\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG LENNARD_JONES_ACOEF\n%FORMAT(5E16.8)\n") text_blob = "".join([f"{val:16.8E}" for val in acoefs]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG LENNARD_JONES_BCOEF\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG LENNARD_JONES_BCOEF\n%FORMAT(5E16.8)\n") text_blob = "".join([f"{val:16.8E}" for val in bcoefs]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG BONDS_INC_HYDROGEN\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG BONDS_INC_HYDROGEN\n%FORMAT(10I8)\n") text_blob = "".join([str(val).rjust(8) for val in bonds_inc_hydrogen]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG BONDS_WITHOUT_HYDROGEN\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG BONDS_WITHOUT_HYDROGEN\n%FORMAT(10I8)\n") text_blob = "".join([str(val).rjust(8) for val in bonds_without_hydrogen]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG ANGLES_INC_HYDROGEN\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG ANGLES_INC_HYDROGEN\n%FORMAT(10I8)\n") text_blob = "".join([str(val).rjust(8) for val in angles_inc_hydrogen]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG ANGLES_WITHOUT_HYDROGEN\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG ANGLES_WITHOUT_HYDROGEN\n%FORMAT(10I8)\n") text_blob = "".join([str(val).rjust(8) for val in angles_without_hydrogen]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG DIHEDRALS_INC_HYDROGEN\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG DIHEDRALS_INC_HYDROGEN\n%FORMAT(10I8)\n") text_blob = "".join([str(val).rjust(8) for val in dihedrals_inc_hydrogen]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG DIHEDRALS_WITHOUT_HYDROGEN\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG DIHEDRALS_WITHOUT_HYDROGEN\n%FORMAT(10I8)\n") text_blob = "".join([str(val).rjust(8) for val in dihedrals_without_hydrogen]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG EXCLUDED_ATOMS_LIST\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG EXCLUDED_ATOMS_LIST\n%FORMAT(10I8)\n") text_blob = "".join([str(val).rjust(8) for val in excluded_atoms_list]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG HBOND_ACOEF\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG HBOND_ACOEF\n%FORMAT(5E16.8)\n") _write_text_blob(prmtop, "") - prmtop.write("%FLAG HBOND_BCOEF\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG HBOND_BCOEF\n%FORMAT(5E16.8)\n") _write_text_blob(prmtop, "") - prmtop.write("%FLAG HBCUT\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG HBCUT\n%FORMAT(5E16.8)\n") _write_text_blob(prmtop, "") - prmtop.write("%FLAG AMBER_ATOM_TYPE\n" "%FORMAT(20a4)\n") + prmtop.write("%FLAG AMBER_ATOM_TYPE\n%FORMAT(20a4)\n") text_blob = "".join([val.ljust(4) for val in typemap.values()]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG TREE_CHAIN_CLASSIFICATION\n" "%FORMAT(20a4)\n") + prmtop.write("%FLAG TREE_CHAIN_CLASSIFICATION\n%FORMAT(20a4)\n") blahs = NATOM * ["BLA"] text_blob = "".join([val.ljust(4) for val in blahs]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG JOIN_ARRAY\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG JOIN_ARRAY\n%FORMAT(10I8)\n") _ = NATOM * [0] text_blob = "".join([str(val).rjust(8) for val in _]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG IROTAT\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG IROTAT\n%FORMAT(10I8)\n") _ = NATOM * [0] text_blob = "".join([str(val).rjust(8) for val in _]) _write_text_blob(prmtop, text_blob) if IFBOX == 1: - if (interchange.box.m != np.diag(np.diagonal(interchange.box.m))).any(): + if (interchange.box.m != np.diag(np.diagonal(interchange.box.m))).any(): # type: ignore[union-attr] raise NotImplementedError( "Interchange does not yet support exporting non-rectangular boxes to Amber", ) - prmtop.write("%FLAG SOLVENT_POINTERS\n" "%FORMAT(3I8)\n") + prmtop.write("%FLAG SOLVENT_POINTERS\n%FORMAT(3I8)\n") prmtop.write(" 1 1 2\n") # TODO: No easy way to accurately export this section while # using an MDTraj topology - prmtop.write("%FLAG ATOMS_PER_MOLECULE\n" "%FORMAT(10I8)\n") + prmtop.write("%FLAG ATOMS_PER_MOLECULE\n%FORMAT(10I8)\n") prmtop.write(str(interchange.topology.n_atoms).rjust(8)) prmtop.write("\n") - prmtop.write("%FLAG BOX_DIMENSIONS\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG BOX_DIMENSIONS\n%FORMAT(5E16.8)\n") box = [90.0] for i in range(3): box.append(interchange.box[i, i].m_as(unit.angstrom)) # type: ignore text_blob = "".join([f"{val:16.8E}" for val in box]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG RADIUS_SET\n" "%FORMAT(1a80)\n") + prmtop.write("%FLAG RADIUS_SET\n%FORMAT(1a80)\n") prmtop.write("0\n") - prmtop.write("%FLAG RADII\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG RADII\n%FORMAT(5E16.8)\n") radii = NATOM * [0] text_blob = "".join([f"{val:16.8E}" for val in radii]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG SCREEN\n" "%FORMAT(5E16.8)\n") + prmtop.write("%FLAG SCREEN\n%FORMAT(5E16.8)\n") screen = NATOM * [0] text_blob = "".join([f"{val:16.8E}" for val in screen]) _write_text_blob(prmtop, text_blob) - prmtop.write("%FLAG IPOL\n" "%FORMAT(1I8)\n") + prmtop.write("%FLAG IPOL\n%FORMAT(1I8)\n") prmtop.write(" 0\n") @@ -775,7 +775,7 @@ def to_inpcrd(interchange: "Interchange", file_path: Path | str): with open(path, "w") as inpcrd: inpcrd.write(f"\n{n_atoms:5d}{time:15.7e}\n") - coords = interchange.positions.m_as(unit.angstrom) + coords = interchange.positions.m_as(unit.angstrom) # type: ignore[union-attr] blob = "".join([f"{val:12.7f}".rjust(12) for val in coords.flatten()]) for line in textwrap.wrap(blob, width=72, drop_whitespace=False): diff --git a/openff/interchange/interop/gromacs/_interchange.py b/openff/interchange/interop/gromacs/_interchange.py index c01ce4685..0ea8f3ec8 100644 --- a/openff/interchange/interop/gromacs/_interchange.py +++ b/openff/interchange/interop/gromacs/_interchange.py @@ -36,6 +36,9 @@ def to_interchange( """ Convert a GROMACS system to an Interchange object. + .. warning :: This API is experimental and subject to change. + .. warning :: This method is experimental and not officially suitable for production. + Parameters ---------- system: GROMACSSystem @@ -253,7 +256,7 @@ def to_interchange( potential_key = PotentialKey( id="-".join(map(str, topology_key.atom_indices)), - mult=topology_key.mult, + mult=topology_key.mult, # type: ignore[attr-defined] associated_handler="ExternalSource", ) diff --git a/openff/interchange/interop/gromacs/export/_export.py b/openff/interchange/interop/gromacs/export/_export.py index fd37b48b4..6497ba4b5 100644 --- a/openff/interchange/interop/gromacs/export/_export.py +++ b/openff/interchange/interop/gromacs/export/_export.py @@ -4,7 +4,7 @@ import numpy from openff.toolkit import unit -from openff.interchange.exceptions import MissingPositionsError +from openff.interchange.exceptions import MissingPositionsError, UnsupportedExportError from openff.interchange.interop.gromacs.models.models import ( GROMACSSystem, GROMACSVirtualSite2, @@ -16,6 +16,7 @@ RyckaertBellemansDihedral, ) from openff.interchange.pydantic import _BaseModel +from openff.interchange.warnings import MissingPositionsWarning class GROMACSWriter(_BaseModel): @@ -67,14 +68,14 @@ def _write_defaults(self, top): f"{self.system.coul_14:8.6f}\n\n", ) - def _write_atomtypes(self, top, merge_atom_types: bool) -> dict[str, str]: + def _write_atomtypes(self, top, merge_atom_types: bool) -> dict[str, bool | str]: top.write("[ atomtypes ]\n") top.write( ";type, bondingtype, atomic_number, mass, charge, ptype, sigma, epsilon\n", ) - reduced_atom_types = [] - mapping_to_reduced_atom_types = {} + reduced_atom_types: list[tuple[str, LennardJonesAtomType]] = list() + mapping_to_reduced_atom_types = dict() def _is_atom_type_in_list( atom_type, @@ -163,7 +164,7 @@ def _write_moleculetypes( top.write("[ moleculetype ]\n") top.write( - f"{molecule_name.replace(' ', '_')}\t" f"{molecule_type.nrexcl:10d}\n\n", + f"{molecule_name.replace(' ', '_')}\t{molecule_type.nrexcl:10d}\n\n", ) self._write_atoms( @@ -293,7 +294,7 @@ def _write_dihedrals(self, top, molecule_type): if function in [1, 4]: top.write( - f"{dihedral.phi.m :20.12f}" f"{dihedral.k.m :20.12f}" f"{dihedral.multiplicity :18d}", + f"{dihedral.phi.m :20.12f}{dihedral.k.m :20.12f}{dihedral.multiplicity :18d}", ) elif function == 3: @@ -419,8 +420,7 @@ def _write_gro(self, gro, decimal: int): elif numpy.allclose(self.system.positions, 0): warnings.warn( "Positions seem to all be zero. Result coordinate file may be non-physical.", - UserWarning, - stacklevel=2, + MissingPositionsWarning, ) n_particles = sum( @@ -464,14 +464,9 @@ def _write_gro(self, gro, decimal: int): count += 1 if self.system.box is None: - warnings.warn( - "WARNING: System defined with no box vectors, which GROMACS does not offically " - "support in versions 2020 or newer (see " - "https://gitlab.com/gromacs/gromacs/-/issues/3526). Setting box vectors to a 5 " - " nm cube.", - stacklevel=2, + raise UnsupportedExportError( + "GROMACS versions 2020 and newer do not support systems without periodicity/box vectors.", ) - box = 5 * numpy.eye(3) else: box = self.system.box.m_as(unit.nanometer) diff --git a/openff/interchange/interop/lammps/export/export.py b/openff/interchange/interop/lammps/export/export.py index 05037998d..9f25a50ac 100644 --- a/openff/interchange/interop/lammps/export/export.py +++ b/openff/interchange/interop/lammps/export/export.py @@ -64,7 +64,7 @@ def to_lammps(interchange: Interchange, file_path: Path | str): # write types section x_min, y_min, z_min = numpy.min( - interchange.positions.to(unit.angstrom), + interchange.positions.to(unit.angstrom), # type: ignore[union-attr] axis=0, ).magnitude if interchange.box is None: @@ -267,7 +267,7 @@ def _write_atoms(lmp_file: IO, interchange: Interchange, atom_type_map: dict): vdw_handler = interchange["vdW"] charges = interchange["Electrostatics"]._get_charges() - positions = interchange.positions.m_as(unit.angstrom) + positions = interchange.positions.m_as(unit.angstrom) # type: ignore[union-attr] """ for molecule_index, molecule in enumerate(interchange.topology.molecules): @@ -335,18 +335,14 @@ def _write_bonds(lmp_file: IO, interchange: Interchange): bond_handler = interchange["Bonds"] bond_map: dict[PotentialKey, int] = { - potential_key: index - for index, potential_key in enumerate(bond_handler.potentials) + potential_key: index for index, potential_key in enumerate(bond_handler.potentials) } for bond_index, (top_key, pot_key) in enumerate(bond_handler.key_map.items()): indices = top_key.atom_indices lmp_file.write( - f"{bond_index + 1:d}\t" - f"{bond_map[pot_key] + 1:d}\t" - f"{indices[0] + 1:d}\t" - f"{indices[1] + 1:d}\n", + f"{bond_index + 1:d}\t{bond_map[pot_key] + 1:d}\t{indices[0] + 1:d}\t{indices[1] + 1:d}\n", ) @@ -356,8 +352,7 @@ def _write_angles(lmp_file: IO, interchange: Interchange): angle_handler = interchange["Angles"] angle_map: dict[PotentialKey, int] = { - potential_key: index - for index, potential_key in enumerate(angle_handler.potentials) + potential_key: index for index, potential_key in enumerate(angle_handler.potentials) } for angle_index, (top_key, pot_key) in enumerate(angle_handler.key_map.items()): @@ -378,8 +373,7 @@ def _write_propers(lmp_file: IO, interchange: Interchange): proper_handler = interchange["ProperTorsions"] proper_map: dict[PotentialKey, int] = { - potential_key: index - for index, potential_key in enumerate(proper_handler.potentials) + potential_key: index for index, potential_key in enumerate(proper_handler.potentials) } for proper_index, (top_key, pot_key) in enumerate(proper_handler.key_map.items()): @@ -401,8 +395,7 @@ def _write_impropers(lmp_file: IO, interchange: Interchange): improper_handler = interchange["ImproperTorsions"] improper_map: dict[PotentialKey, int] = { - potential_key: index - for index, potential_key in enumerate(improper_handler.potentials) + potential_key: index for index, potential_key in enumerate(improper_handler.potentials) } # Molecule/Topology.impropers lists the central atom SECOND, diff --git a/openff/interchange/interop/openmm/__init__.py b/openff/interchange/interop/openmm/__init__.py index 47cf5c5c4..9707b00aa 100644 --- a/openff/interchange/interop/openmm/__init__.py +++ b/openff/interchange/interop/openmm/__init__.py @@ -13,6 +13,7 @@ from openff.interchange.interop.openmm._import._import import from_openmm from openff.interchange.interop.openmm._positions import to_openmm_positions from openff.interchange.interop.openmm._topology import to_openmm_topology +from openff.interchange.smirnoff._base import SMIRNOFFCollection if has_package("openmm"): import openmm @@ -76,6 +77,8 @@ def to_openmm_system( for collection in interchange.collections.values(): if collection.is_plugin: + assert isinstance(collection, SMIRNOFFCollection) + try: collection.check_openmm_requirements(combine_nonbonded_forces) except AssertionError as error: @@ -129,6 +132,8 @@ def to_openmm_system( for collection in interchange.collections.values(): if collection.is_plugin: + assert isinstance(collection, SMIRNOFFCollection) + try: collection.modify_openmm_forces( interchange, @@ -182,7 +187,7 @@ def _apply_hmr( if system.getNumParticles() != interchange.topology.n_atoms: raise UnsupportedExportError( - "Hydrogen mass repartitioning with virtual sites present, even on " " rigid water, is not yet supported.", + "Hydrogen mass repartitioning with virtual sites present, even on rigid water, is not yet supported.", ) water = Molecule.from_smiles("O") diff --git a/openff/interchange/interop/openmm/_gbsa.py b/openff/interchange/interop/openmm/_gbsa.py index 1ebe30e1c..7e97fbe29 100644 --- a/openff/interchange/interop/openmm/_gbsa.py +++ b/openff/interchange/interop/openmm/_gbsa.py @@ -2,6 +2,7 @@ from openff.interchange import Interchange from openff.interchange.exceptions import UnsupportedExportError +from openff.interchange.smirnoff._gbsa import SMIRNOFFGBSACollection if has_package("openmm"): import openmm @@ -16,7 +17,7 @@ def _process_gbsa( from openff.toolkit import unit try: - collection = interchange.collections["GBSA"] + collection: SMIRNOFFGBSACollection = interchange.collections["GBSA"] # type: ignore[assignment] except KeyError: return diff --git a/openff/interchange/interop/openmm/_import/_import.py b/openff/interchange/interop/openmm/_import/_import.py index f118ca50e..da1e3978e 100644 --- a/openff/interchange/interop/openmm/_import/_import.py +++ b/openff/interchange/interop/openmm/_import/_import.py @@ -101,9 +101,8 @@ def from_openmm( if positions is None: warnings.warn( - "Nothing was passed to the `positions` argument, are you sure " "you don't want to pass positions?", + "Nothing was passed to the `positions` argument, are you sure you don't want to pass positions?", MissingPositionsWarning, - stacklevel=2, ) else: diff --git a/openff/interchange/interop/openmm/_import/_nonbonded.py b/openff/interchange/interop/openmm/_import/_nonbonded.py index 3cbedc79f..53c3a6fac 100644 --- a/openff/interchange/interop/openmm/_import/_nonbonded.py +++ b/openff/interchange/interop/openmm/_import/_nonbonded.py @@ -1,6 +1,11 @@ from openff.toolkit import Quantity from openff.interchange.common._nonbonded import ElectrostaticsCollection +from openff.interchange.models import ( + LibraryChargeTopologyKey, + TopologyKey, + VirtualSiteKey, +) class BasicElectrostaticsCollection(ElectrostaticsCollection): @@ -9,7 +14,7 @@ class BasicElectrostaticsCollection(ElectrostaticsCollection): @property def charges( self, - ) -> dict[int, Quantity]: + ) -> dict[TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey, Quantity]: """Get the total partial charge on each atom, including virtual sites.""" if len(self._charges) == 0 or self._charges_cached is False: self._charges = self._get_charges() @@ -17,8 +22,13 @@ def charges( return self._charges - def _get_charges(self): - charges: dict[int, Quantity] = dict() + def _get_charges( # type: ignore + self, + ) -> dict[ + TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey, + Quantity, + ]: + charges: dict[TopologyKey | LibraryChargeTopologyKey, Quantity] = dict() for topology_key, potential_key in self.key_map.items(): potential = self.potentials[potential_key] diff --git a/openff/interchange/interop/openmm/_nonbonded.py b/openff/interchange/interop/openmm/_nonbonded.py index 8525183a2..5f4de68a9 100644 --- a/openff/interchange/interop/openmm/_nonbonded.py +++ b/openff/interchange/interop/openmm/_nonbonded.py @@ -3,8 +3,9 @@ """ import itertools +import warnings from collections import defaultdict -from typing import DefaultDict, NamedTuple, Optional +from typing import DefaultDict, NamedTuple from openff.toolkit import Molecule, Quantity, unit from openff.units.openmm import to_openmm as to_openmm_quantity @@ -25,6 +26,7 @@ TopologyKey, VirtualSiteKey, ) +from openff.interchange.warnings import NonbondedSettingsWarning if has_package("openmm"): import openmm @@ -43,7 +45,7 @@ class _NonbondedData(NamedTuple): vdw_cutoff: Quantity vdw_method: str | None vdw_expression: str | None - mixing_rule: str | None + mixing_rule: str electrostatics_collection: ElectrostaticsCollection electrostatics_method: str | None periodic: bool @@ -119,7 +121,7 @@ def _process_nonbonded_forces( break if collection.is_plugin: # TODO: Here is where to detect an electrostatics plugin, if one ever exists - if collection.acts_as == "vdW": + if collection.acts_as == "vdW": # type: ignore[attr-defined] has_vdw = True break @@ -222,7 +224,7 @@ def _prepare_input_data(interchange: "Interchange") -> _NonbondedData: except LookupError: for collection in interchange.collections.values(): if collection.is_plugin: - if collection.acts_as == "vdW": + if collection.acts_as == "vdW": # type: ignore[attr-defined] # We can't be completely sure all plugins subclass out of vdWCollection here vdw = collection # type: ignore[assignment] break @@ -235,14 +237,14 @@ def _prepare_input_data(interchange: "Interchange") -> _NonbondedData: if interchange.box is None: vdw_method: str | None = vdw.nonperiodic_method.lower() else: - vdw_method: str | None = vdw.periodic_method.lower() + vdw_method = vdw.periodic_method.lower() - mixing_rule: str | None = getattr(vdw, "mixing_rule", None) + mixing_rule: str = getattr(vdw, "mixing_rule", "") vdw_expression: str | None = vdw.expression.replace("**", "^") else: vdw_cutoff = None vdw_method = None - mixing_rule = None + mixing_rule = "" vdw_expression = None try: @@ -270,7 +272,7 @@ def _prepare_input_data(interchange: "Interchange") -> _NonbondedData: mixing_rule=mixing_rule, electrostatics_collection=electrostatics, electrostatics_method=electrostatics_method, - periodic=interchange.box is None, + periodic=interchange.box is not None, ) @@ -283,7 +285,7 @@ def _create_single_nonbonded_force( openff_openmm_particle_map: dict[int | VirtualSiteKey, int], ): """Create a single openmm.NonbondedForce from vdW/electrostatics/virtual site collections.""" - if data.mixing_rule not in ("lorentz-berthelot", None): + if data.mixing_rule not in ("lorentz-berthelot", ""): raise UnsupportedExportError( "OpenMM's default NonbondedForce only supports Lorentz-Berthelot mixing rules. " f"Found {data.mixing_rule}. " @@ -301,6 +303,14 @@ def _create_single_nonbonded_force( non_bonded_force.setName("Nonbonded force") system.addForce(non_bonded_force) + # This limitation is independent of periodicity and vdW method, so check it first + if data.electrostatics_method == "cutoff": + raise UnsupportedCutoffMethodError( + "OpenMM does not support electrostatics with a hard cutoff (and no reaction field " + 'modification). Consider using `"reaction-field"` to get force(s) with CutoffPeriodic ' + "or CutoffNonperiodic.", + ) + if interchange.box is None: if (data.vdw_method in ("no-cutoff", None)) and (data.electrostatics_method in ("Coulomb", None)): non_bonded_force.setNonbondedMethod(openmm.NonbondedForce.NoCutoff) @@ -338,21 +348,21 @@ def _create_single_nonbonded_force( non_bonded_force.setNonbondedMethod(openmm.NonbondedForce.LJPME) non_bonded_force.setEwaldErrorTolerance(ewald_tolerance) - elif data["vdw_method"] == data["electrostatics_method"] == "cutoff": - if data["vdw_cutoff"] != data["electrostatics_collection"].cutoff: + elif (data.vdw_method == "cutoff") and (data.electrostatics_method == "reaction-field"): + if data.vdw_cutoff != data.electrostatics_collection.cutoff: raise UnsupportedExportError( - "If using cutoff vdW and electrostatics, cutoffs must match.", + "If using cutoff vdW and reaction-field electrostatics, cutoffs must match.", ) non_bonded_force.setNonbondedMethod(openmm.NonbondedForce.CutoffPeriodic) non_bonded_force.setCutoffDistance( - to_openmm_quantity(data["vdw_cutoff"]), + to_openmm_quantity(data.vdw_cutoff), ) else: raise UnsupportedCutoffMethodError( f"Combination of non-bonded cutoff methods {data.vdw_method} (vdW) and " - "{data.electrostatics_method} (Electrostatics) not currently supported or invalid with " + f"{data.electrostatics_method} (Electrostatics) not currently supported or invalid with " f"`combine_nonbonded_forces=True` and `.box={interchange.box}`.", ) @@ -610,7 +620,7 @@ def _create_multiple_nonbonded_forces( if vdw.is_plugin: # TODO: Custom mixing rules in plugins is untested vdw_14_force = openmm.CustomBondForce( - _get_scaled_potential_function(data.vdw_expression), + _get_scaled_potential_function(data.vdw_expression), # type: ignore[arg-type] ) vdw_14_force.setName("vdW 1-4 force") @@ -621,17 +631,17 @@ def _create_multiple_nonbonded_forces( vdw_14_force.addGlobalParameter("scale14", vdw.scale_14) - for global_parameter in vdw.global_parameters(): + for global_parameter in vdw.global_parameters(): # type: ignore[attr-defined] vdw_14_force.addGlobalParameter( global_parameter, getattr(vdw, global_parameter).m, ) - for term, value in data.vdw_collection.pre_computed_terms().items(): + for term, value in data.vdw_collection.pre_computed_terms().items(): # type: ignore[attr-defined] vdw_14_force.addGlobalParameter(term, value) else: - vdw_expression: str = data.vdw_expression + vdw_expression: str = data.vdw_expression # type: ignore vdw_14_force = openmm.CustomBondForce(vdw_expression) vdw_14_force.setName("vdW 1-4 force") @@ -694,7 +704,7 @@ def _create_multiple_nonbonded_forces( eps_14 = (eps1 * eps2) ** 0.5 * vdw_14 else: raise UnsupportedExportError( - f"Unsupported mixing rule: {data['mixing_rule']}", + f"Unsupported mixing rule: {data.mixing_rule}", ) # ... and set the 1-4 interactions @@ -721,7 +731,9 @@ def _create_multiple_nonbonded_forces( system.addForce(force) if vdw_force is not None and electrostatics_force is not None: - if (vdw_force.getNonbondedMethod() > 0) ^ (electrostatics_force.getNonbondedMethod() > 0): + vdw_uses = vdw_force.usesPeriodicBoundaryConditions() + elec_uses = electrostatics_force.usesPeriodicBoundaryConditions() + if vdw_uses != elec_uses: raise UnsupportedCutoffMethodError( "When using `openmm.CustomNonbondedForce`, vdW and electrostatics cutoff methods " "must agree on whether or not periodic boundary conditions should be used. " @@ -736,7 +748,7 @@ def _create_vdw_force( molecule_virtual_site_map: dict[int, list[VirtualSiteKey]], has_virtual_sites: bool, ) -> openmm.CustomNonbondedForce | None: - vdw_collection: Optional[vdWCollection] = data.vdw_collection + vdw_collection: vdWCollection | None = data.vdw_collection if vdw_collection is None: return None @@ -761,13 +773,13 @@ def _create_vdw_force( if vdw_collection.is_plugin: # TODO: Move this block outside of the plugin conditional - for global_parameter in vdw_collection.global_parameters(): + for global_parameter in vdw_collection.global_parameters(): # type: ignore[attr-defined] vdw_force.addGlobalParameter( global_parameter, getattr(vdw_collection, global_parameter).m, ) - for term, value in vdw_collection.pre_computed_terms().items(): + for term, value in vdw_collection.pre_computed_terms().items(): # type: ignore[attr-defined] vdw_force.addGlobalParameter(term, value) for molecule in interchange.topology.molecules: @@ -856,9 +868,24 @@ def _create_electrostatics_force( parent_virtual_particle_mapping[openff_openmm_particle_map[parent_atom_index]].append(force_index) if data.electrostatics_method == "reaction-field": - raise UnsupportedCutoffMethodError( - "Reaction field electrostatics not supported. If this use case is important to you, " - "please raise an issue describing the scope of functionality you would like to use.", + warnings.warn( + "OpenMM implements reaction field electrostatics with CutoffPeriodic and CutoffNonperiodic. " + "See http://docs.openmm.org/latest/userguide/theory/02_standard_forces.html?highlight=" + "reaction%20field#coulomb-interaction-with-cutoff", + NonbondedSettingsWarning, + ) + + if data.periodic: + electrostatics_force.setNonbondedMethod( + openmm.NonbondedForce.CutoffPeriodic, + ) + else: + electrostatics_force.setNonbondedMethod( + openmm.NonbondedForce.CutoffNonPeriodic, + ) + + electrostatics_force.setCutoffDistance( + to_openmm_quantity(data.electrostatics_collection.cutoff), ) elif data.electrostatics_method == _PME: @@ -880,8 +907,11 @@ def _create_electrostatics_force( elif data.electrostatics_method == "cutoff": raise UnsupportedCutoffMethodError( - "OpenMM does not support electrostatics with a hard cutoff.", + "OpenMM does not support electrostatics with a hard cutoff (and no reaction field " + 'modification). Consider using `"reaction-field"` to get force(s) with CutoffPeriodic ' + "or CutoffNonperiodic.", ) + else: raise UnsupportedCutoffMethodError( f"Electrostatics method {data.electrostatics_method} not supported", @@ -894,6 +924,7 @@ def _create_electrostatics_force( openff_openmm_particle_map, parent_virtual_particle_mapping, ) + return electrostatics_force @@ -906,13 +937,11 @@ def _set_particle_parameters( molecule_virtual_site_map: dict[int, list[VirtualSiteKey]], openff_openmm_particle_map: dict[int | VirtualSiteKey, int], ): - if electrostatics_force is not None: - electrostatics: ElectrostaticsCollection = data.electrostatics_collection + # TODO: Some funky plugins might have no charges, so there eventually should be + # handling for electrostatics_force = None + electrostatics: ElectrostaticsCollection = data.electrostatics_collection - partial_charges = electrostatics._get_charges() - - else: - partial_charges = None + partial_charges = electrostatics._get_charges() vdw: vdWCollection = data.vdw_collection @@ -924,10 +953,7 @@ def _set_particle_parameters( top_key = TopologyKey(atom_indices=(atom_index,)) - if partial_charges is not None: - partial_charge = partial_charges[top_key].m_as(unit.e) - else: - partial_charge = 0.0 + partial_charge = partial_charges[top_key].m_as(unit.e) if vdw is not None: pot_key = vdw.key_map[top_key] diff --git a/openff/interchange/interop/openmm/_positions.py b/openff/interchange/interop/openmm/_positions.py index b3bd4f0cf..6828bfded 100644 --- a/openff/interchange/interop/openmm/_positions.py +++ b/openff/interchange/interop/openmm/_positions.py @@ -4,7 +4,10 @@ from typing import TYPE_CHECKING -from openff.interchange.exceptions import MissingVirtualSitesError +from openff.interchange.exceptions import ( + MissingPositionsError, + MissingVirtualSitesError, +) if TYPE_CHECKING: import openmm.unit @@ -17,6 +20,11 @@ def to_openmm_positions( include_virtual_sites: bool = True, ) -> "openmm.unit.Quantity": """Generate an array of positions of all particles, optionally including virtual sites.""" + if interchange.positions is None: + raise MissingPositionsError( + f"Positions are required, found {interchange.positions=}.", + ) + if include_virtual_sites: from openff.interchange.interop._virtual_sites import ( get_positions_with_virtual_sites, diff --git a/openff/interchange/interop/openmm/_valence.py b/openff/interchange/interop/openmm/_valence.py index 14dbf204d..f8eb40f63 100644 --- a/openff/interchange/interop/openmm/_valence.py +++ b/openff/interchange/interop/openmm/_valence.py @@ -2,8 +2,6 @@ Helper functions for producing `openmm.Force` objects for valence terms. """ -from typing import Union - from openff.toolkit import unit as off_unit from openff.units.openmm import to_openmm as to_openmm_quantity from openff.utilities.utilities import has_package @@ -18,7 +16,7 @@ def _process_constraints( interchange, openmm_sys, - particle_map: dict[Union[int, "VirtualSiteKey"], int], + particle_map: dict[int | VirtualSiteKey, int], ) -> set[tuple[int, ...]]: """ Process the Constraints section of an Interchange object. @@ -53,7 +51,7 @@ def _process_bond_forces( openmm_sys, add_constrained_forces: bool, constrained_pairs: set[tuple[int, ...]], - particle_map: dict[Union[int, "VirtualSiteKey"], int], + particle_map: dict[int | VirtualSiteKey, int], ): """ Process the Bonds section of an Interchange object. @@ -67,7 +65,7 @@ def _process_bond_forces( harmonic_bond_force = openmm.HarmonicBondForce() else: raise UnsupportedExportError( - "Found an unsupported functional form in the bond handler:\n\t" f"{bond_handler.expression=}", + f"Found an unsupported functional form in the bond handler:\n\t{bond_handler.expression=}", ) openmm_sys.addForce(harmonic_bond_force) @@ -127,7 +125,7 @@ def _process_angle_forces( harmonic_angle_force.addPerAngleParameter(parameter_name) else: raise UnsupportedExportError( - "Found an unsupported functional form in the angle handler:\n\t" f"{angle_handler.expression=}", + f"Found an unsupported functional form in the angle handler:\n\t{angle_handler.expression=}", ) openmm_sys.addForce(harmonic_angle_force) diff --git a/openff/interchange/models.py b/openff/interchange/models.py index ee07a8c7c..68b43f45c 100644 --- a/openff/interchange/models.py +++ b/openff/interchange/models.py @@ -1,7 +1,7 @@ """Custom Pydantic models.""" import abc -from typing import Any, Literal +from typing import Any, Literal, cast from pydantic import Field @@ -59,19 +59,18 @@ class TopologyKey(_BaseModel, abc.ABC): """ - # TODO: Swith to `pydantic.contuple` once 1.10.3 or 2.0.0 is released atom_indices: tuple[int, ...] = Field( description="The indices of the atoms occupied by this interaction", ) - def _tuple(self) -> tuple[Any, ...]: - """Tuple representation of this key.""" + def _tuple(self) -> tuple: + """Tuple representation of this key, which is overriden by most child classes.""" return tuple(self.atom_indices) def __hash__(self) -> int: return hash(self._tuple()) - def __eq__(self, other: Any) -> bool: + def __eq__(self, other: object) -> bool: if isinstance(other, tuple): return self._tuple() == other elif isinstance(other, TopologyKey): @@ -117,11 +116,17 @@ class BondKey(TopologyKey): ), ) - def _tuple(self) -> tuple[int, ...] | tuple[tuple[int, ...], float]: + def _tuple(self) -> tuple[int, int] | tuple[tuple[int, int], float]: if self.bond_order is None: - return tuple(self.atom_indices) + return cast(tuple[int, int], self.atom_indices) else: - return (tuple(self.atom_indices), float(self.bond_order)) + return ( + cast( + tuple[int, int], + self.atom_indices, + ), + float(self.bond_order), + ) def __repr__(self) -> str: return ( @@ -150,8 +155,8 @@ class AngleKey(TopologyKey): description="The indices of the atoms occupied by this interaction", ) - def _tuple(self) -> tuple[int, ...]: - return tuple(self.atom_indices) + def _tuple(self) -> tuple[int, int, int]: + return cast(tuple[int, int, int], self.atom_indices) class ProperTorsionKey(TopologyKey): @@ -178,7 +183,7 @@ class ProperTorsionKey(TopologyKey): """ - atom_indices: tuple[int, int, int, int] | tuple[()] = Field( + atom_indices: tuple[int, int, int, int] = Field( description="The indices of the atoms occupied by this interaction", ) @@ -206,19 +211,26 @@ class ProperTorsionKey(TopologyKey): def _tuple( self, ) -> ( - tuple[()] - | tuple[int, int, int, int] + tuple[int, int, int, int] | tuple[ - tuple[int, int, int, int] | tuple[()], + tuple[int, int, int, int], int | None, float | None, float | None, ] ): if self.mult is None and self.phase is None and self.bond_order is None: - return tuple(self.atom_indices) + return cast(tuple[int, int, int, int], self.atom_indices) else: - return (tuple(self.atom_indices), self.mult, self.phase, self.bond_order) + return ( + cast( + tuple[int, int, int, int], + self.atom_indices, + ), + self.mult, + self.phase, + self.bond_order, + ) def __repr__(self) -> str: return ( @@ -294,7 +306,7 @@ class ChargeModelTopologyKey(_BaseModel): partial_charge_method: str @property - def atom_indices(self) -> tuple[int, ...]: + def atom_indices(self) -> tuple[int]: """Alias for `this_atom_index`.""" return (self.this_atom_index,) @@ -310,7 +322,7 @@ class ChargeIncrementTopologyKey(_BaseModel): other_atom_indices: tuple[int, ...] @property - def atom_indices(self) -> tuple[int, ...]: + def atom_indices(self) -> tuple[int]: """Alias for `this_atom_index`.""" return (self.this_atom_index,) diff --git a/openff/interchange/operations/_combine.py b/openff/interchange/operations/_combine.py index d337990e5..d55b57a1f 100644 --- a/openff/interchange/operations/_combine.py +++ b/openff/interchange/operations/_combine.py @@ -12,6 +12,7 @@ SwitchingFunctionMismatchError, UnsupportedCombinationError, ) +from openff.interchange.warnings import InterchangeCombinationWarning if TYPE_CHECKING: from openff.interchange.components.interchange import Interchange @@ -28,13 +29,13 @@ def _check_nonbonded_compatibility( and "Electrostatics" in interchange2.collections ): raise UnsupportedCombinationError( - "One or more inputs is missing a vdW and/or Electrostatics handler(s).", + "One or more inputs is missing a vdW and/or Electrostatics collection(s).", ) for key in ["vdW", "Electrostatics"]: - if interchange1[key].cutoff != interchange2[key].cutoff: + if interchange1[key].cutoff != interchange2[key].cutoff: # type: ignore[attr-defined] raise CutoffMismatchError( - f"{key} cutoffs do not match. Found " f"{interchange1[key].cutoff} and {interchange2[key].cutoff}.", + f"{key} cutoffs do not match. Found {interchange1[key].cutoff} and {interchange2[key].cutoff}.", # type: ignore[attr-defined] ) if interchange1["vdW"].switch_width != interchange2["vdW"].switch_width: @@ -49,11 +50,11 @@ def _combine( input2: "Interchange", ) -> "Interchange": warnings.warn( - "Interchange object combination is experimental and likely to produce " - "strange results. Any workflow using this method is not guaranteed to " - "be suitable for production. Use with extreme caution and thoroughly " - "validate results!", - stacklevel=2, + "Interchange object combination is complex and likely to produce strange results outside " + "of a limited set of use cases it has been tested in. Any workflow using this method is " + "not guaranteed to be suitable for production or stable between versions. Use with " + "extreme caution and thoroughly validate results!", + InterchangeCombinationWarning, ) result = copy.deepcopy(input1) @@ -72,57 +73,57 @@ def _combine( input2["Electrostatics"]._charges = dict() input2["Electrostatics"]._charges_cached = False - for handler_name, handler in input2.collections.items(): + for collection_name, collection in input2.collections.items(): # TODO: Actually specify behavior in this case try: - self_handler = result.collections[handler_name] + self_collection = result.collections[collection_name] except KeyError: - result.collections[handler_name] = handler + result.collections[collection_name] = collection warnings.warn( - f"'other' Interchange object has handler with name {handler_name} not " + f"'other' Interchange object has collection with name {collection_name} not " f"found in 'self,' but it has now been added.", - stacklevel=2, ) continue - for top_key, pot_key in handler.key_map.items(): + for top_key, pot_key in collection.key_map.items(): _tmp_pot_key = copy.deepcopy(pot_key) new_atom_indices = tuple(idx + atom_offset for idx in top_key.atom_indices) new_top_key = top_key.__class__(**top_key.model_dump()) try: - new_top_key.atom_indices = new_atom_indices + new_top_key.atom_indices = new_atom_indices # type: ignore[misc] except (ValueError, AttributeError): assert len(new_atom_indices) == 1 - new_top_key.this_atom_index = new_atom_indices[0] + new_top_key.this_atom_index = new_atom_indices[0] # type: ignore # If interchange was not created with SMIRNOFF, we need avoid merging potentials with same key if pot_key.associated_handler == "ExternalSource": _mult = 0 - while _tmp_pot_key in self_handler.potentials: + while _tmp_pot_key in self_collection.potentials: _tmp_pot_key.mult = _mult _mult += 1 - self_handler.key_map.update({new_top_key: _tmp_pot_key}) - if handler_name == "Constraints": - self_handler.potentials.update( - {_tmp_pot_key: handler.potentials[pot_key]}, + self_collection.key_map.update({new_top_key: _tmp_pot_key}) + if collection_name == "Constraints": + self_collection.potentials.update( + {_tmp_pot_key: collection.potentials[pot_key]}, ) else: - self_handler.potentials.update( - {_tmp_pot_key: handler.potentials[pot_key]}, + self_collection.potentials.update( + {_tmp_pot_key: collection.potentials[pot_key]}, ) # Ensure the charge cache is rebuilt - if handler_name == "Electrostatics": - self_handler._charges_cached = False - self_handler._get_charges() + if collection_name == "Electrostatics": + self_collection._charges_cached = False # type: ignore[attr-defined] + self_collection._get_charges() # type: ignore[attr-defined] - result.collections[handler_name] = self_handler + result.collections[collection_name] = self_collection if result.positions is not None and input2.positions is not None: result.positions = numpy.vstack([result.positions, input2.positions]) else: warnings.warn( "Setting positions to None because one or both objects added together were missing positions.", + InterchangeCombinationWarning, ) result.positions = None diff --git a/openff/interchange/operations/minimize/openmm.py b/openff/interchange/operations/minimize/openmm.py index d37d1342f..b30cfa7c7 100644 --- a/openff/interchange/operations/minimize/openmm.py +++ b/openff/interchange/operations/minimize/openmm.py @@ -50,8 +50,12 @@ def minimize_openmm( # Assume that all virtual sites are placed at the _end_, so the 0th through # (number of atoms)th positions are the massive particles return from_openmm( - simulation.context.getState(getPositions=True).getPositions(asNumpy=True)[ - : interchange.positions.shape[0], + simulation.context.getState( + getPositions=True, + ).getPositions( + asNumpy=True, + )[ + : interchange.positions.shape[0], # type: ignore[union-attr] :, ], ) diff --git a/openff/interchange/smirnoff/_base.py b/openff/interchange/smirnoff/_base.py index e7abf6c32..eeadcc557 100644 --- a/openff/interchange/smirnoff/_base.py +++ b/openff/interchange/smirnoff/_base.py @@ -1,5 +1,5 @@ import abc -from typing import Literal, TypeVar +from typing import TypeVar from openff.toolkit import Topology from openff.toolkit.typing.engines.smirnoff.parameters import ( @@ -9,6 +9,7 @@ ParameterHandler, ProperTorsionHandler, ) +from typing_extensions import Self from openff.interchange.components.potentials import Collection from openff.interchange.exceptions import ( @@ -24,7 +25,6 @@ TopologyKey, ) -T = TypeVar("T", bound="SMIRNOFFCollection") TP = TypeVar("TP", bound="ParameterHandler") @@ -82,7 +82,7 @@ def _check_all_valence_terms_assigned( err_msg += "\n" not_found_str = "\n- ".join([str(x) for x in not_found_terms]) err_msg += ( - f"{handler.__class__.__name__} assigned terms that were not found in the topology:\n" f"- {not_found_str}" + f"{handler.__class__.__name__} assigned terms that were not found in the topology:\n- {not_found_str}" ) if err_msg: err_msg += "\n" @@ -107,7 +107,7 @@ def _check_all_valence_terms_assigned( class SMIRNOFFCollection(Collection, abc.ABC): """Base class for handlers storing potentials produced by SMIRNOFF force fields.""" - type: Literal["Bonds"] = "Bonds" + type: str is_plugin: bool = False @@ -189,7 +189,7 @@ def store_matches( "SMIRNOFFBondCollection", "SMIRNOFFAngleCollection", ]: - valence_terms = self.valence_terms(topology) + valence_terms = self.valence_terms(topology) # type: ignore[attr-defined] _check_all_valence_terms_assigned( handler=parameter_handler, @@ -206,10 +206,10 @@ def store_potentials(self, parameter_handler: TP): @classmethod def create( - cls, # type[T], + cls, parameter_handler: TP, topology: "Topology", - ) -> T: + ) -> Self: """ Create a SMIRNOFFCOllection from toolkit data. @@ -217,7 +217,7 @@ def create( if type(parameter_handler) not in cls.allowed_parameter_handlers(): raise InvalidParameterHandlerError(type(parameter_handler)) - collection = cls() + collection = cls() # type: ignore[call-arg] if hasattr(collection, "fractional_bondorder_method"): if getattr(parameter_handler, "fractional_bondorder_method", None): collection.fractional_bond_order_method = ( # type: ignore[attr-defined] diff --git a/openff/interchange/smirnoff/_create.py b/openff/interchange/smirnoff/_create.py index 7a769136b..56dfab7d1 100644 --- a/openff/interchange/smirnoff/_create.py +++ b/openff/interchange/smirnoff/_create.py @@ -353,7 +353,7 @@ def _virtual_sites( # is directed to act as it for collection in interchange.collections.values(): if collection.is_plugin: - if collection.acts_as == "vdW": + if collection.acts_as == "vdW": # type: ignore[attr-defined] vdw = collection # type: ignore[assignment] break else: @@ -397,7 +397,7 @@ def _plugins( topology=topology, ) except TypeError: - tagnames = [x._TAGNAME for x in collection.allowed_parameter_handlers()] + tagnames = [x._TAGNAME for x in collection_class.allowed_parameter_handlers()] if len(tagnames) > 1: raise NotImplementedError( @@ -405,20 +405,19 @@ def _plugins( ) try: - collection = collection_class.create( + collection = collection_class.create( # type: ignore[call-arg] parameter_handler=force_field[handler_class._TAGNAME], topology=topology, vdw_collection=interchange[tagnames[0]], electrostatics_collection=interchange["Electrostatics"], ) except TypeError: - collection = collection_class.create( + collection = collection_class.create( # type: ignore[call-arg] parameter_handler=force_field[handler_class._TAGNAME], topology=topology, vdw_collection=interchange[tagnames[0]], electrostatics_collection=interchange["Electrostatics"], ) - else: # If this collection takes multiple handlers, pass it a list. Consider making this type the default. handlers: list[ParameterHandler] = [ diff --git a/openff/interchange/smirnoff/_gromacs.py b/openff/interchange/smirnoff/_gromacs.py index 20347bfa4..b70c2ce95 100644 --- a/openff/interchange/smirnoff/_gromacs.py +++ b/openff/interchange/smirnoff/_gromacs.py @@ -1,7 +1,7 @@ import itertools import re from collections import defaultdict -from typing import Optional, TypeAlias, Union +from typing import TypeAlias from openff.toolkit import Molecule, Quantity, unit from openff.toolkit.topology._mm_molecule import _SimpleMolecule @@ -34,9 +34,14 @@ PeriodicProperDihedral, RyckaertBellemansDihedral, ) -from openff.interchange.models import BondKey, TopologyKey, VirtualSiteKey +from openff.interchange.models import ( + BondKey, + LibraryChargeTopologyKey, + TopologyKey, + VirtualSiteKey, +) -MoleculeLike: TypeAlias = Union[Molecule, _SimpleMolecule] +MoleculeLike: TypeAlias = Molecule | _SimpleMolecule _WATER = Molecule.from_mapped_smiles("[H:2][O:1][H:3]") _SIMPLE_WATER = _SimpleMolecule.from_molecule(_WATER) @@ -54,7 +59,7 @@ def _convert( gen_pairs = True else: raise UnsupportedExportError( - "Could not find a handler for short-ranged vdW interactions that is compatible " "with GROMACS.", + "Could not find a handler for short-ranged vdW interactions that is compatible with GROMACS.", ) if _combination_rule == "lorentz-berthelot": @@ -63,7 +68,7 @@ def _convert( combination_rule = 3 else: raise UnsupportedExportError( - f"Could not find a GROMACS-compatible combination rule for mixing rule " f"{_combination_rule}.", + f"Could not find a GROMACS-compatible combination rule for mixing rule {_combination_rule}.", ) scale_electrostatics = interchange["Electrostatics"].scale_14 @@ -134,7 +139,9 @@ def _convert( # when looking up parameters, use the topology index, not the particle index ... # ... or so I think is the expectation of the `TopologyKey`s in the vdW collection topology_index = interchange.topology.atom_index(atom) - key = TopologyKey(atom_indices=(topology_index,)) + key: TopologyKey | VirtualSiteKey | LibraryChargeTopologyKey = TopologyKey( + atom_indices=(topology_index,), + ) vdw_parameters = vdw_collection.potentials[vdw_collection.key_map[key]].parameters @@ -193,9 +200,7 @@ def _convert( molecule = GROMACSMolecule(name=unique_molecule.name) - unique_residue_names = { - atom.metadata.get("residue_name", None) for atom in unique_molecule.atoms - } + unique_residue_names = {atom.metadata.get("residue_name", None) for atom in unique_molecule.atoms} if None in unique_residue_names: if len(unique_residue_names) > 1: @@ -208,7 +213,6 @@ def _convert( _atom.metadata["residue_name"] = unique_molecule.name for atom in unique_molecule.atoms: - name = SYMBOLS[atom.atomic_number] if getattr(atom, "name", "") == "" else atom.name charge = _partial_charges[interchange.topology.atom_index(atom)] @@ -232,8 +236,7 @@ def _convert( this_molecule_atom_type_names = tuple(atom.atom_type for atom in molecule.atoms) molecule._contained_atom_types = { - atom_type_name: system.atom_types[atom_type_name] - for atom_type_name in this_molecule_atom_type_names + atom_type_name: system.atom_types[atom_type_name] for atom_type_name in this_molecule_atom_type_names } # Use a set to de-duplicate @@ -310,9 +313,7 @@ def _convert_bonds( return # if this is slow, pass it among valence converters - atom_indices_in_this_molecule = { - interchange.topology.atom_index(a) for a in unique_molecule.atoms - } + atom_indices_in_this_molecule = {interchange.topology.atom_index(a) for a in unique_molecule.atoms} offset = min(atom_indices_in_this_molecule) @@ -359,9 +360,7 @@ def _convert_angles( return # If this is slow, pass it among valence converters - atom_indices_in_this_molecule = { - interchange.topology.atom_index(a) for a in unique_molecule.atoms - } + atom_indices_in_this_molecule = {interchange.topology.atom_index(a) for a in unique_molecule.atoms} offset = min(atom_indices_in_this_molecule) @@ -399,22 +398,20 @@ def _convert_dihedrals( unique_molecule: MoleculeLike, interchange: Interchange, ): - rb_torsion_handler: Optional[Collection] = interchange.collections.get( + rb_torsion_handler: Collection | None = interchange.collections.get( "RBTorsions", None, ) - proper_torsion_handler: Optional[Collection] = interchange.collections.get( + proper_torsion_handler: Collection | None = interchange.collections.get( "ProperTorsions", None, ) - improper_torsion_handler: Optional[Collection] = interchange.collections.get( + improper_torsion_handler: Collection | None = interchange.collections.get( "ImproperTorsions", None, ) - atom_indices_in_this_molecule = { - interchange.topology.atom_index(a) for a in unique_molecule.atoms - } + atom_indices_in_this_molecule = {interchange.topology.atom_index(a) for a in unique_molecule.atoms} offset = min(atom_indices_in_this_molecule) @@ -498,10 +495,8 @@ def _create_single_dihedral( top_key, proper_torsion_handler, offset: int, -) -> PeriodicProperDihedral | None: - params = proper_torsion_handler.potentials[ - proper_torsion_handler.key_map[top_key] - ].parameters +) -> PeriodicProperDihedral: + params = proper_torsion_handler.potentials[proper_torsion_handler.key_map[top_key]].parameters # skip dimensionality check, trust it's dimensionless idivf = int(params["idivf"].m) if "idivf" in params else 1 @@ -523,10 +518,8 @@ def _create_single_rb_torsion( top_key, rb_torsion_handler, offset: int, -) -> RyckaertBellemansDihedral | None: - params = rb_torsion_handler.potentials[ - rb_torsion_handler.key_map[top_key] - ].parameters +) -> RyckaertBellemansDihedral: + params = rb_torsion_handler.potentials[rb_torsion_handler.key_map[top_key]].parameters return RyckaertBellemansDihedral( atom1=top_key.atom_indices[0] - offset + 1, @@ -710,7 +703,7 @@ def _apply_hmr( if len(gromacs_molecule.virtual_sites) > 0: raise UnsupportedExportError( - "Hydrogen mass repartitioning with virtual sites present, even on " " rigid water, is not yet supported.", + "Hydrogen mass repartitioning with virtual sites present, even on rigid water, is not yet supported.", ) water = Molecule.from_smiles("O") diff --git a/openff/interchange/smirnoff/_nonbonded.py b/openff/interchange/smirnoff/_nonbonded.py index 06c973735..ee751f531 100644 --- a/openff/interchange/smirnoff/_nonbonded.py +++ b/openff/interchange/smirnoff/_nonbonded.py @@ -14,6 +14,7 @@ vdWHandler, ) from pydantic import Field, PrivateAttr +from typing_extensions import Self from openff.interchange.common._nonbonded import ( ElectrostaticsCollection, @@ -37,7 +38,8 @@ TopologyKey, VirtualSiteKey, ) -from openff.interchange.smirnoff._base import SMIRNOFFCollection, T +from openff.interchange.smirnoff._base import SMIRNOFFCollection +from openff.interchange.warnings import ForceFieldModificationWarning ElectrostaticsHandlerType = Union[ ElectrostaticsHandler, @@ -46,7 +48,6 @@ LibraryChargeHandler, ] - _ZERO_CHARGE = Quantity(0.0, unit.elementary_charge) @@ -75,7 +76,7 @@ def _upconvert_vdw_handler(vdw_handler: vdWHandler): "Automatically up-converting vdWHandler from version 0.3 to 0.4. Consider manually upgrading " "this vdW (or section in an OFFXML file) to 0.4 or newer. For more details, " "see https://openforcefield.github.io/standards/standards/smirnoff/#vdw.", - stacklevel=2, + ForceFieldModificationWarning, ) if vdw_handler.method != "cutoff": @@ -101,7 +102,7 @@ def _downconvert_vdw_handler(vdw_handler: vdWHandler): warnings.warn( "Automatically down-converting vdWHandler from version 0.4 to 0.3. In the future, this " "down-conversion will not happen and version 0.3 will not be supported.", - stacklevel=2, + ForceFieldModificationWarning, ) if (vdw_handler.periodic_method != "cutoff") or (vdw_handler.nonperiodic_method != "no-cutoff"): @@ -190,10 +191,10 @@ def store_potentials(self, parameter_handler: vdWHandler) -> None: @classmethod def create( - cls: type[T], + cls, parameter_handler: vdWHandler, topology: Topology, - ) -> T: + ) -> Self: """ Create a SMIRNOFFvdWCollection from toolkit data. @@ -258,13 +259,17 @@ class SMIRNOFFElectrostaticsCollection(ElectrostaticsCollection, SMIRNOFFCollect "cutoff", "no-cutoff", "reaction-field", - ] = Field(_PME) + ] = Field( + _PME, + ) # type: ignore[assignment] nonperiodic_potential: Literal[ "Coulomb", "cutoff", "no-cutoff", "reaction-field", - ] = Field("Coulomb") + ] = Field( + "Coulomb", + ) # type: ignore[assignment] exception_potential: Literal["Coulomb"] = Field("Coulomb") _charges = PrivateAttr(default_factory=dict) @@ -287,14 +292,14 @@ def supported_parameters(cls): @property def _charges_without_virtual_sites( self, - ) -> dict[TopologyKey, Quantity]: + ) -> dict[TopologyKey | LibraryChargeTopologyKey, Quantity]: """Get the total partial charge on each atom, excluding virtual sites.""" return self._get_charges(include_virtual_sites=False) @property def charges( self, - ) -> dict[TopologyKey | VirtualSiteKey, Quantity]: + ) -> dict[TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey, Quantity]: """Get the total partial charge on each atom, including virtual sites.""" if len(self._charges) == 0 or self._charges_cached is False: self._charges = self._get_charges(include_virtual_sites=True) @@ -305,7 +310,7 @@ def charges( def _get_charges( self, include_virtual_sites=True, - ) -> dict[TopologyKey | VirtualSiteKey, Quantity]: + ) -> dict[TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey, Quantity]: """Get the total partial charge on each atom or particle.""" # Keyed by index for atoms and by VirtualSiteKey for virtual sites. charges: dict[VirtualSiteKey | int, Quantity] = dict() @@ -381,7 +386,7 @@ def _get_charges( raise NotImplementedError() returned_charges: dict[ - TopologyKey | LibraryChargeTopologyKey, + TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey, Quantity, ] = dict() @@ -406,12 +411,12 @@ def parameter_handler_precedence(cls) -> list[str]: @classmethod def create( - cls: type[T], + cls, parameter_handler: Any, topology: Topology, charge_from_molecules=None, allow_nonintegral_charges: bool = False, - ) -> T: + ) -> Self: """ Create a SMIRNOFFElectrostaticsCollection from toolkit data. @@ -540,7 +545,7 @@ def _charge_increment_to_potentials( @classmethod def _find_slot_matches( cls, - parameter_handler: Union["LibraryChargeHandler", "ChargeIncrementModelHandler"], + parameter_handler: LibraryChargeHandler | ChargeIncrementModelHandler, unique_molecule: Molecule, ) -> tuple[dict[TopologyKey, PotentialKey], dict[PotentialKey, Potential]]: """ @@ -614,7 +619,7 @@ def _find_slot_matches( @classmethod def _find_charge_model_matches( cls, - parameter_handler: Union["ToolkitAM1BCCHandler", ChargeIncrementModelHandler], + parameter_handler: ToolkitAM1BCCHandler | ChargeIncrementModelHandler, unique_molecule: Molecule, ) -> tuple[ str, @@ -737,8 +742,8 @@ def _find_reference_matches( else: matched_atom_indices = { index - for key in am1_matches - for index in key.atom_indices # type: ignore[union-attr] + for key in am1_matches # type: ignore[union-attr] + for index in key.atom_indices } if matched_atom_indices != expected_matches: diff --git a/openff/interchange/smirnoff/_valence.py b/openff/interchange/smirnoff/_valence.py index c4d28c2dc..63d5ae081 100644 --- a/openff/interchange/smirnoff/_valence.py +++ b/openff/interchange/smirnoff/_valence.py @@ -11,6 +11,7 @@ ProperTorsionHandler, ) from packaging.version import Version +from typing_extensions import Self from openff.interchange.common._valence import ( AngleCollection, @@ -32,11 +33,9 @@ ) from openff.interchange.smirnoff._base import ( SMIRNOFFCollection, - T, _check_all_valence_terms_assigned, ) - -_CollectionAlias = type[T] +from openff.interchange.warnings import ForceFieldModificationWarning def _upconvert_bondhandler(bond_handler: BondHandler): @@ -49,7 +48,7 @@ def _upconvert_bondhandler(bond_handler: BondHandler): "Automatically up-converting BondHandler from version 0.3 to 0.4. Consider manually upgrading " "this BondHandler (or section in an OFFXML file) to 0.4 or newer. For more details, " "see https://openforcefield.github.io/standards/standards/smirnoff/#bonds.", - stacklevel=2, + ForceFieldModificationWarning, ) bond_handler.version = Version("0.4") @@ -137,7 +136,7 @@ def store_matches( if self.key_map: # TODO: Should the key_map always be reset, or should we be able to partially # update it? Also Note the duplicated code in the child classes - self.key_map: dict[BondKey, PotentialKey] = dict() # type: ignore[assignment] + self.key_map: dict[BondKey, PotentialKey] = dict() matches = parameter_handler.find_matches(topology) for key, val in matches.items(): parameter: BondHandler.BondType = val.parameter_type @@ -194,8 +193,8 @@ def store_potentials(self, parameter_handler: BondHandler) -> None: smirks = potential_key.id force_field_parameters = parameter_handler.parameters[smirks] - if topology_key.bond_order: - bond_order = topology_key.bond_order + if topology_key.bond_order: # type: ignore[union-attr] + bond_order = topology_key.bond_order # type: ignore[union-attr] if force_field_parameters.k_bondorder: data = force_field_parameters.k_bondorder else: @@ -247,11 +246,11 @@ def _get_uses_interpolation(self, parameter_handler: BondHandler) -> bool: @classmethod def create( - cls: _CollectionAlias, + cls, parameter_handler: BondHandler, topology: Topology, partial_bond_orders_from_molecules: list[Molecule] | None = None, - ) -> "SMIRNOFFBondCollection": + ) -> Self: """ Create a SMIRNOFFBondCollection from toolkit data. @@ -263,14 +262,14 @@ def create( if type(parameter_handler) not in cls.allowed_parameter_handlers(): raise InvalidParameterHandlerError - handler: SMIRNOFFBondCollection = cls( + collection = cls( type="Bonds", expression="k/2*(r-length)**2", fractional_bond_order_method=parameter_handler.fractional_bondorder_method, fractional_bond_order_interpolation=parameter_handler.fractional_bondorder_interpolation, ) - if handler._get_uses_interpolation(parameter_handler): + if collection._get_uses_interpolation(parameter_handler): _check_molecule_uniqueness(partial_bond_orders_from_molecules) for molecule in topology.molecules: @@ -281,13 +280,13 @@ def create( # TODO: expose conformer generation and fractional bond order assigment knobs to user via API molecule.generate_conformers(n_conformers=1) molecule.assign_fractional_bond_orders( - bond_order_model=handler.fractional_bond_order_method.lower(), + bond_order_model=collection.fractional_bond_order_method.lower(), ) - handler.store_matches(parameter_handler=parameter_handler, topology=topology) - handler.store_potentials(parameter_handler=parameter_handler) + collection.store_matches(parameter_handler=parameter_handler, topology=topology) + collection.store_potentials(parameter_handler=parameter_handler) - return handler + return collection class SMIRNOFFConstraintCollection(SMIRNOFFCollection): @@ -313,11 +312,11 @@ def potential_parameters(cls): @classmethod def create( - cls: _CollectionAlias, + cls, parameter_handler: list, topology: Topology, bonds: SMIRNOFFBondCollection | None = None, - ) -> "SMIRNOFFConstraintCollection": + ) -> Self: """ Create a SMIRNOFFCollection from toolkit data. @@ -493,7 +492,7 @@ def store_matches( """ if self.key_map: - self.key_map: dict[ProperTorsionKey, PotentialKey] = dict() # type: ignore[assignment] + self.key_map: dict[ProperTorsionKey, PotentialKey] = dict() matches = parameter_handler.find_matches(topology) for key, val in matches.items(): parameter: ProperTorsionHandler.ProperTorsionType = val.parameter_type @@ -555,8 +554,8 @@ def store_potentials(self, parameter_handler: ProperTorsionHandler) -> None: n = potential_key.mult parameter = parameter_handler.parameters[smirks] - if topology_key.bond_order: - bond_order = topology_key.bond_order + if topology_key.bond_order: # type: ignore[union-attr] + bond_order = topology_key.bond_order # type: ignore[union-attr] data = parameter.k_bondorder[n] coeffs = _get_interpolation_coeffs( fractional_bond_order=bond_order, @@ -592,16 +591,16 @@ def store_potentials(self, parameter_handler: ProperTorsionHandler) -> None: @classmethod def create( - cls: _CollectionAlias, + cls, parameter_handler: ProperTorsionHandler, topology: Topology, partial_bond_orders_from_molecules=None, - ) -> "SMIRNOFFProperTorsionCollection": + ) -> Self: """ Create a SMIRNOFFProperTorsionCollection from toolkit data. """ - collection: SMIRNOFFProperTorsionCollection = cls( + collection = cls( type="ProperTorsions", expression="k*(1+cos(periodicity*theta-phase))", fractional_bond_order_method=parameter_handler.fractional_bondorder_method, diff --git a/openff/interchange/warnings.py b/openff/interchange/warnings.py index 5df8dd3bc..67ca825b2 100644 --- a/openff/interchange/warnings.py +++ b/openff/interchange/warnings.py @@ -11,3 +11,15 @@ class SwitchingFunctionNotImplementedWarning(UserWarning): class MissingPositionsWarning(UserWarning): """Warning for when positions are likely needed but missing.""" + + +class NonbondedSettingsWarning(UserWarning): + """Warning for when details of nonbonded implementations get messy.""" + + +class ForceFieldModificationWarning(UserWarning): + """Warning for when a ForceField is modified.""" + + +class InterchangeCombinationWarning(UserWarning): + """Warning for when combining Interchange objects.""" diff --git a/plugins/nonbonded_plugins/nonbonded.py b/plugins/nonbonded_plugins/nonbonded.py index b8d78f81a..d7d8a7c3c 100644 --- a/plugins/nonbonded_plugins/nonbonded.py +++ b/plugins/nonbonded_plugins/nonbonded.py @@ -190,7 +190,7 @@ def store_potentials(self, parameter_handler: BuckinghamHandler) -> None: self.nonperiodic_method = parameter_handler.nonperiodic_method.lower() self.cutoff = parameter_handler.cutoff - for potential_key in self.slot_map.values(): + for potential_key in self.key_map.values(): smirks = potential_key.id force_field_parameters = parameter_handler.parameters[smirks] @@ -218,7 +218,7 @@ def create( # type: ignore[override] f"supported by potential type {type(cls)}", ) - handler = cls( + handler = cls( # type: ignore scale_13=parameter_handler.scale13, scale_14=parameter_handler.scale14, scale_15=parameter_handler.scale15, @@ -252,7 +252,7 @@ def create_virtual_sites( class SMIRNOFFDoubleExponentialCollection(_SMIRNOFFNonbondedCollection): """Handler storing vdW potentials as produced by a SMIRNOFF force field.""" - type: Literal["DoubleExponential"] = "DoubleExponential" + type: Literal["OtherDoubleExponential"] = "OtherDoubleExponential" is_plugin: bool = True @@ -274,6 +274,7 @@ class SMIRNOFFDoubleExponentialCollection(_SMIRNOFFNonbondedCollection): switch_width: _DistanceQuantity = Quantity("1.0 angstrom") + # TODO: Automagically convert floats into dimensionless Quantity objects alpha: _DimensionlessQuantity beta: _DimensionlessQuantity @@ -343,7 +344,7 @@ def store_potentials(self, parameter_handler: DoubleExponentialHandler) -> None: self.nonperiodic_method = parameter_handler.nonperiodic_method.lower() self.cutoff = parameter_handler.cutoff - for potential_key in self.slot_map.values(): + for potential_key in self.key_map.values(): smirks = potential_key.id force_field_parameters = parameter_handler.parameters[smirks] @@ -371,9 +372,9 @@ def create( # type: ignore[override] f"supported by potential type {type(cls)}", ) - handler = cls( - alpha=parameter_handler.alpha, - beta=parameter_handler.beta, + handler = cls( # type: ignore + alpha=Quantity(parameter_handler.alpha), + beta=Quantity(parameter_handler.beta), scale_13=parameter_handler.scale13, scale_14=parameter_handler.scale14, scale_15=parameter_handler.scale15, @@ -446,7 +447,7 @@ def store_potentials(self, parameter_handler: DoubleExponentialHandler) -> None: Populate self.potentials with key-val pairs of [TopologyKey, PotentialKey]. """ - for potential_key in self.slot_map.values(): + for potential_key in self.key_map.values(): smirks = potential_key.id force_field_parameters = parameter_handler.parameters[smirks] diff --git a/plugins/nonbonded_plugins/virtual_sites.py b/plugins/nonbonded_plugins/virtual_sites.py index 8ab6075e3..66cc3f7e4 100644 --- a/plugins/nonbonded_plugins/virtual_sites.py +++ b/plugins/nonbonded_plugins/virtual_sites.py @@ -1,6 +1,5 @@ """Plugins handling virtual sites.""" -from nonbonded_plugins.nonbonded import SMIRNOFFBuckinghamCollection from openff.toolkit.typing.engines.smirnoff.parameters import ( ParameterAttribute, VirtualSiteHandler, @@ -8,6 +7,7 @@ ) from openff.units import unit +from nonbonded_plugins.nonbonded import SMIRNOFFBuckinghamCollection from openff.interchange.components.potentials import Potential from openff.interchange.components.toolkit import _validated_list_to_array from openff.interchange.exceptions import InvalidParameterHandlerError @@ -40,6 +40,8 @@ class BuckinghamVirtualSiteType(_BaseVirtualSiteType): class SMIRNOFFBuckinghamVirtualSiteCollection(SMIRNOFFVirtualSiteCollection): """A collection storing virtual sites compatible with the Buckingham (exp-6) functional form.""" + is_plugin: bool = True + @classmethod def supported_parameters(cls): """Return a list of parameter attributes supported by this handler.""" diff --git a/plugins/setup.cfg b/plugins/setup.cfg new file mode 100644 index 000000000..2c5b803f8 --- /dev/null +++ b/plugins/setup.cfg @@ -0,0 +1,6 @@ +[mypy] +plugins = numpy.typing.mypy_plugin,pydantic.mypy +warn_unused_configs = True +warn_unused_ignores = True +warn_incomplete_stub = True +show_error_codes = True diff --git a/pyproject.toml b/pyproject.toml index 4df020ffe..fb79f2dca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,10 +25,11 @@ fail-under = 90 [tool.ruff] line-length = 119 +namespace-packages = ["openff/interchange/"] [tool.ruff.lint] ignore = ["E721","D105","D107","D200","D203","D212"] -select = ["E", "F", "W", "NPY", "UP", "RUF"] +select = ["F", "E", "W", "NPY", "UP", "RUF", "I"] [tool.ruff.lint.per-file-ignores] "openff/interchange/**/__init__.py" = ["F401"] @@ -43,9 +44,13 @@ select = ["E", "F", "W", "NPY", "UP", "RUF"] "openff/interchange/_tests/unit_tests/test_types.py" = ["F821"] "openff/interchange/foyer/_nonbonded.py" = ["F821"] "openff/interchange/_tests/data/*" = ["INP001"] -"versioneer.py" = ["UP", "RUF"] "openff/interchange/_tests/*" = ["RUF015"] "openff/interchange/smirnoff/_*.py" = ["RUF015"] +[tool.ruff.lint.isort] +# can't find a clean way to get Rust's globset to handle this via regex ... +known-third-party = ["openff.toolkit", "openff.utilities", "openff.units"] +known-first-party = ["openff.interchange"] + [tool.ruff.lint.pydocstyle] property-decorators=["validator"] diff --git a/pytest.ini b/pytest.ini index a997e0e7f..761785364 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,4 +1,3 @@ [pytest] markers = slow: marks tests as slow (deselect with '-m "not slow"') -addopts = -m "not slow" diff --git a/setup.cfg b/setup.cfg index 67525d271..4aa3f4299 100644 --- a/setup.cfg +++ b/setup.cfg @@ -10,27 +10,6 @@ exclude_lines = raise NotImplementedError @overload -[flake8] -max-line-length = 119 -ignore = E203,B028,W503 -per-file-ignores = - openff/interchange/_tests/unit_tests/test_types.py:F821 - openff/interchange/**/__init__.py:F401 - openff/interchange/*_pydantic.py:F401 - openff/interchange/smirnoff/_nonbonded.py:F821 - openff/interchange/smirnoff/_gbsa.py:F821 - openff/interchange/smirnoff/_virtual_sites.py:F821 - openff/interchange/foyer/_nonbonded.py:F821 - openff/interchange/components/interchange.py:E704,F821 - openff/interchange/components/*.py:F821 - openff/interchange/components/foyer.py:F401 - openff/interchange/components/_packmol.py:W503 - openff/interchange/components/toolkit.py:W503 - openff/interchange/operations/_combine.py:W503 - openff/interchange/interop/gromacs/export/_export.py:W503 - openff/interchange/_tests/data/*:INP001 - plugins/*:INP001 - [mypy] mypy_path = stubs/ plugins = numpy.typing.mypy_plugin,pydantic.mypy @@ -105,3 +84,6 @@ ignore_missing_imports = True [mypy-nonbonded_plugins.*] ignore_missing_imports = True + +[mypy-lammps] +ignore_missing_imports = True diff --git a/setup.py b/setup.py index d3aa8186f..175e40feb 100644 --- a/setup.py +++ b/setup.py @@ -1,19 +1,13 @@ -import sys -from setuptools import setup, find_namespace_packages import versioneer +from setuptools import find_namespace_packages, setup short_description = "A project (and object) for storing, manipulating, and converting molecular mechanics data." -# from https://github.com/pytest-dev/pytest-runner#conditional-requirement -needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv) -pytest_runner = ["pytest-runner"] if needs_pytest else [] - with open("README.md") as handle: long_description = handle.read() setup( - # Self-descriptive entries which should always be present name="openff-interchange", author="Open Force Field Initiative", author_email="info@openforcefield.org", diff --git a/stubs/foyer/atomtyper.pyi b/stubs/foyer/atomtyper.pyi index fb124923d..6dc0ca6a4 100644 --- a/stubs/foyer/atomtyper.pyi +++ b/stubs/foyer/atomtyper.pyi @@ -5,4 +5,8 @@ class _AtomTypeInfo(TypedDict): blacklist: set[str] atomtype: str -def find_atomtypes(structure: Any, forcefield: Any, max_iter: int = 10) -> dict[int, _AtomTypeInfo]: ... +def find_atomtypes( + structure: Any, + forcefield: Any, + max_iter: int = 10, +) -> dict[int, _AtomTypeInfo]: ... diff --git a/stubs/mbuild/__init__.pyi b/stubs/mbuild/__init__.pyi index 1b30f1b46..9f9b1be16 100644 --- a/stubs/mbuild/__init__.pyi +++ b/stubs/mbuild/__init__.pyi @@ -4,7 +4,11 @@ class Particle: def __init__(self, name: str | None) -> None: ... class Compound: - def __init__(self, name: str = "Compound", subcompounds: list | None = None) -> None: ... + def __init__( + self, + name: str = "Compound", + subcompounds: list | None = None, + ) -> None: ... name: str xyz: Any def add( diff --git a/stubs/mdtraj/core/residue_names.pyi b/stubs/mdtraj/core/residue_names.pyi index 47bc30326..69b2d56b2 100644 --- a/stubs/mdtraj/core/residue_names.pyi +++ b/stubs/mdtraj/core/residue_names.pyi @@ -1,4 +1,3 @@ - _SOLVENT_TYPES: frozenset[str] _WATER_RESIDUES: frozenset[str] _AMINO_ACID_CODES: dict[str, str | None] diff --git a/stubs/nglview/__init__.pyi b/stubs/nglview/__init__.pyi index ebb90d60d..135042fea 100644 --- a/stubs/nglview/__init__.pyi +++ b/stubs/nglview/__init__.pyi @@ -1,7 +1,13 @@ from typing import Iterable class NGLWidget: - ... + def __init__( + self, + structure=None, + representations=None, + parameters=None, + **kwargs, + ): ... def add_representation( self, repr_type: str,