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SMIRNOFF: multiple force field files, virtual sites, and constraints (#423)
* Support virtual sites and multiple SMIRNOFF force fields * Put test files where tests can actually find them * Clean up some changes in template_generators.py * Clean up virtual site permutation handling in test cases * Unfinished draft * Allow specifying multiple force fields * Support constraints and virtual sites * Add more tests for constraints * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Run tests on OpenMM 8.5.0 beta since we need ForceField changes * Need openmm_dev channel * Use correct channel names (openmm_rc for beta) * Minor improvement to torsion handling, fix incorrect comment * Default to unconstrained variant of force field when given name * Test molecule is unstable due to vsite/H overlap * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update vsite tests with more varieties of molecules * Autoformatter * Update openmmforcefields/generators/template_generators.py Co-authored-by: Josh Horton <[email protected]> * 1-4 exception check (not vsites) now uses non-zero scalings * Use preset list of known force field names, update documentation * Reduce test set size after Interchange cache behavior change * Update openmmforcefields/tests/test_template_generators.py Co-authored-by: Jeff Wagner <[email protected]> * Water constraints test also checks TIP3P inside openff_unconstrained * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix error message if preset force field file can't be located --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Josh Horton <[email protected]> Co-authored-by: Jeff Wagner <[email protected]>
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‎.github/workflows/ci.yaml‎

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os: [ubuntu-latest, macos-latest]
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python-version: ["3.11", "3.12", "3.13"]
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amber-conversion: [false]
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openmm-version: ["8.3.1", "8.4.0"]
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openmm-version: ["8.5.0beta"]
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steps:
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- uses: actions/checkout@v6

‎README.md‎

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@@ -189,12 +189,10 @@ Create a SMIRNOFF template generator for a single molecule (benzene, created fro
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from openff.toolkit import Molecule
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molecule = Molecule.from_smiles("c1ccccc1")
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# Create the SMIRNOFF template generator with the default installed force field (openff-2.2.1)
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from openmmforcefields.generators import (
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SMIRNOFFTemplateGenerator,
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)
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# Create the SMIRNOFF template generator with the openff-2.3.0 force field
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from openmmforcefields.generators import SMIRNOFFTemplateGenerator
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smirnoff = SMIRNOFFTemplateGenerator(molecules=molecule)
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smirnoff = SMIRNOFFTemplateGenerator(molecules=molecule, forcefield="openff-2.3.0")
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# Create an OpenMM ForceField object with AMBER ff14SB and TIP3P with compatible ions
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from openmm.app import ForceField
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# create a System with the non-bonded settings of mainline OpenFF force fields
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# (9 Angstrom cut-off, switching distance applied at 8 Angstrom)
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import openmm.unit
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system = forcefield.createSystem(
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topology=molecule.to_topology().to_openmm(),
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nonbondedCutoff=0.9 * openmm.unit.nanometer,
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switchDistance=0.8 * openmm.unit.nanometer,
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)
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```
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The latest official Open Force Field Initiative release ([`openff-2.2.1`](https://github.com/openforcefield/openff-forcefields) of the ["Sage" small molecule force field](https://openforcefield.org/force-fields/force-fields/)) is used if none is specified.
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You can check which SMIRNOFF force field is in use with
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You can create a template generator capable of recognizing multiple molecules,
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*e.g.*, read from an SDF file:
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```pycon
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>>> smirnoff.smirnoff_filename
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'/Users/mattthompson/mambaforge/envs/openmmforcefields/lib/python3.11/site-packages/openforcefields/offxml/openff-2.2.1.offxml'
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```python
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molecules = Molecule.from_file("molecules.sdf")
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smirnoff = SMIRNOFFTemplateGenerator(molecules=molecules, forcefield="openff-2.3.0")
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```
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Create a template generator for a specific SMIRNOFF force field for multiple molecules read from an SDF file:
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You can also add molecules to the generator later, even after the generator has been registered:
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```python
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molecules = Molecule.from_file("molecules.sdf")
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# Create a SMIRNOFF residue template generator from the official openff-2.2.1 release,
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# which is installed automatically
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smirnoff = SMIRNOFFTemplateGenerator(molecules=molecules, forcefield="openff-2.2.1")
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smirnoff.add_molecules(molecule)
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smirnoff.add_molecules([molecule1, molecule2])
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```
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You must specify the desired SMIRNOFF force field with the `forcefield` keyword
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argument when you create a `SMIRNOFFTemplateGenerator` by providing at least one
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force field name, path to an OFFXML force field file, file object, or XML in a
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string. An iterable can be provided to the `forcefield` argument to load from
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multiple sources if desired. For exapmle:
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```
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# Create a SMIRNOFF residue template generator from an older Sage or Parsley version
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smirnoff = SMIRNOFFTemplateGenerator(molecules=molecules, forcefield="openff-1.3.0")
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# Request a specific SMIRNOFF force field installed with OpenFF by its full name
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smirnoff = SMIRNOFFTemplateGenerator(molecules=molecules, forcefield="openff_unconstrained-1.3.0.offxml")
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# Use a local .offxml file instead
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smirnoff = SMIRNOFFTemplateGenerator(molecules=molecules, forcefield="local-file.offxml")
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# Load from multiple sources at once
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smirnoff = SMIRNOFFTemplateGenerator(molecules=molecule, forcefield=['openff-2.3.0', 'tip5p.offxml'])
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```
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You can also add molecules to the generator later, even after the generator has been registered:
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You can check the full paths of the force field files that have been loaded:
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```python
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smirnoff.add_molecules(molecule)
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smirnoff.add_molecules([molecule1, molecule2])
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```pycon
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>>> smirnoff.smirnoff_filenames
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['/.../offxml/openff_unconstrained-2.3.0.offxml', '/.../offxml/tip5p.offxml']
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```
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To check which SMIRNOFF force fields are automatically installed, examine the `INSTALLED_FORCEFIELDS` attribute:
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Any force field installed with the OpenFF Toolkit can be requested by its
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filename, *e.g.*, `openff_unconstrained-2.3.0.offxml`. To see which force
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fields can be requested by an abbreviated name, examine `INSTALLED_FORCEFIELDS`:
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```pycon
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>>> print(SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS)
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['ff14sb_off_impropers_0.0.2', 'ff14sb_off_impropers_0.0.4', 'ff14sb_off_impropers_0.0.1', 'ff14sb_off_impropers_0.0.3', 'tip3p_fb-1.1.0', 'tip3p_fb-1.0.0', 'openff-2.2.1-rc1', 'openff-1.0.1', 'openff-1.1.1', 'spce-1.0.0', 'openff_no_water-3.0.0-alpha0', 'openff-1.0.0-RC1', 'opc3', 'opc3-1.0.0', 'openff-2.1.0-rc.1', 'openff-2.3.0-rc2', 'openff-1.2.0', 'openff-1.3.0', 'tip3p-1.0.0', 'opc-1.0.2', 'openff-2.2.1', 'openff-2.0.0-rc.2', 'opc-1.0.0', 'openff-2.1.0', 'openff-2.0.0', 'tip4p_fb-1.0.1', 'tip3p', 'tip4p_ew', 'opc3-1.0.1', 'opc', 'openff-2.3.0-rc1', 'tip3p_fb-1.1.1', 'openff-1.1.0', 'openff-1.0.0', 'openff-1.0.0-RC2', 'openff-2.2.0-rc1', 'tip3p-1.0.1', 'openff-1.3.1', 'openff-1.2.1', 'tip4p_ew-1.0.0', 'openff-1.3.1-alpha.1', 'tip4p_fb', 'tip3p_fb', 'openff-2.2.0', 'spce', 'tip5p', 'tip4p_fb-1.0.0', 'openff-2.1.1', 'openff-2.0.0-rc.1', 'tip5p-1.0.0', 'opc-1.0.1']
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>>> SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS
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['openff-1.0.0', 'openff-1.0.1', 'openff-1.1.0', 'openff-1.1.1', ...]
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```
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The names in this list are of the form `openff-x.y.z` and will resolve to the
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"unconstrained" variants of standard OpenFF force fields, which can also be
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loaded with filenames of the form `openff_unconstrained-x.y.z.offxml`. To
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obtain the "constrained" variants, use filenames `openff-x.y.z.offxml`. When
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the constrained variants are used, bonds to hydrogen atoms in molecules
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parameterized by the template generator will be constrained unconditionally,
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regardless of the constraint options given in `ForceField.createSystem()`. The
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unconstrained variants, which are the defaults selected if one of the predefined
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names in `INSTALLED_FORCEFIELDS` is used, do not force these constraints to be
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present, and the option of which degrees of freedom should be constrained are
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left up to the user by passing any desired `constraint` setting to
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[`ForceField.createSystem()`](https://docs.openmm.org/latest/api-python/generated/openmm.app.forcefield.ForceField.html#openmm.app.forcefield.ForceField.createSystem).
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You can optionally specify a file that contains a cache of pre-parameterized molecules:
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```python
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smirnoff = SMIRNOFFTemplateGenerator(
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cache="smirnoff-molecules.json",
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forcefield="openff-2.2.1",
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forcefield="openff-2.3.0",
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)
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```
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‎devtools/conda-envs/test_charmm_env.yaml‎

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name: openmmforcefields-test-charmm
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channels:
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- conda-forge/label/openmm_dev
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- conda-forge
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dependencies:
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- numpy <2.3

‎devtools/conda-envs/test_env.yaml‎

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name: openmmforcefields-test
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channels:
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- conda-forge/label/openmm_rc
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- conda-forge
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dependencies:
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- ambertools >=24

‎openmmforcefields/data/test-virtual-sites.offxml‎

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<?xml version="1.0" encoding="utf-8"?>
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<!--
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MIT License
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Copyright (c) 2020 Open Force Field Initiative
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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-->
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<SMIRNOFF version="0.3" aromaticity_model="OEAroModel_MDL">
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<VirtualSites version="0.3" exclusion_policy="parents">
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<!-- A chlorine bound to (any) carbon, for fixing sigma holes -->
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<VirtualSite
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smirks="[#6:2]-[#17X1:1]"
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epsilon="0.5 * kilojoules_per_mole ** 1"
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type="BondCharge"
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match="all_permutations"
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distance="0.13 * angstrom ** 1"
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outOfPlaneAngle="None"
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inPlaneAngle="None"
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charge_increment1="-0.063 * elementary_charge ** 1"
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charge_increment2="0.1 * elementary_charge ** 1"
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sigma="2.0 * angstrom ** 1"
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name="sigma_hole">
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</VirtualSite>
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<!-- An oxygen in a carbonyl group, flip outOfPlaneAngle to 41 -->
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<VirtualSite
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smirks="[#8:1]=[#6X3+0:2]-[#6:3]"
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epsilon="0.1 * kilocalories_per_mole ** 1"
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type="MonovalentLonePair"
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match="all_permutations"
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distance="0.15 * angstrom ** 1"
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outOfPlaneAngle="0 * degree ** 1"
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inPlaneAngle="110 * degree ** 1"
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charge_increment1="0.1 * elementary_charge ** 1"
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charge_increment2="-0.2 * elementary_charge ** 1"
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charge_increment3="0.3 * elementary_charge ** 1"
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sigma="0.05 * angstrom ** 1"
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name="planar_carbonyl">
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</VirtualSite>
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<!-- A conventional five-site water model -->
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<VirtualSite
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smirks="[#1:2]-[#8X2H2+0:1]-[#1:3]"
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epsilon="0.0 * kilocalorie_per_mole ** 1"
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type="DivalentLonePair"
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match="all_permutations"
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distance="0.07 * nanometer ** 1"
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outOfPlaneAngle="54.735 * degree ** 1"
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inPlaneAngle="None"
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charge_increment1="0.0 * elementary_charge ** 1"
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charge_increment2="0.1205 * elementary_charge ** 1"
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charge_increment3="0.1205 * elementary_charge ** 1"
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sigma="10.0 * angstrom ** 1"
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name="5_site_water"
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></VirtualSite>
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<!-- On order to avoid applying two water models at the same time, this file -->
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<!-- only includes five-site water parameters. To see a conventional -->
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<!-- four-site water model, load ForceField("tip4p.offxml") -->
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<!-- -->
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<!-- A trivalent nitrogen, occupying the location of the lone pair -->
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<!-- 5 nm distance looks comically large - can we do 0.5 or 1 A? -->
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<VirtualSite
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smirks="[*:2][#7:1]([*:3])[*:4]"
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epsilon="0.5 * kilojoules_per_mole ** 1"
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type="TrivalentLonePair"
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match="once"
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distance="0.17 * angstrom ** 1"
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outOfPlaneAngle="None"
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inPlaneAngle="None"
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charge_increment1="0.2 * elementary_charge ** 1"
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charge_increment2="0.05 * elementary_charge ** 1"
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charge_increment3="-0.1 * elementary_charge ** 1"
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charge_increment4="-0.15 * elementary_charge ** 1"
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sigma="1.0 * angstrom ** 1"
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name="trivalent_nitrogen">
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</VirtualSite>
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</VirtualSites>
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</SMIRNOFF>

‎openmmforcefields/data/test_vsites_mols/C13H9ClN2O4.sdf‎

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RDKit 3D
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3.0787 1.9191 -1.7909 H 0 0 0 0 0 0 0 0 0 0 0 0
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18 29 1 0
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M END
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> <atom.dprop.PartialCharge> (1)
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-0.56515204431167965 0.74306053398498173 -0.13963260771385555 -0.050116802469409742 -0.11601972104660396 0.03780772639759656 -0.080641309634364888 -0.053396160617984571
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-0.12579522551647548 0.74183500288375492 -0.56509708882919674 -0.53693997384659176 0.06700046090730305 -0.089005465522922322 -0.15062590958229427 0.71034175632842655 -0.59908800841919307
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-0.60823964597336178 0.69618905065902348 -0.59525155545822506 0.16555642066844578 0.15883733807452793 0.17739490149863835 0.10420614956267948 0.077082541867576793 0.077082541867576793
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0.087043036803089335 0.087043036803089335 0.34452102063544865
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$$$$
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17 6 1 1
112+
7 22 1 0
113+
8 25 1 0
114+
9 26 1 0
115+
10 11 2 0
116+
11 12 1 0
117+
11 17 1 0
118+
12 14 1 0
119+
13 14 2 0
120+
14 15 1 0
121+
15 16 1 0
122+
16 17 1 0
123+
17 18 1 0
124+
18 20 1 0
125+
18 28 1 0
126+
19 20 2 0
127+
20 21 1 0
128+
21 22 1 0
129+
21 27 2 0
130+
22 24 2 0
131+
23 24 1 0
132+
24 25 1 0
133+
25 26 2 0
134+
26 27 1 0
135+
27 28 1 0
136+
28 29 2 0
137+
M END
138+
> <atom.dprop.PartialCharge> (1)
139+
0.34452102063544865 0.087043036803089335 0.087043036803089335 0.077082541867576793 0.077082541867576793 0.10420614956267948 0.17739490149863835 0.15883733807452793 0.16555642066844578
140+
-0.59525155545822506 0.69618905065902348 -0.60823964597336178 -0.59908800841919307 0.71034175632842655 -0.15062590958229427 -0.089005465522922322 0.06700046090730305 -0.53693997384659176
141+
-0.56509708882919674 0.74183500288375492 -0.12579522551647548 -0.053396160617984571 -0.080641309634364888 0.03780772639759656 -0.11601972104660396 -0.050116802469409742
142+
-0.13963260771385555 0.74306053398498173 -0.56515204431167965
143+
144+
$$$$

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