Merge remote-tracking branch 'upstream/main' into lammps-constraints

.github/workflows/beta.yaml

@@ -21,6 +21,7 @@ jobs:
  python-version:
  - "3.9"
  - "3.10"
+ - "3.11"
  openeye:
  - true
  - false
@@ -46,9 +47,7 @@ jobs:
  python -m pip install . plugins/
 
  - name: Environment Information
- run: |
- conda info
- conda list
+ run: conda info && conda list
 
  - name: License OpenEye
  if: ${{ matrix.openeye == true }}
@@ -60,13 +59,11 @@ jobs:
 
  - name: Run mypy
  continue-on-error: true
- run: |
- mypy --show-error-codes --namespace-packages -p "openff.interchange"
+ run: mypy --show-error-codes --namespace-packages -p "openff.interchange"
 
  - 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/ -m "slow or not slow"
 
  - name: Codecov
  uses: codecov/codecov-action@v4

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
  hooks:
  - id: add-trailing-comma
 - repo: https:/psf/black
- rev: 24.1.1
+ rev: 24.2.0
  hooks:
  - id: black
  files: ^openff|plugins|stubs
@@ -23,6 +23,10 @@ repos:
  hooks:
  - id: isort
  files: ^openff|plugins|stubs
+- repo: https:/asottile/yesqa
+ rev: v1.5.0
+ hooks:
+ - id: yesqa
 - repo: https:/PyCQA/flake8
  rev: 7.0.0
  hooks:

devtools/conda-envs/beta_env.yaml

@@ -2,14 +2,13 @@ name: beta-env
 channels:
  - jaimergp/label/unsupported-cudatoolkit-shim
  - conda-forge/label/openmm_rc
- - conda-forge/label/openff-models_rc
  - conda-forge
  - openeye
 dependencies:
  # Core
  - python
  - numpy >=1.21
- - pydantic =1
+ - pydantic
  - openmm >=7.6
  # OpenFF stack
  - openff-toolkit >=0.15.2
@@ -39,7 +38,7 @@ dependencies:
  - pytest
  - nbval
  # Typing
- - mypy =1.3
+ - mypy
  - typing-extensions
  - types-setuptools
  - pandas-stubs >=1.2.0.56

devtools/conda-envs/examples_env.yaml

@@ -12,8 +12,9 @@ dependencies:
  # OpenFF stack
  - openff-toolkit =0.15.2
  - openff-models
- - openff-nagl ==0.3.1
+ - openff-nagl ==0.3
  - openff-nagl-models ==0.1
+ - dgl =1
  # Optional features
  - unyt
  - mbuild

docs/releasehistory.md

@@ -11,7 +11,7 @@ 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.
 
-## Current development
+## 0.3.20 - 2023-02-12
 
 * #891 Adds support for hydrogen mass repartitioning (HMR) in GROMACS export. Note that this implementaiton never modifies masses in waters and requires the system contains no virtual sites.
 * #887 Adds support for hydrogen mass repartitioning (HMR) in OpenMM export. Note that this implementaiton never modifies masses in waters and requires the system contains no virtual sites.

examples/host-guest/host_guest.ipynb

@@ -195,7 +195,7 @@
  "name": "python",
  "nbconvert_exporter": "python",
  "pygments_lexer": "ipython3",
- "version": "3.11.6"
+ "version": "3.11.7"
  }
  },
  "nbformat": 4,

openff/interchange/_tests/__init__.py

@@ -2,22 +2,18 @@
 
 import pathlib
 import sys
-from collections import defaultdict
-from typing import DefaultDict, Optional
+from typing import Optional
 
-import numpy as np
 import pytest
-from openff.toolkit import ForceField, Molecule, Topology
+from openff.toolkit import Molecule
 from openff.toolkit.utils import (
  AmberToolsToolkitWrapper,
  OpenEyeToolkitWrapper,
  RDKitToolkitWrapper,
 )
-from openff.utilities import get_data_file_path
-from openff.utilities.utilities import has_executable, has_package, requires_package
+from openff.utilities.utilities import has_executable, has_package
 
 from openff.interchange.drivers.gromacs import _find_gromacs_executable
-from openff.interchange.drivers.lammps import _find_lammps_executable
 
 if sys.version_info >= (3, 10):
  from importlib import resources
@@ -98,94 +94,8 @@ def from_mapped_smiles(self, smiles, name="", **kwargs):
  return molecule
 
 
-class _BaseTest:
- @pytest.fixture(autouse=True)
- def _initdir(self, tmpdir):
- tmpdir.chdir()
-
- @pytest.fixture()
- def ethanol_top(self, ethanol):
- """Fixture that builds a simple four ethanol topology."""
- return Topology.from_molecules(4 * [ethanol])
-
- @pytest.fixture()
- def mainchain_ala(self):
- molecule = Molecule.from_file(
- get_data_file_path("proteins/MainChain_ALA.sdf", "openff.toolkit"),
- )
- molecule._add_default_hierarchy_schemes()
- molecule.perceive_residues()
- molecule.perceive_hierarchy()
-
- return molecule
-
- @pytest.fixture()
- def mainchain_arg(self):
- molecule = Molecule.from_file(
- get_data_file_path("proteins/MainChain_ARG.sdf", "openff.toolkit"),
- )
- molecule._add_default_hierarchy_schemes()
- molecule.perceive_residues()
- molecule.perceive_hierarchy()
-
- return molecule
-
- @pytest.fixture()
- def two_peptides(self, mainchain_ala, mainchain_arg):
- return Topology.from_molecules([mainchain_ala, mainchain_arg])
-
- xml_ff_bo_bonds = """<?xml version='1.0' encoding='ASCII'?>
- <SMIRNOFF version="0.3" aromaticity_model="OEAroModel_MDL">
- <Bonds version="0.3" fractional_bondorder_method="AM1-Wiberg" fractional_bondorder_interpolation="linear">
- <Bond smirks="[#6:1]~[#8:2]" id="bbo1"
- k_bondorder1="100.0*kilocalories_per_mole/angstrom**2"
- k_bondorder2="1000.0*kilocalories_per_mole/angstrom**2"
- length_bondorder1="1.5*angstrom"
- length_bondorder2="1.0*angstrom"/>
- </Bonds>
- </SMIRNOFF>
- """
-
- @pytest.fixture()
- def methane(self):
- return Molecule.from_smiles("C")
-
- @pytest.fixture()
- def parsley(self):
- return ForceField("openff-1.0.0.offxml")
-
- @pytest.fixture()
- def hydrogen_cyanide(self):
- return Molecule.from_mapped_smiles("[H:1][C:2]#[N:3]")
-
- @pytest.fixture()
- def hydrogen_cyanide_reversed(self):
- return Molecule.from_mapped_smiles("[H:3][C:2]#[N:1]")
-
- @pytest.fixture()
- def hexane_diol(self):
- molecule = Molecule.from_smiles("OCCCCCCO")
- molecule.assign_partial_charges(partial_charge_method="gasteiger")
- molecule.partial_charges.m
- return molecule
-
- @pytest.fixture()
- def hydrogen_chloride(self):
- return Molecule.from_mapped_smiles("[Cl:1][H:2]")
-
- @pytest.fixture()
- def formaldehyde(self):
- return Molecule.from_mapped_smiles("[H:3][C:1]([H:4])=[O:2]")
-
- @pytest.fixture()
- def acetaldehyde(self):
- return Molecule.from_mapped_smiles(
- "[C:1]([C:2](=[O:3])[H:7])([H:4])([H:5])[H:6]",
- )
-
-
 HAS_GROMACS = _find_gromacs_executable() is not None
-HAS_LAMMPS = _find_lammps_executable() is not None
+HAS_LAMMPS = has_package("lammps")
 HAS_SANDER = has_executable("sander")
 
 needs_gmx = pytest.mark.skipif(not HAS_GROMACS, reason="Needs GROMACS")
@@ -203,161 +113,3 @@ def acetaldehyde(self):
  HAS_SANDER,
  reason="sander needs to NOT be installed",
 )
-
-
-def _get_charges_from_openff_interchange(interchange):
- charges_ = [*interchange["Electrostatics"].charges.values()]
- charges = np.asarray([charge.magnitude for charge in charges_])
- return charges
-
-
-def _create_torsion_dict(torsion_force) -> dict[tuple[int], list[tuple]]:
- torsions: DefaultDict = defaultdict(list)
-
- for i in range(torsion_force.getNumTorsions()):
- p1, p2, p3, p4, periodicity, phase, k = torsion_force.getTorsionParameters(i)
- key = (p1, p2, p3, p4)
- torsions[key]
- torsions[key].append((periodicity, phase, k))
-
- return torsions
-
-
-def _create_bond_dict(bond_force):
- bonds = dict()
-
- for i in range(bond_force.getNumBonds()):
- p1, p2, length, k = bond_force.getBondParameters(i)
- key = (p1, p2)
- bonds[key] = (length, k)
-
- return bonds
-
-
-def _create_angle_dict(angle_force):
- angles = dict()
-
- for i in range(angle_force.getNumAngles()):
- p1, p2, p3, theta, k = angle_force.getAngleParameters(i)
- key = (p1, p2, p3)
- angles[key] = (theta, k)
-
- return angles
-
-
-@requires_package("openmm")
-def _compare_individual_torsions(x, y):
- assert x[0] == y[0]
- assert x[1] == y[1]
- assert (x[2] - y[2]) < 1e-15 * openmm.unit.kilojoule_per_mole
-
-
-def _compare_torsion_forces(force1, force2):
- sorted1 = _create_torsion_dict(torsion_force=force1)
- sorted2 = _create_torsion_dict(torsion_force=force2)
-
- assert sum(len(v) for v in sorted1.values()) == force1.getNumTorsions()
- assert sum(len(v) for v in sorted2.values()) == force2.getNumTorsions()
- assert len(sorted1) == len(sorted2)
-
- for key in sorted1:
- for i in range(len(sorted1[key])):
- _compare_individual_torsions(sorted1[key][i], sorted2[key][i])
-
-
-@requires_package("openmm")
-def _compare_bond_forces(force1, force2):
- assert force1.getNumBonds() == force2.getNumBonds()
-
- bonds1 = _create_bond_dict(force1)
- bonds2 = _create_bond_dict(force2)
-
- for key in bonds1:
- length_diff = bonds2[key][0] - bonds1[key][0]
- assert (
- abs(length_diff) < 1e-15 * openmm.unit.nanometer
- ), f"Bond lengths differ by {length_diff}"
- k_diff = bonds2[key][1] - bonds1[key][1]
- assert abs(k_diff) < 1e-9 * kj_nm2_mol, f"bond k differ by {k_diff}"
-
-
-@requires_package("openmm")
-def _compare_angle_forces(force1, force2):
- assert force1.getNumAngles() == force2.getNumAngles()
-
- angles1 = _create_angle_dict(force1)
- angles2 = _create_angle_dict(force2)
-
- for key in angles1:
- angle_diff = angles2[key][0] - angles1[key][0]
- assert (
- abs(angle_diff) < 1e-15 * openmm.unit.radian
- ), f"angles differ by {angle_diff}"
- k_diff = angles2[key][1] - angles1[key][1]
- assert abs(k_diff) < 1e-10 * kj_rad2_mol, f"angle k differ by {k_diff}"
-
-
-def _compare_nonbonded_settings(force1, force2):
- for attr in dir(force1):
- if not attr.startswith("get") or attr in [
- "getExceptionParameterOffset",
- "getExceptionParameters",
- "getGlobalParameterDefaultValue",
- "getGlobalParameterName",
- "getLJPMEParametersInContext",
- "getPMEParametersInContext",
- "getParticleParameterOffset",
- "getParticleParameters",
- "getForceGroup",
- ]:
- continue
- assert getattr(force1, attr)() == getattr(force2, attr)(), attr
-
-
-@requires_package("openmm")
-def _compare_nonbonded_parameters(force1, force2):
- assert (
- force1.getNumParticles() == force2.getNumParticles()
- ), "found different number of particles"
-
- for i in range(force1.getNumParticles()):
- q1, sig1, eps1 = force1.getParticleParameters(i)
- q2, sig2, eps2 = force2.getParticleParameters(i)
- assert (
- abs(q2 - q1) < 1e-8 * openmm.unit.elementary_charge
- ), f"charge mismatch in particle {i}: {q1} vs {q2}"
- assert (
- abs(sig2 - sig1) < 1e-12 * openmm.unit.nanometer
- ), f"sigma mismatch in particle {i}: {sig1} vs {sig2}"
- assert (
- abs(eps2 - eps1) < 1e-12 * openmm.unit.kilojoule_per_mole
- ), f"epsilon mismatch in particle {i}: {eps1} vs {eps2}"
-
-
-@requires_package("openmm")
-def _compare_exceptions(force1, force2):
- assert (
- force1.getNumExceptions() == force2.getNumExceptions()
- ), "found different number of exceptions"
-
- for i in range(force1.getNumExceptions()):
- _, _, q1, sig1, eps1 = force1.getExceptionParameters(i)
- _, _, q2, sig2, eps2 = force2.getExceptionParameters(i)
- assert (
- abs(q2 - q1) < 1e-12 * openmm.unit.elementary_charge**2
- ), f"charge mismatch in exception {i}"
- assert (
- abs(sig2 - sig1) < 1e-12 * openmm.unit.nanometer
- ), f"sigma mismatch in exception {i}"
- assert (
- abs(eps2 - eps1) < 1e-12 * openmm.unit.kilojoule_per_mole
- ), f"epsilon mismatch in exception {i}"
-
-
-@requires_package("openmm")
-def _get_force(openmm_sys: "openmm.System", force_type):
- forces = [f for f in openmm_sys.getForces() if type(f) is force_type]
-
- if len(forces) > 1:
- raise NotImplementedError("Not yet able to process duplicate forces types")
- return forces[0]