Release History

Releases follow the major.minor.micro scheme recommended by PEP440, where

  • major increments denote a change that may break API compatibility with previous major releases

  • minor increments add features but do not break API compatibility

  • micro increments represent bugfix releases or improvements in documentation

0.16.7

Bugfixes

  • PR #1971: Fixes bug where OpenEyeToolkitWrapper would write coordinate-less PDB atoms if insertion_code or chain_id was an empty string (Issue #1967)

Tests updated

  • PR #1965: Fixes slight difference in GBSA energy reported in Issue #1964 by forcing the use of the Reference platform in OpenMM for both calculations.

  • PR #1965: Disables testing of parmed-dependent notebook in external examples, since ParmEd 3 is no longer compatible with our upstreams and ParmEd 4 raises an error for our use cases.

  • PR #1965: Uses a different molecule in test_nagl’s test_unsupported_molecule_bond to avoid having molecule handled successfully by nagl’s new lookup table.

Miscellaneous

  • PR #1970: Consolidates config files into pyproject.toml.

  • PR #1968: Switches version handling to versioningit.

0.16.6

Behavior changes

  • PR #1954: Topology.from_openmm no longer casts residue numbers to int.

  • PR #1959: Speeds up import times.

Bugfixes

  • PR #1961: Fix Issue #1960, where lazy-loading machinery in openff-toolkit would clash with newly added lazy-loading code in openff-units 0.2.3.

New features

  • PR #1958: Allows serialization of _SimpleMolecules (relevant to serialization of Topology objects created by Interchange.from_openmm)

Improved documentation and warnings

  • PR #1957: Fixed a misleading typo in an error message.

Tests updated

  • PR #1942: Update tests for newer versions of RDKit, while stepping around recent RDKit conda-forge packages that fail when run natively on osx-arm64.

0.16.5

Improved documentation and warnings

Miscellaneous

  • PR #1940: Fixes an esoteric issue in which optional upstream packages resulted in import errors.

0.16.4

Bugfixes

  • PR #1928: Fixes a bug in which atom names were lost when adding _SimpleMolecule to a topology or serializing through a dictionary.

Improved documentation and warnings

  • PR #1925: Adds a FAQ entry describing how to send a prepared system to HPC resources.

  • PR #1926: Improves hints in UnAssignedChemistryInPDBError.

0.16.3

New features

  • PR #1920: Adds Topology.add_molecules, which takes a list of Molecules and is faster when adding many molecules.

Bugfixes

  • PR #1923: Topology.add_molecule and Topology.add_molecules now return indices starting at 0. Previously, these indices started at 1, which does not match other indexing in the toolkit.

  • PR #1926: Less noisy hints when the chemistry of a PDB file cannot be identified.

0.16.2

Bugfixes

  • PR #1898 and PR #1904: Fixes #1897 in which to_inchi and to_inchikey methods would return an empty string in some rare cases. Now these cases result in an EmptyInchiError being raised.

  • PR #1890: Fixes #1888 in which ParameterAttribute.unit was sometimes not validated when stringified.

  • PR #1894: Fixes #1893 in which int-based virtual site parameter lookups were mistakenly forbidden in changes in 0.16.0.

0.16.1

  • PR #1861: Fixes [#1857] by forbidding looking up virtual site parameters by SMIRKS, since a valid SMIRNOFF force field can have several virtual site parameters with identical SMIRKS.

Bugfixes

  • PR #1868: Fixes issue #1868 in which Topology.set_positions would sometimes fail if it contained _SimpleMolecules.

New features

  • PR #1866: Implements a safer AmberTools version check.

  • PR #1874: Improves some loading times by lazy-loading networkx.

  • PR #1881: Adds an optional suffix parameter to generate_unique_atom_names.

  • PR #1887: Allows skipping vsite valence check for parent atoms using the OPENFF_UNSAFE_VSITES environment variable.

Improved documentation and warnings

  • PR #1878: docs: updated docs for SMIRNOFF spec around AMBER/GROMACS

  • PR #1870: Updates examples to use openff-2.2.0, and modernizes use of some API points.

  • PR #1787: Improve documentation for toolkit wrappers and registries

  • PR #1886: Update docs to build with myst-parser version 3.

0.16.0

Behavior changes

  • PR #1852: Fixes issue #1363: If multiple parameters have identical SMIRKS, calls to ParameterHandler[smirks] and ParameterList[smirks] will now return the LAST parameter with a matching SMIRKS. Previously this would return the FIRST parameter with a matching SMIRKS, which was a confusing behavior given SMIRNOFF hierarchy rules.

Bugfixes

  • PR #1846: Band-aids issue #1842, where the Toolkit Showcase example would sporadically fail when run with one core.

New features

  • PR #1827: Adds Topology.clear_positions

  • PR #1852: Adds the allow_duplicate_smirks named argument to ParameterHandler.add_parameter. Previously it was possible to make a force field with duplicate SMIRKS by loading it from file or combining multiple FFs, so this also lets you do it using the API.

  • PR #1826: Allow writing molecules to Paths

  • PR #1797: Topology.from_pdb can now load more file-like objects, including io.StringIO.

  • PR #1808: Improves default representation of ValenceDict.

  • PR #1834: Adds Molecule.get_available_charge_methods and BaseWrapper.supported_charge_methods.

  • PR #1837: Decouples vdW and virtual site parameters.

Improved documentation and warnings

  • PR #1795: Add NAGLToolkitWrapper to API reference

  • PR #1796: Update docs tooling and fix warnings

  • PR #1786: Describe contributing to documentation notebooks in developers guide.

  • PR #1845: Update convert_all_strings_to_quantity docstring.

  • PR #1849: Add “how are charges assigned?” section to FAQ.

  • PR #1798: Adds type annotations to most of the codebase.

Tests updated

  • PR #1836: Update tests to not directly call numpy.random.random any more (per NEP 19)

0.15.2

New features

  • PR #1818: Several improvements to enable the practical use of Interchange.from_openmm.

0.15.1

Tests updated

  • PR #1814: Fixes a test to be compatible with both pydantic 1 and 2.

0.15.0

This release adds compatibility with QCFractal >=0.50.0, but removes compatibiltiy with QCFractal <0.50.0.

API-breaking changes

  • PR #1760: Removes the private, unused ParameterHandler._OPENMMTYPE attribute.

  • PR #1763: Updates the OpenFF Toolkit to be compatible with QCFractal >= 0.50. Removes the client named argument from Molecule.from_qcschema.

Behavior changes

  • PR #1779: Overhauls Molecule.enumerate_protomers:

    • By default, max_states=0 and there is no limit to the number of returned protomers

    • The input molecule is returned if it is enumerated with default Quacpac formal charge enumeration settings

Bugfixes

  • PR #1778: Ensures SD data tags are preserved in Molecule.from_openeye if the input is of type oechem.OEGraphMol.

  • PR #1811: Preserves hierarchy data in _SimpleMolecule.from_molecule

New features

  • PR #1775: Re-exports openff.units.unit and Quantity at openff.toolkit.unit and Quantity.

  • PR #1805: Adds _SimpleMolecule.__deepcopy__ and _SimpleMolecule.to_topology.

Improved documentation and warnings

  • PR #1732: Add documentation describing the use of PDB files with the toolkit.

  • PR #1804: Makes ForceField.parse_sources docstring consistent with implementation.

0.14.5

Bugfixes

  • PR #1740: Updates for Mypy 1.6.

  • PR #1749: Updates versioneer for Python 3.12 compatibility.

  • PR #1756: Fixes issue #1739, where virtual sites would be double-created under some circumstances.

New features

  • PR #1731: Support SMIRNOFF vdW version 0.5.

Improved documentation and warnings

  • PR #1747: Warns if a SMILES with full atom mappings is passed to Molecule.from_smiles, which does not use the atom map for atom ordering (Molecule.from_mapped_smiles does).

  • PR #1743: Uses a longer stride in OpenMM DCD reporter in the toolkit showcase and should better utilize GPU resources, if available.

  • PR #1744: Updates the virtual site notebook to use new Interchange behavior.

0.14.4

Behavior changes

  • PR #1705: Do not raise warning when allow_undefined_stereo=True.

  • PR #1695: ChemicalEnvironmentParsingError is now raised when an underlying toolkit fails to parse a SMARTS/SMIRKS pattern it is given during substructure matching.

  • PR #1716: Adds deprecation warnings to Molecule.from_polymer_pdb, Molecule.from_pdb_and_smiles, and RDKitToolkitWrapper.from_pdb_and_smiles instead pointing users toward Topology.from_pdb.

Bugfixes

  • PR #1726: Fix error message in setting scale12, scale13, and scale15 attributes.

  • PR #1728: Adds support for loading deprotonated cysteine (sometimes labeled as “CYM”) residues in Topology.from_pdb

New features

  • PR #1733: Makes NAGLToolkitWrapper and its associated module public.

  • PR #1698: Makes openff.toolkit.utils.toolkit_registry.toolkit_registry_manager public.

  • PR #1662: Adds hierarchy scheme iterators to Topology, i.e. Topology.residues, when schemes of the same iterator name are defines on all constituent Molecules.

  • PR #1700: Use openff-nagl v0.3.0.

  • PR #1623: Adds Topology.visualize.

Improved documentation and warnings

  • PR #1709: Update molecule cookbook to use the maximally capable Topology.from_pdb in lieu of the more limited Molecule.from_pdb_and_smiles and Molecule.from_polymer_pdb.

  • PR #1719: Remove out-of-date and unused examples/environment.yaml and various examples updates.

0.14.3

Bugfixes

  • PR #1689: Fixes #1688 in which automatic up-conversion of version 0.3 of vdWHandler created via the Python API errored out if method was not specified.

  • PR #1690: Fixes a circular-import bug that occurs when attempting to print a “no cheminformatics toolkits available” warning.

0.14.2

Behavior changes

  • PR #1679: Version 0.3 <vdW> sections of OFFXML files will automatically be up-converted (in memory) to version 0.4 according to the recomendations provided in OFF-EP 0008.

New features

  • PR #1631: Adds support for Python 3.11.

0.14.1

API-breaking changes

  • PR #1664: Removes ChemicalEnvironment and the entire openff.toolkit.typing.chemistry submodule, which was deprecated in 0.12.0.

Behavior changes

  • PR #1675: Makes InChI parsing failures more informative and gives them their own exception type, InChIParseError.

New features

  • PR #1627: (beta release of major new feature by @connordavel) Adds experimental support for custom substructure loading in Topology.from_pdb, via the _custom_substructures keyword argument. This will be added to the public API (by removing the leading underscore) in a future feature release, but is available for testing now. This feature should allow for easier loading of modified amino acids, nucleic acids, and other polymers.

Bugfixes

  • PR #1662: Fixes issue #1660 by forbidding the registration of HierarchySchemes with iterator names that conflict with existing Molecule attributes.

  • PR #1667: A more helpful exception is now raised when Topology.from_openmm is given an OpenMM Topology with virtual sites.

Examples updated

  • PR #1671: Re-rendered all examples using RDKit+AmberTools backend, and using most recent version of OFF Toolkit.

Improved documentation and warnings

0.14.0

API-breaking changes

  • PR #1649: Removes tests and associated modules from the public API.

  • PR #1508: Removes the return_topology kwawrg from ForceField.create_openmm_system which was deprecated in version 0.11.0. To access the Topology that results from parametrization, call ForceField.create_interchange and access the .topology attribute of the returned Interchange object.

  • PR #1506: Removes several classes and properties in the topology submodule that were deprecated in version 0.11.0.

Behavior changes

  • PR #1652: Fixes issue #1642 by making AmberToolsToolkitWrapper thread-safe (previously AmberToolsToolkitWrapper.assign_partial_charges and assign_fractional_bond_orders were not)

Bugfixes

  • PR #1654: Fixes issue #1653, where a test that expected RDKit to fail began returning an error when RDKit became able to generate conformers for octahedral molecules.

Improved documentation and warnings

  • PR #1572: Improved installation guide in line with ecosystem docs.

Examples updated

  • PR #1644: Streamlines several examples by using Interchange.to_openmm_simulation.

  • PR #1651: Fix broken links in several examples.

  • PR #1648: Update examples to use Topology.from_pdb and other small cleanups.

0.13.2

Bugfixes

  • PR #1640: Fixes issue #1633 in which some force field attributes were erroneously parsed as Quantity objects and issue #1635 in which OpenFF 2.1.0 (“Sage”) could not be loaded with Pint 0.22.

Improved documentation and warnings

  • PR #1636 and PR #1643: Make the Molecule Cookbook and Molecule.from_qcschema docstring only pull down QCF records with fully defined stereo.

0.13.1

Behavior changes

  • PR #1619: Fixes silent error #1618, by making partial_charges.setter more comprehensive in type and shape checking.

Bugfixes

  • PR #1617: Fixes #1616, by converting NAGL charges to float and converting partial_charges to float before converting to_openeye()

  • PR #1622: Fixes #1621 and #1346 in which some file-loading methods would fail on pathlib.Path.

0.13.0

New features

  • PR #1567: Allows setting Molecule.name in Molecule.from_smiles, from_inchi, from_polymer_pdb, and from_pdb_and_smiles.

  • PR #1565: Adds Topology.from_pdb.

Behavior changes

  • PR #1569: Several instances of Exception being raised are now replaced with other exceptions being raised.

  • PR #1577: Drops support for Python 3.8, following NEP-29.

Bugfixes

  • PR #1589: Fixes Issue #1579, where Molecule.from_polymer_pdb could not handle NH2 caps at C termini.

  • PR #1591: Fixes #1563, where from_rdkit would sometimes raise an error about radicals if a molecule using a non-MDL aromaticity model was provided.

Improved documentation and warnings

  • PR #1564: Improve documentation of conformer selection in Molecule.assign_partial_charges()

  • PR #1574: Fix class method signature rendering throughout API docs

  • PR #1584: Update some outdated docstrings and add some annotations.

Examples updates

  • PR #1575: The Toolkit Showcase example has been simplified via use of Topology.from_pdb

0.12.1

New features

  • PR #1502: Adds Gasteiger charge computation using the RDKit backend.

  • PR #1498: Molecule.remap() now supports partial mappings with the partial argument.

  • PR #1528: Topology.box_vectors are can now be set with openmm.unit.Quantitys, which are internally converted.

Behavior changes

  • PR #1498: New, more complete, and more descriptive errors for Molecule.remap().

  • PR #1525: Some unreleased force fields previously accessible from "openff/toolkit/data/test_forcefields/" are no longer implicitly available to the ForceField constructor.

  • PR #1545: Replaced the logic that sorts HierarchyElements with dedicated code in the OpenFF Toolkit instead of relying on deprecated features in the packaging module.

Bugfixes

  • PR #1543: Fixes a bug in which plugins are not loaded if a ForceField is constructed prior without plugins.

Improved documentation and warnings

  • PR #1498: Improved documentation for Molecule.remap(), Molecule.from_smiles(), and Molecule.from_mapped_smiles(), emphasizing the relationships between these methods. In particular, the documentation now clearly states that from_smiles() will not reorder atoms based on SMILES atom mapping.

  • PR #1525: Improves reporting failures when loading force fields.

  • PR #1513: Improves error messages and documentation around supported aromaticity models (currently only “OEAroModel_MDL”).

0.12.0

New features

  • PR #1484: A positions argument has been added to Topology.from_openmm() and Topology.from_mdtraj(), which allows the topology’s positions to be set more conveniently.

  • PR #1468: Track which ParameterHandlers are loaded as plugins.

Behavior changes

  • PR #1481: Removes compute_partial_charges_am1bcc, which was deprecated in 0.11.0.

  • PR #1466: Replaces the use of collections.OrderedDict throughout the toolkit with the built-in dict. attach_units, detach_units, and extract_serialized_units_from_dict have been removed from openff.toolkit.utils.utils.

  • PR #1472: Removes ParameterHandler._VALENCE_TYPE and the same attribute of its subclasses, which were previously not used. Also deprecates ChemicalEnvironment and, by extension, the openff.toolkit.typing.chemistry submodule.

Bugfixes

  • PR #1476: Fixes #1475 by also registering a ParameterHandler’s class when calling ForceField.register_parameter_handler.

  • PR #1480: Fixes #1479 by requiring that Atom.atomic_number is a positive integer.

  • PR #1494: Fixes #1493 in which some OFFXML file contents were parsed to unit.Quantity objects despite not representing physical quantities.

Improved documentation and warnings

  • PR #1484: The docstrings for Topology.from_openmm() and Topology.from_mdtraj() have been improved.

  • PR #1483: Simplified and clarified errors and warnings related to undefined stereochemistry with RDKit.

0.11.4 Bugfix release

Behavior changes

  • PR #1462: Makes residue numbers added by Molecule.perceive_residues strings (previously they were ints), to match the behavior of Topology.from_openmm and other hierarchy info-setting methods.

Bugfixes

  • PR #1459: Fixes #1430, where Topology.from_openmm would mis-assign atom names (and probably also hierarchy metadata as well).

  • PR #1462: Fixes #1461, where the default Molecule.residues iterator wouldn’t sort by residue number correctly when residue information was added by Molecule.perceive_residues.

0.11.3 Bugfix release

  • PR #1460: Disables error causing Issue #1432, where Molecule.from_polymer_pdb would sometimes issue stereochemistry errors when reading valid PDBs using the RDKit backend.

Bugfixes

  • PR #1436: Fix a small bug introduced in 0.11.2, where running with OpenEye installed but not licensed could lead to a crash.

  • PR #1444: Update for pint 0.20.

Examples updates

  • PR #1447: Fixed units of tolerance used in OpenMM minimization in Toolkit Showcase example notebook (from @ziyuanzhao2000)

Improved documentation and warnings

  • PR #1442: Doctests added to CI, leading to numerous fixed docstrings and examples therein.

Miscellaneous

  • PR #1413: Remove some large and unused data files from the test suite.

  • PR #1434: Remove dependency on typing_extensions.

0.11.2 Bugfix release

Behavior changes

  • PR #1421: Allow Molecule.from_rdkit() to load D- and F- block radicals, which cannot have implicit hydrogens.

Bug fixes

  • PR #1417: Ensure the properties dict is copied when a Molecule is.

Improved documentation and warnings

  • PR #1426: A warning about OpenEye Toolkits being unavailable is only emitted when they are installed but the license file is not found.

0.11.1 Minor release forbidding loading radicals

Behavior changes

  • PR #1398: Updates the Bond.bond_order setter to only accept int values.

  • PR #1236: from_rdkit and from_openeye now raise an RadicalsNotSupportedError when loading radicals. It’s not clear that the OpenFF Toolkit was ever safely handling radicals - they appear to be the root cause of many instances of unintended hydrogen addition and other connection table changes. If this change affects a workflow that was previously working correctly, please let us know on this issue so we can refine this behavior.

Examples changed

  • PR #1236: examples/check_dataset_parameter_coverage has been deprecated.

Bug fixes

  • PR #1400: Fixes a bug where Molecule.from_pdb_and_smiles could incorrectly order coordinates.

  • PR #1404: Support default hierarchy schemes in outputs of Molecule.from_pdb_and_smiles() and Topology.from_openmm()

0.11.0 Major release adding support for proteins and refactoring the Topology class.

Migration guide

New Molecule.from_polymer_pdb() method for loading proteins from PDB files

The Toolkit now supports loading protein PDB files through the Molecule.from_polymer_pdb() class method. For now, PDB files must consist of only a single protein molecule composed only of the 20 standard amino acids, their common protonated and deprotonated conjugates, and the N-methyl and acetyl caps.

Important API points re-exported from openff.toolkit

A number of commonly used API points have been re-exported from the package root. This should make using the Toolkit simpler for most people. The previous API points remain available. These API points are lazy-loaded so that parts of the toolkit can still be loaded without loading the entire code-base.

The most important of these are the ForceField, Molecule, and Topology classes:

- from openff.toolkit.typing.engines.smirnoff import ForceField
- from openff.toolkit.topology import Molecule, Topology
+ from openff.toolkit import ForceField, Molecule, Topology

A number of other useful API points are also available through this mechanism:

- from openff.toolkit.typing.engines.smirnoff import get_available_force_fields
- from openff.toolkit.utils.toolkits import (
-     GLOBAL_TOOLKIT_REGISTRY,
-     AmberToolsToolkitWrapper,
-     BuiltInToolkitWrapper,
-     OpenEyeToolkitWrapper,
-     RDKitToolkitWrapper,
-     ToolkitRegistry,
- )
+ from openff.toolkit import (
+     get_available_force_fields,
+     GLOBAL_TOOLKIT_REGISTRY,
+     AmberToolsToolkitWrapper,
+     BuiltInToolkitWrapper,
+     OpenEyeToolkitWrapper,
+     RDKitToolkitWrapper,
+     ToolkitRegistry,
+ )

The topology, typing, and utils modules can also be lazy loaded after importing only the top-level module:

- import openff.toolkit.topology
+ import openff.toolkit
  atom = openff.toolkit.topology.Atom()

Units

The use of OpenMM units has been replaced by the new OpenFF Units package, based on Pint.

Import the unit registry provided by openff-units:

from openff.units import unit

Create a unit.Quantity object:

value = unit.Quantity(1.0, unit.nanometer)  # or 1.0 * unit.nanometer

Inspect the value and unit of this quantity:

print(value.magnitude)  # or value.m
# 1.0
print(value.units)
# <Unit('nanometer')>

Convert to compatible units:

converted = value.to(unit.angstrom)
print(converted)
# 10.0 <Unit('angstrom')>

Report the value in compatible units:

print(value.m_as(unit.angstrom))  # Note that value.magnitude_as() does not exist
# 10.0 <Unit('angstrom')>

Convert to and from OpenMM quantities:

from openff.units.openmm import to_openmm, from_openmm
value_openmm = to_openmm(value)
print(value_openmm)
# Quantity(value=1.0, unit=nanometer)
print(type(value_openmm))
# 1.0 <Unit('nanometer')>
value_roundtrip = from_openmm(value_openmm)
print(value_roundtrip)
# 1.0 <Unit('nanometer')>

Breaking change: Removal of openff.toolkit.utils.check_units_are_compatible()

The openff.toolkit.utils.check_units_are_compatible() function has been removed. Use openff.units.Quantity.is_compatible_with() and openff.units.openmm.from_openmm() instead:

- check_units_are_compatible("length", length, openmm.unit.angstrom)
+ from_openmm(length).is_compatible_with(openff.units.unit.angstrom)

Breaking change: Interchange now responsible for system parametrization

Code for applying parameters to topologies has been removed from the Toolkit. This is now the responsibility of OpenFF Interchange. This change improves support for working with parametrized systems (through the Interchange class), and adds support for working with simulation engines other than OpenMM.

The ForceField.create_interchange() method has been added, and the ForceField.create_openmm_system() method now uses Interchange under the hood.

As part of this change, the UnsupportedKeywordArgumentsError has been removed; passing unknown arguments to create_openmm_system now raises a TypeError, as is normal in Python.

The following classes and methods have been removed from openff.toolkit.typing.engines.smirnoff.parameters:

  • NonintegralMoleculeChargeException

  • NonbondedMethod

  • ParameterHandler.assign_parameters()

  • ParameterHandler.postprocess_system()

  • ParameterHandler.check_partial_bond_orders_from_molecules_duplicates()

  • ParameterHandler.assign_partial_bond_orders_from_molecules()

In addition, the ParameterHandler.create_force() method has been deprecated and its functionality has been removed. It will be removed in a future release.

The return_topology argument of create_openmm_system has also been deprecated, and will be removed in 0.12.0. To create an OpenMM topology, use Interchange:

- omm_sys, off_top = force_field.create_openmm_system(
-     topology,
-     return_topology=True,
- )
- omm_top = off_top.to_openmm()
+ interchange = force_field.create_interchange(topology)
+ omm_sys = interchange.to_openmm(combine_nonbonded_forces=True)
+ omm_top = interchange.to_openmm_topology()

If you need access to the modified OpenFF topology for some other reason, create an Interchange and retrieve it there:

- omm_sys, off_top = force_field.create_openmm_system(
-     topology,
-     return_topology=True,
- )
+ interchange = force_field.create_interchange(topology)
+ off_top = interchange.topology
+ omm_sys = interchange.to_openmm(combine_nonbonded_forces=True)

Breaking change: Topology molecule representation

Topology objects now store complete copies of their constituent Molecule objects, rather than using simplified classes specific to Topology. This dramatically simplifies the code base and allows the use of the full Molecule API on molecules inside topologies.

The following classes have been removed:

  • TopologyAtom (use Atom instead)

  • TopologyBond (use Bond instead)

  • TopologyMolecule (use Molecule instead)

The following properties have been deprecated and will be removed in a future release:

In addition, the Topology.identical_molecule_groups property has been added, to facilitate iterating over copies of isomorphic molecules in a Topology.

Breaking change: Removed virtual site handling from topologies

To maintain a clear distinction between a model and the chemistry it represents, virtual site handling has been removed from the Toolkit’s Topology and Molecule classes. Virtual site support remains in the force field side of the toolkit, but creating virtual sites for particular molecules is now the responsibility of OpenFF Interchange. This allows the same Topology to be used for force fields that use different virtual sites; for example, a topology representing a solvated protein might be parametrized separately with a 3-point and 4-point water model.

As part of this change, the distinction between Atom and Particle is deprecated. The Particle class will be removed in a future release.

The following classes have been removed:

  • BondChargeVirtualSite

  • DivalentLonePairVirtualSite

  • MonovalentLonePairVirtualSite

  • TrivalentLonePairVirtualSite

  • VirtualParticle

  • VirtualSite

  • TopologyVirtualParticle

  • TopologyVirtualSite

The following methods and properties have been removed:

  • Atom.add_virtual_site()

  • Atom.virtual_sites

  • FrozenMolecule.compute_virtual_site_positions_from_conformer()

  • FrozenMolecule.compute_virtual_site_positions_from_atom_positions()

  • FrozenMolecule.n_virtual_sites

  • FrozenMolecule.n_virtual_particles

  • FrozenMolecule.virtual_sites()

  • Molecule.add_bond_charge_virtual_site()

  • Molecule.add_monovalent_lone_pair_virtual_site()

  • Molecule.add_divalent_lone_pair_virtual_site()

  • Molecule.add_trivalent_lone_pair_virtual_site()

  • Molecule.add_bond_charge_virtual_site()

  • Topology.n_topology_virtual_sites

  • Topology.topology_virtual_sites

  • Topology.virtual_site()

  • Topology.add_particle()

The following properties have been deprecated and will be removed in a future release:

Atom metadata and hierarchy schemes for iterating over residues, chains, etc.

The new Atom.metadata attribute is a dictionary that can store arbitrary metadata. Atom metadata commonly includes residue names, residue sequence numbers, chain identifiers, and other metadata that is not essential to the functioning of the Toolkit. Metadata can then be passed on when a Molecule is converted to another package; see Molecule conversion to other packages.

Metadata can also support iteration through the HierarchyScheme class. A hierarchy scheme is defined by some uniqueness criteria. Iterating over the scheme iterates over groups of atoms that have identical metadata values for the defined uniqueness criteria. For more information, see the API docs for HierarchyScheme and its related methods.

Breaking change: Removed Topology.charge_model and Topology.fractional_bond_order_model

Due to flaws in previous versions of the OFF Toolkit, these properties never had an effect on the assigned parameters. To resolve this bug and maintain a clear distinction between a model and the chemistry it represents, the Topology.charge_model and Topology.fractional_bond_order_model properties have been removed. Charge models and FBOs are now the responsibility of the ForceField.

Breaking change: Removed Atom.element

Atom.element has been removed to reduce our dependency on OpenMM for core functions:

- atomic_number = atom.element.atomic_number
+ atomic_number = atom.atomic_number
- atom_mass = atom.element.mass
+ atom_mass = atom.mass
- atom_elem_symbol = atom.element.symbol
+ atom_elem_symbol = atom.symbol

Topology.to_file()

The Topology.to_file() method has been significantly revised, including three breaking changes.

Breaking change: filename argument renamed file

The filename argument has been renamed file, and now supports file-like objects in addition to file names:

-  topology.to_file(filename="out.pdb", positions=xyz)
+  topology.to_file(file="out.pdb", positions=xyz)

Breaking change: Atom names guaranteed unique per residue by default

The default behavior is now to ensure that atom names are unique within a residue, rather than within a molecule. The ensure_unique_atom_names argument has been added to control this behavior. The previous behavior can be achieved by passing True to ensure_unique_atom_names:

- topology.to_file("out.pdb", xyz)
+ topology.to_file("out.pdb", xyz, ensure_unique_atom_names=True)

The ensure_unique_atom_names argument can also take the name of a HierarchyScheme, in which case atom names will be unique within the elements of that scheme (instead of within the atoms of a molecule). If the scheme is missing from a molecule, atom names will be unique within that molecule. The default value of this argument is "residues" to preserve atom names from the PDB.

Breaking change: keepIds argument renamed keep_ids

The keepIds argument has been renamed to the more Pythonic keep_ids. Its behavior and position in the argument list has not changed.

- topology.to_file("out.pdb", xyz, keepIds=True)
+ topology.to_file("out.pdb", xyz, keep_ids=True)

Non-breaking changes

In addition to these breaking changes, the positions argument is now optional. If it is not provided, positions will be taken from the first conformer of each molecule in the topology. If any molecule has no conformers, an error will be raised.

Positions in topologies

The Topology.get_positions() and Topology.set_positions() methods have been added to facilitate working with coordinates in topologies. A topology’s positions are defined by the zeroth conformer of each molecule. If any molecule lacks conformers, the entire topology has no positions.

Parameter types moved out of handler classes

To facilitate their discovery and documentation, re-exports for the ParameterType classes have been added to the openff.toolkit.typing.engines.smirnoff.parameters module. Previously, they were accessible only within their associated ParameterHandler classes. This is not a breaking change.

- from openff.toolkit.typing.engines.smirnoff.parameters import BondHandler
- BondType = BondHandler.BondType
+ from openff.toolkit.typing.engines.smirnoff.parameters import BondType

Breaking change: MissingDependencyError renamed MissingPackageError

The MissingDependencyError exception has been renamed MissingPackageError to better reflect its purpose.

  try:
      ...
- except MissingDependencyError:
+ except MissingPackageError:
      pass

compute_partial_charges_am1bcc() deprecated

The compute_partial_charges_am1bcc() methods of the Molecule, AmberToolsToolkitWrapper and OpenEyeToolkitWrapper classes have been deprecated and will be removed in a future release. Their functionality has been incorporated into assign_partial_charges() for more consistency with other charge generation methods:

- mol.compute_partial_charges_am1bcc()
+ mol.assign_partial_charges(partial_charge_method='am1bcc')

Additional changes and bugfixes

  • PR #1105, PR #1195, PR #1301, PR #1331, PR #1322, PR #1372: Add Molecule.from_polymer_pdb

  • PR #1377: Adds Topology.unique_molecules, which largely replaces Topology.reference_molecules.

  • PR #1313: Fixes Issue #1287, where OpenEyeToolkitWrapper.assign_partial_charges didn’t request symmetrized charges when the charge model was set to AM1-Mulliken.

  • PR #1348: Allows pathlib.Path objects to be passed to Molecule.from_file.

  • PR #1276: Removes the use_interchange argument to create_openmm_system. Deletes the create_force and postprocess_system methods of ParameterHandler and other methods related to creating OpenMM systems and forces. This is now handled in Interchange.

  • PR #1303: Deprecates Topology.particles, Topology.n_particles, Topology.particle_index as Molecule objects do not store virtual sites, only atoms.

  • PR #1297: Drops support for Python 3.7, following NEP-29.

  • PR #1194: Adds Topology.__add__, allowing Topology objects to be added together, including added in-place, using the + operator.

  • PR #1277: Adds support for version 0.4 of the <Electrostatics> section of the SMIRNOFF specification.

  • PR #1279: ParameterHandler.version and the .version attribute of its subclasses is now a Version object. Previously it was a string, which is not safe for PEP440-style versioning.

  • PR #1250: Adds support for return_topology in the Interchange code path in create_openmm_system.

  • PR #964: Adds initial implementation of atom metadata dictionaries.

  • PR #1097: Deprecates TopologyMolecule.

  • PR #1097: Topology.from_openmm is no longer guaranteed to maintain the ordering of bonds, but now explicitly guarantees that it maintains the order of atoms (Neither of these ordering guarantees were explicitly documented before, but this may be a change from the previous behavior).

  • PR #1165: Adds the boolean argument use_interchange to create_openmm_system with a default value of False. Setting it to True routes openmm.System creation through Interchange.

  • PR #1192: Add re-exports for core classes to the new openff.toolkit.app module and re-exports for parameter types to the new openff.toolkit.topology.parametertypes module. This does not affect existing paths and gives some new, easier to remember paths to core objects.

  • PR #1198: Ensure the vdW switch width is correctly set and enabled.

  • PR #1213: Removes Topology.charge_model and Topology.fractional_bond_order_model.

  • PR #1140: Adds the Topology.identical_molecule_groups property, which provides a way of grouping the instances of a specific chemical species in the topology.

  • PR #1200: Fixes a bug (Issue #1199) in which library charges were ignored in some force fields, including openff-2.0.0 code name “Sage.” This resulted in the TIP3P partial charges included Sage not being applied correctly in versions 0.10.1 and 0.10.2 of the OpenFF Toolkit. This regression was not present in version 0.10.0 and earlier and therefore is not believed to have any impact on the fitting or benchmarking of the first release of Sage (version 2.0.0). The change causing regression only affected library charges and therefore no other parameter types are believed to be affected.

  • PR #1346: Conformer generation with RDKit will use useRandomCoords=True on a second attempt if the first attempt fails, which sometimes happens with large molecules.

  • PR #1277: Version 0.3 <Electrostatics> sections of OFFXML files will automatically be up-converted (in memory) to version 0.4 according to the recomendations provided in OFF-EP 0005. Note this means the method attribute is replaced by periodic_potential, nonperiodic_potential, and exception_potential.

  • PR #1277: Fixes a bug in which attempting to convert ElectrostaticsHandler.switch_width did nothing.

  • PR #1130: Running unit tests will no longer generate force field files in the local directory.

  • PR #1182: Removes Atom.element, thereby also removing Atom.element.symbol, Atom.element.mass and Atom.element.atomic_number. These are replaced with corresponding properties directly on the Atom class: Atom.symbol, Atom.mass, and Atom.atomic_number.

  • PR #1209: Fixes Issue #1073, where the fractional_bondorder_method kwarg to the BondHandler initializer was being ignored.

  • PR #1214: A long overdue fix for Issue #837! If OpenEye is available, the ToolkitAM1BCCHandler will use the ELF10 method to select conformers for AM1BCC charge assignment.

  • PR #1160: Fixes the bug identified in Issue #1159, in which the order of atoms defining a BondChargeVirtualSite (and possibly other virtual sites types too) might be reversed if the match attribute of the virtual site has a value of "once".

  • PR #1231: Fixes Issue #1181 and Issue #1190, where in rare cases double bond stereo would cause to_rdkit to raise an error. The transfer of double bond stereochemistry from OpenFF’s E/Z representation to RDKit’s local representation is now handled as a constraint satisfaction problem.

  • PR #1368: Adds the Topology.get_positions() and Topology.set_positions() methods for working with topology positions. Positions are represented as the first conformer of each molecule in the topology.

  • PR #1368: Allows setting the ensure_unique_atom_names argument of Topology.to_openmm()to the name of a hierarchy scheme, in which case atom names are guaranteed unique per element of that scheme rather than per molecule. Changes the default value to "residues".

  • PR #1368: Adds the ensure_unique_atom_names argument to the Topology.to_file(), which mimics the same argument in Topology.to_openmm(). Renames the keepIds argument to keep_ids. Renames the filename argument to file and allows a file-like object to be passed instead of a filename. Makes the positions argument optional; if it is not given, positions are take from the first conformer of each molecule in the Topology.

  • PR #1290: Fixes Issue #1216 by adding internal logic to handle the possibility that multiple vsites share the same parent atom, and makes the return value of VirtualSiteHandler.find_matches be closer to the base class.

Examples added

  • PR #1113: Updates the Amber/GROMACS example to use Interchange.

  • PR #1368: Updates the Toolkit showcase with the new polymer handling and Interchange support

Tests updated

  • PR #1188: Add an <Electrostatics> section to the TIP3P force field file used in testing (test_forcefields/tip3p.offxml)

0.10.5 Bugfix release

  • PR #1252: Refactors virtual site support, resolving Issue #1235, Issue #1233, Issue #1222, Issue #1221, and Issue #1206.

    • Attempts to make virtual site handler more resilient through code simplification.

    • Virtual sites are now associated with a particular ‘parent’ atom, rather than with a set of atoms. In particular, when checking if a v-site has been assigned we now only check the main ‘parent’ atom associated with the v-site, rather than all additional orientation atoms. As an example, if a force field contained a bond-charge v-site that matches [O:1]=[C:2] and a monovalent lone pair that matches [O:1]=[C:2]-[*:3] in that order, then only the monovalent lone pair will be assigned to formaldehyde as the oxygen is the main atom that would be associated with both v-sites, and the monovalent lone pair appears later in the hierarchy. This constitutes a behaviour change over previous versions.

    • All v-site exclusion policies have been removed except for ‘parents’ which has been updated to match OFF-EP 0006.

    • checks have been added to enforce that the ‘match’ keyword complies with the SMIRNOFF spec.

    • Molecule virtual site classes no longer store FF data such as epsilon and sigma.

    • Sanity checks have been added when matching chemical environments for v-sites that ensure the environment looks like one of our expected test cases.

    • Fixes di- and trivalent lone pairs mixing the :1 and :2 indices.

    • Fixes trivalent v-site positioning.

    • Correctly splits TopologyVirtualSite and TopologyVirtualParticle so that virtual particles no longer have attributes such as particles, and ensure that indexing methods now work correctly.

0.10.4 Bugfix release

Critical bugfixes

  • PR #1242: Fixes Issue #837. If OpenEye Toolkits are available, ToolkitAM1BCCHandler will use the ELF10 method to select conformers for AM1-BCC charge assignment.

  • PR #1184: Fixes Issue #1181 and Issue #1190, where in rare cases double bond stereochemistry would cause Molecule.to_rdkit to raise an error. The transfer of double bond stereochemistry from OpenFF’s E/Z representation to RDKit’s local representation is now handled as a constraint satisfaction problem.

0.10.3 Bugfix release

Critical bugfixes

  • PR #1200: Fixes a bug (Issue #1199) in which library charges were ignored in some force fields, including openff-2.0.0 code name “Sage.” This resulted in the TIP3P partial charges included Sage not being applied correctly in versions 0.10.1 and 0.10.2 of the OpenFF Toolkit. This regression was not present in version 0.10.0 and earlier and therefore is not believed to have any impact on the fitting or benchmarking of the first release of Sage (version 2.0.0). The change causing the regression only affected library charges and therefore no other parameter types are believed to be affected.

API breaking changes

  • PR #855: In earlier versions of the toolkit, we had mistakenly made the assumption that cheminformatics toolkits agreed on the number and membership of rings. However we later learned that this was not true. This PR removes Molecule.rings and Molecule.n_rings. To find rings in a molecule, directly use a cheminformatics toolkit after using Molecule.to_rdkit or Molecule.to_openeye. Atom.is_in_ring and Bond.is_in_ring are now methods, not properties.

Behaviors changed and bugfixes

Behaviors changed and bugfixes

  • PR #1185: Removed length check in ValenceDict and fixed checking the permutations of dihedrals

Improved documentation and warnings

API breaking changes

0.10.2 Bugfix release

API-breaking changes

Behaviors changed and bugfixes

  • PR #1160: Fixes a major bug identified in Issue #1159, in which the order of atoms defining a BondChargeVirtualSite (and possibly other virtual sites types too) might be reversed if the match attribute of the virtual site has a value of "once".

  • PR #1130: Running unit tests will no longer generate force field files in the local directory.

  • PR #1148: Adds a new exception UnsupportedFileTypeError and descriptive error message when attempting to use Molecule.from_file to parse XYZ/.xyz files.

  • PR #1153: Fixes Issue #1152 in which running Molecule.generate_conformers using the OpenEye backend would use the stereochemistry from an existing conformer instead of the stereochemistry from the molecular graph, leading to undefined behavior if the molecule had a 2D conformer.

  • PR #1158: Fixes the default representation of Molecule failing in Jupyter notebooks when NGLview is not installed.

  • PR #1151: Fixes Issue #1150, in which calling Molecule.assign_fractional_bond_orders with all default arguments would lead to an error as a result of trying to lowercase None.

  • PR #1149: TopologyAtom, TopologyBond, and TopologyVirtualSite now properly reference their reference molecule from their .molecule attribute.

  • PR #1155: Ensures big-endian byte order of NumPy arrays when serialized to dictionaries or files formats except JSON.

  • PR #1163: Fixes the bug identified in Issue #1161, which was caused by the use of the deprecated pkg_resources package. Now the recommended importlib_metadata package is used instead.

Breaking changes

  • PR #1118: Molecule.to_hill_formula is now a class method and no longer accepts input of NetworkX graphs.

  • PR #1156: Removes ParseError and MessageException, which has been deprecated since version 0.10.0.

Examples added

  • PR #1113: Updates the Amber/GROMACS example to use Interchange.

0.10.1 Minor feature and bugfix release

Behaviors changed and bugfixes

  • PR #1096: Atom names generated by Molecule.generate_unique_atom_names are now appended with an "x". See the linked issue for more details.

  • PR #1050: In Molecule.generate_conformers, a single toolkit wrapper failing to generate conformers is no longer fatal, but if all wrappers in a registry fail, then a ValueError will be raised. This mirrors the behavior of Molecule.assign_partial_charges.

  • PR #1050: Conformer generation failures in OpenEyeToolkitWrapper.generate_conformers, and RDKitToolkitWrapper.generate_conformers now each raise openff.toolkit.utils.exceptions.ConformerGenerationError if conformer generation fails. The same behavior occurs in Molecule.generate_conformers, but only when the toolkit_registry argument is a ToolkitWrapper, not when it is a ToolkitRegistry.

  • PR #1046: Changes OFFXML output to replace tabs with 4 spaces to standardize representation in different text viewers.

  • PR #1001: RDKit Mol objects created through the Molecule.to_rdkit() method have the NoImplicit property set to True on all atoms. This prevents RDKit from incorrectly adding hydrogen atoms to to molecule.

  • PR #1058: Removes the unimplemented methods ForceField.create_parmed_structure, Topology.to_parmed, and Topology.from_parmed.

  • PR #1065: The example conformer_energies.py script now uses the Sage 2.0.0 force field.

  • PR #1036: SMARTS matching logic for library charges was updated to use only one unique match instead of enumerating all possible matches. This results in faster matching, particularly with larger molecules. No adverse side effects were found in testing, but bad behavior may possibly exist in some unknown cases. Note that the default behavior for other parameter handlers was not updated.

  • PR #1001: Revamped the Molecule.visualize() method’s rdkit backend for more pleasing and idiomatic 2D visualization by default.

  • PR #1087: Fixes Issue #1073 in which Molecule.__repr__ fails if the molecule can not be represented as a SMILES pattern. Now, if SMILES generation fails, the molecule will be described by its Hill formula.

  • PR #1052: Fixes Issue #986 by raising a subclass of AttributeError in _ParameterAttributeHandler.__getattr__

  • PR #1030: Fixes a bug in which the expectations for capitalization for values of bond_order_model attributes and keywords are inconsistent.

  • PR #1101: Fixes a bug in which calling to_qcschema on a molecule with no connectivity feeds QCElemental.Molecule an empty list for the connectivity field; now feeds None.

Tests updated

  • PR #1017: Ensures that OpenEye-only CI builds really do lack both AmberTools and RDKit.

Improved documentation and warnings

  • PR #1065: Example notebooks were updated to use the Sage Open Force Field

  • PR #1062: Rewrote installation guide for clarity and comprehensiveness.

0.10.0 Improvements for force field fitting

Behaviors changed

New features and behaviors changed

  • PR #1027: Corrects interconversion of Molecule objects with OEMol objects by ensuring atom names are correctly accessible via the OEAtomBase.GetName() and OEAtomBase.SetName() methods, rather that the non-standard OEAtomBase.GetData("name") and OEAtomBase.SetData("name", name).

  • PR #1007: Resolves Issue #456 by adding the normalize_partial_charges (default is True) keyword argument to Molecule.assign_partial_charges, AmberToolsToolkitWrapper.assign_partial_charges, OpenEyeToolkitWrapper.assign_partial_charges, RDKitToolkitWrapper.assign_partial_charges, and BuiltInToolkitWrapper.assign_partial_charges. This adds an offset to each atom’s partial charge to ensure that their sum is equal to the net charge on the molecule (to the limit of a python float’s precision, generally less than 1e-6 electron charge). Note that, because this new behavior is ON by default, it may slightly affect the partial charges and energies of systems generated by running create_openmm_system.

  • PR #954: Adds LibraryChargeType.from_molecule which returns a LibraryChargeType object that will match the full molecule being parameterized, and assign it the same partial charges as are set on the input molecule.

  • PR #923: Adds Molecule.nth_degree_neighbors, Topology.nth_degree_neighbors, TopologyMolecule.nth_degree_neighbors, which returns pairs of atoms that are separated in a molecule or topology by exactly N atoms.

  • PR #917: ForceField.create_openmm_system now ensures that the cutoff of the NonbondedForce is set to the cutoff of the vdWHandler when it and a Electrostatics handler are present in the force field.

  • PR #850: OpenEyeToolkitWrapper.is_available now returns True if any OpenEye tools are licensed (and installed). This allows, i.e, use of functionality that requires OEChem without having an OEOmega license.

  • PR #909: Virtual site positions can now be computed directly in the toolkit. This functionality is accessed through

    • FrozenMolecule.compute_virtual_site_positions_from_conformer

    • VirtualSite.compute_positions_from_conformer

    • VirtualParticle.compute_position_from_conformer

    • FrozenMolecule.compute_virtual_site_positions_from_atom_positions

    • VirtualSite.compute_positions_from_atom_positions

    • VirtualParticle.compute_position_from_atom_positions where the positions can be computed from a stored conformer, or an input vector of atom positions.

    • Tests have been added (TestMolecule.test_*_virtual_site_position) to check for sane behavior. The tests do not directly compare OpenMM position equivalence, but offline tests show that they are equivalent.

    • The helper method VirtualSiteHandler.create_openff_virtual_sites is now public, which returns a modified topology with virtual sites added.

    • Virtual sites now expose the parameters used to create its local frame via the read-only properties

      • VirtualSite.local_frame_weights

      • VirtualSite.local_frame_position

    • Adding virtual sites via the Molecule API now have defaults for sigma, epsilon, and charge_increment set to 0 with appropriate units, rather than None

  • PR #956: Added ForceField.get_partial_charges() to more easily compute the partial charges assigned by a force field for a molecule.

  • PR #1006: Two behavior changes in the SMILES output for to_file() and to_file_obj():

    • The RDKit and OpenEye wrappers now output the same SMILES as to_smiles(). This uses explicit hydrogens rather than the toolkit’s default of implicit hydrogens.

    • The RDKit wrapper no longer includes a header line. This improves the consistency between the OpenEye and RDKit outputs.

Bugfixes

  • PR #1024: Small changes for compatibility with OpenMM 7.6.

  • PR #1003: Fixes Issue #1000, where a stereochemistry warning is sometimes erroneously emitted when loading a stereogenic molecule using Molecule.from_pdb_and_smiles

  • PR #1002: Fixes a bug in which OFFXML files could inadvertently be loaded from subdirectories.

  • PR #969: Fixes a bug in which the cutoff distance of the NonbondedForce generated by ForceField.create_openmm_system was not set to the value specified by the vdW and Electrostatics handlers.

  • PR #909: Fixed several bugs related to creating an OpenMM system with virtual sites created via the Molecule virtual site API

  • PR #1006: Many small fixes to the toolkit wrapper I/O for better error handling, improved consistency between reading from a file vs. file object, and improved consistency between the RDKit and OEChem toolkit wrappers. For the full list see Issue #1005. Some of the more significant fixes are:

    • RDKitToolkitWrapper.from_file_obj() now uses the same structure normaliation as from_file().

    • from_smiles() now raises an openff.toolkit.utils.exceptions.SMILESParsingError if the SMILES could not be parsed.

    • OEChem input and output files now raise an OSError if the file could not be opened.

    • All input file object readers now support file objects open in binary mode.

Examples added

  • PR #763: Adds an introductory example showcasing the toolkit parameterizing a protein-ligand simulation.

  • PR #955: Refreshed the force field modification example

  • PR #934 and conda-forge/openff-toolkit-feedstock#9: Added openff-toolkit-examples Conda package for easy installation of examples and their dependencies. Simply conda install -c conda-forge openff-toolkit-examples and then run the openff-toolkit-examples script to copy the examples suite to a convenient place to run them!

Tests updated

  • PR #963: Several tests modules used functions from test_forcefield.py that created an OpenFF Molecule without a toolkit. These functions are now in their own module so they can be imported directly, without the overhead of going through test_forcefield.

  • PR #997: Several XML snippets in test_forcefield.py that were scattered around inside of classes and functions are now moved to the module level.

0.9.2 Minor feature and bugfix release

New features and behaviors changed

Bugfixes

Improved documentation and warnings

  • PR #862: Clarify that System objects produced by the toolkit are OpenMM Systems in anticipation of forthcoming OpenFF Systems. Fixes Issue #618.

  • PR #863: Documented how to build the docs in the developers guide.

  • PR #870: Reorganised documentation to improve discoverability and allow future additions.

  • PR #871: Changed Markdown parser from m2r2 to MyST for improved documentation rendering.

  • PR #880: Cleanup and partial rewrite of the developer’s guide.

  • PR #906: Cleaner instructions on how to setup development environment.

0.9.1 - Minor feature and bugfix release

New features

Behavior changed

  • PR #802: Fixes Issue #408. The 1-4 scaling factor for electrostatic interactions is now properly set by the value specified in the force field. Previously it fell back to a default value of 0.83333. The toolkit may now produce slightly different energies as a result of this change.

  • PR #839: The average WBO will now be returned when multiple conformers are provided to assign_fractional_bond_orders using use_conformers.

  • PR #816: Force field file paths are now loaded in a case-insensitive manner.

Bugfixes

  • PR #849: Changes create_openmm_system so that it no longer uses the conformers on existing reference molecules (if present) to calculate Wiberg bond orders. Instead, new conformers are always generated during parameterization.

Improved documentation and warnings

  • PR #838: Corrects spacing of “forcefield” to “force field” throughout documentation. Fixes Issue #112.

  • PR #846: Corrects dead links throughout release history. Fixes Issue #835.

  • PR #847: Documentation now compiles with far fewer warnings, and in many cases more correctly. Additionally, ParameterAttribute documentation no longer appears incorrectly in classes where it is used. Fixes Issue #397 .

0.9.0 - Namespace Migration

This release marks the transition from the old openforcefield branding over to its new identity as openff-toolkit. This change has been made to better represent the role of the toolkit, and highlight its place in the larger Open Force Field (OpenFF) ecosystem.

From version 0.9.0 onwards the toolkit will need to be imported as import openff.toolkit.XXX and from openff.toolkit import XXX.

API-breaking changes

  • PR #803: Migrates openforcefield imports to openff.toolkit.

0.8.4 - Minor feature and bugfix release

This release is intended to be functionally identical to 0.9.1. The only difference is that it uses the “openforcefield” namespace.

This release is a final patch for the 0.8.X series of releases of the toolkit, and also marks the last version of the toolkit which will be imported as import openforcefield.XXX / from openforcefield import XXX. From version 0.9.0 onwards the toolkit will be importable only as import openff.toolkit.XXX / from openff.toolkit import XXX.

Note This change will also be accompanied by a renaming of the package from openforcefield to openff-toolkit, so users need not worry about accidentally pulling in a version with changed imports. Users will have to explicitly choose to install the openff-toolkit package once released which will contain the breaking import changes.

0.8.3 - Major bugfix release

This release fixes a critical bug in van der Waals parameter assignment.

This release is also a final patch for the 0.8.X series of releases of the toolkit, and also marks the last version of the toolkit which will be imported as import openforcefield.XXX / from openforcefield import XXX. From version 0.9.0 onwards the toolkit will be importable only as import openff.toolkit.XXX / from openff.toolkit import XXX.

Note This change will also be accompanied by a renaming of the package from openforcefield to openff-toolkit, so users need not worry about accidentally pulling in a version with changed imports. Users will have to explicitly choose to install the openff-toolkit package once released which will contain the breaking import changes.

Bugfixes

  • PR #808: Fixes Issue #807, which tracks a major bug in the interconversion between a vdW sigma and rmin_half parameter.

New features

  • PR #794: Adds a decorator @requires_package that denotes a function requires an optional dependency.

  • PR #805: Adds a deprecation warning for the up-coming release of the openff-toolkit package and its import breaking changes.

0.8.2 - Bugfix release

WARNING: This release was later found to contain a major bug, Issue #807, and produces incorrect energies.

Bugfixes

  • PR #786: Fixes Issue #785 where RDKitToolkitWrapper would sometimes expect stereochemistry to be defined for non-stereogenic bonds when loading from SDF.

  • PR #786: Fixes an issue where using the Molecule copy constructor (newmol = Molecule(oldmol)) would result in the copy sharing the same .properties dict as the original (as in, changes to the .properties dict of the copy would be reflected in the original).

  • PR #789: Fixes a regression noted in Issue #788 where creating vdWHandler.vdWType or setting sigma or rmin_half using Quantities represented as strings resulted in an error.

0.8.1 - Bugfix and minor feature release

WARNING: This release was later found to contain a major bug, Issue #807, and produces incorrect energies.

API-breaking changes

  • PR #757: Renames test_forcefields/smirnoff99Frosst.offxml to test_forcefields/test_forcefield.offxml to avoid confusion with any of the ACTUAL released FFs in the smirnoff99Frosst line

  • PR #751: Removes the optional oetools=("oechem", "oequacpac", "oeiupac", "oeomega") keyword argument from OpenEyeToolkitWrapper.is_available, as there are no special behaviors that are accessed in the case of partially-licensed OpenEye backends. The new behavior of this method is the same as if the default value above is always provided.

Behavior Changed

New features

Bugfixes

0.8.0 - Virtual Sites

Major Feature: Support for the SMIRNOFF VirtualSite tag

This release implements the SMIRNOFF virtual site specification. The implementation enables support for models using off-site charges, including 4- and 5-point water models, in addition to lone pair modeling on various functional groups. The primary focus was on the ability to parameterize a system using virtual sites, and generating an OpenMM system with all virtual sites present and ready for evaluation. Support for formats other than OpenMM has not be implemented in this release, but may come with the appearance of the OpenFF system object. In addition to implementing the specification, the toolkit Molecule objects now allow the creation and manipulation of virtual sites.

This change is documented in the Virtual sites page of the user guide.

Minor Feature: Support for the 0.4 ChargeIncrementModel tag

To allow for more convenient fitting of ChargeIncrement parameters, it is now possible to specify one less charge_increment value than there are tagged atoms in a ChargeIncrement’s smirks. The missing charge_increment value will be calculated at parameterization-time to make the sum of the charge contributions from a ChargeIncrement parameter equal to zero. Since this change allows for force fields that are incompatible with the previous specification, this new style of ChargeIncrement must specify a ChargeIncrementModel section version of 0.4. All 0.3-compatible ChargeIncrement parameters are compatible with the 0.4 ChargeIncrementModel specification.

More details and examples of this change are available in The ChargeIncrementModel tag in the SMIRNOFF specification

New features

  • PR #726: Adds support for the 0.4 ChargeIncrementModel spec, allowing for the specification of one fewer charge_increment values than there are tagged atoms in the smirks, and automatically assigning the final atom an offsetting charge.

  • PR #548: Adds support for the VirtualSites tag in the SMIRNOFF specification

  • PR #548: Adds replace and all_permutations kwarg to

    • Molecule.add_bond_charge_virtual_site

    • Molecule.add_monovalent_lone_pair_virtual_site

    • Molecule.add_divalent_lone_pair_virtual_site

    • Molecule.add_trivalent_lone_pair_virtual_site

  • PR #548: Adds orientations to

    • BondChargeVirtualSite

    • MonovalentLonePairVirtualSite

    • DivalentLonePairVirtualSite

    • TrivalentLonePairVirtualSite

  • PR #548: Adds

  • PR #705: Adds interpolation based on fractional bond orders for harmonic bonds. This includes interpolation for both the force constant k and/or equilibrium bond distance length. This is accompanied by a bump in the <Bonds> section of the SMIRNOFF spec (but not the entire spec).

  • PR #718: Adds .rings and .n_rings to Molecule and .is_in_ring to Atom and Bond

Bugfixes

Behavior changed

  • PR #705: Changes the default values in the <Bonds> section of the SMIRNOFF spec to fractional_bondorder_method="AM1-Wiberg" and potential="(k/2)*(r-length)^2", which is backwards-compatible with and equivalent to potential="harmonic".

Examples added

  • PR #548: Adds a virtual site example notebook to run an OpenMM simulation with virtual sites, and compares positions and potential energy of TIP5P water between OpenFF and OpenMM force fields.

API-breaking changes

  • PR #548: Methods

    • Molecule.add_bond_charge_virtual_site

    • Molecule.add_monovalent_lone_pair_virtual_site

    • Molecule.add_divalent_lone_pair_virtual_site

    • Molecule.add_trivalent_lone_pair_virtual_site

    now only accept a list of atoms, not a list of integers, to define to parent atoms

  • PR #548: Removes VirtualParticle.molecule_particle_index

  • PR #548: Removes outOfPlaneAngle from

    • DivalentLonePairVirtualSite

    • TrivalentLonePairVirtualSite

  • PR #548: Removes inPlaneAngle from TrivalentLonePairVirtualSite

  • PR #548: Removes weights from

    • BondChargeVirtualSite

    • MonovalentLonePairVirtualSite

    • DivalentLonePairVirtualSite

    • TrivalentLonePairVirtualSite

Tests added

  • PR #548: Adds test for

    • The virtual site parameter handler

    • TIP5P water dimer energy and positions

    • Adds tests to for virtual site/particle indexing/counting

0.7.2 - Bugfix and minor feature release

New features

Behavior changed

  • PR #684: Changes ToolkitRegistry to return an empty registry when initialized with no arguments, i.e. ToolkitRegistry() and makes the register_imported_toolkit_wrappers argument private.

  • PR #711: The setter for Topology.box_vectors now infers box vectors (a 3x3 matrix) when box lengths (a 3x1 array) are passed, assuming an orthogonal box.

  • PR #649: Makes SMARTS searches stereochemistry-specific (if stereo is specified in the SMARTS) for both OpenEye and RDKit backends. Also ensures molecule aromaticity is re-perceived according to the ForceField’s specified aromaticity model, which may overwrite user-specified aromaticity on the Molecule

  • PR #648: Removes the utils.structure module, which was deprecated in 0.2.0.

  • PR #670: Makes the Topology returned by create_openmm_system contain the partial charges and partial bond orders (if any) assigned during parameterization.

  • PR #675 changes the exception raised when no antechamber executable is found from IOError to AntechamberNotFoundError

  • PR #696 Adds an aromaticity_model keyword argument to the ForceField constructor, which defaults to DEFAULT_AROMATICITY_MODEL.

Bugfixes

  • PR #715: Closes issue Issue #475 writing a “PDB” file using OE backend rearranges the order of the atoms by pushing the hydrogens to the bottom.

  • PR #649: Prevents 2020 OE toolkit from issuing a warning caused by doing stereo-specific smarts searches on certain structures.

  • PR #724: Closes issue Issue #502 Adding a utility function Topology.to_file() to write topology and positions to a “PDB” file using openmm backend for pdb file write.

Tests added

  • PR #694: Adds automated testing to code snippets in docs.

  • PR #715: Adds tests for pdb file writes using OE backend.

  • PR #724: Adds tests for the utility function Topology.to_file().

0.7.1 - OETK2020 Compatibility and Minor Update

This is the first of our patch releases on our new planned monthly release schedule.

Detailed release notes are below, but the major new features of this release are updates for compatibility with the new 2020 OpenEye Toolkits release, the get_available_force_fields function, and the disregarding of pyrimidal nitrogen stereochemistry in molecule isomorphism checks.

Behavior changed

  • PR #646: Checking for Molecule equality using the == operator now disregards all pyrimidal nitrogen stereochemistry by default. To re-enable, use Molecule.{is|are}_isomorphic with the strip_pyrimidal_n_atom_stereo=False keyword argument.

  • PR #646: Adds an optional toolkit_registry keyword argument to Molecule.are_isomorphic, which identifies the toolkit that should be used to search for pyrimidal nitrogens.

Bugfixes

New features

0.7.0 - Charge Increment Model, Proper Torsion interpolation, and new Molecule methods

This is a relatively large release, motivated by the idea that changing existing functionality is bad so we shouldn’t do it too often, but when we do change things we should do it all at once.

Here’s a brief rundown of what changed, migration tips, and how to find more details in the full release notes below:

  • To provide more consistent partial charges for a given molecule, existing conformers are now disregarded by default by Molecule.assign_partial_charges. Instead, new conformers are generated for use in semiempirical calculations. Search for use_conformers.

  • Formal charges are now always returned as simtk.unit.Quantity objects, with units of elementary charge. To convert them to integers, use from simtk import unit and atom.formal_charge.value_in_unit(unit.elementary_charge) or mol.total_charge.value_in_unit(unit.elementary_charge). Search atom.formal_charge.

  • The OpenFF Toolkit now automatically reads and writes partial charges in SDF files. Search for atom.dprop.PartialCharges.

  • The OpenFF Toolkit now has different behavior for handling multi-molecule and multi-conformer SDF files. Search multi-conformer.

  • The OpenFF Toolkit now distinguishes between partial charges that are all-zero and partial charges that are unknown. Search partial_charges = None.

  • Topology.to_openmm now assigns unique atoms names by default. Search ensure_unique_atom_names.

  • Molecule equality checks are now done by graph comparison instead of SMILES comparison. Search Molecule.are_isomorphic.

  • The ChemicalEnvironment module was almost entirely removed, as it is an outdated duplicate of some Chemper functionality. Search ChemicalEnvironment.

  • TopologyMolecule.topology_particle_start_index has been removed from the TopologyMolecule API, since atoms and virtualsites are no longer contiguous in the Topology particle indexing system. Search topology_particle_start_index.

  • compute_wiberg_bond_orders has been renamed to assign_fractional_bond_orders.

There are also a number of new features, such as:

  • Support for ChargeIncrementModel sections in force fields.

  • Support for ProperTorsion k interpolation in force fields using fractional bond orders.

  • Support for AM1-Mulliken, Gasteiger, and other charge methods using the new assign_partial_charges methods.

  • Support for AM1-Wiberg bond order calculation using either the OpenEye or RDKit/AmberTools backends and the assign_fractional_bond_orders methods.

  • Initial (limited) interoperability with QCArchive, via Molecule.to_qcschema and from_qcschema.

  • A Molecule.visualize method.

  • Several additional Molecule methods, including state enumeration and mapped SMILES creation.

Major Feature: Support for the SMIRNOFF ChargeIncrementModel tag

The ChargeIncrementModel tag in the SMIRNOFF specification provides analagous functionality to AM1-BCC, except that instead of AM1-Mulliken charges, a number of different charge methods can be called, and instead of a fixed library of two-atom charge corrections, an arbitrary number of SMIRKS-based, N-atom charge corrections can be defined in the SMIRNOFF format.

The initial implementation of the SMIRNOFF ChargeIncrementModel tag accepts keywords for version, partial_charge_method, and number_of_conformers. partial_charge_method can be any string, and it is up to the ToolkitWrapper’s compute_partial_charges methods to understand what they mean. For geometry-independent partial_charge_method choices, number_of_conformers should be set to zero.

SMIRKS-based parameter application for ChargeIncrement parameters is different than other SMIRNOFF sections. The initial implementation of ChargeIncrementModelHandler follows these rules:

  • an atom can be subject to many ChargeIncrement parameters, which combine additively.

  • a ChargeIncrement that matches a set of atoms is overwritten only if another ChargeIncrement matches the same group of atoms, regardless of order. This overriding follows the normal SMIRNOFF hierarchy.

To give a concise example, what if a molecule A-B(-C)-D were being parametrized, and the force field defined ChargeIncrement SMIRKS in the following order?

  1. [A:1]-[B:2]

  2. [B:1]-[A:2]

  3. [A:1]-[B:2]-[C:3]

  4. [*:1]-[B:2](-[*:3])-[*:4]

  5. [D:1]-[B:2](-[*:3])-[*:4]

In the case above, the ChargeIncrement from parameters 1 and 4 would NOT be applied to the molecule, since another parameter matching the same set of atoms is specified further down in the parameter hierarchy (despite those subsequent matches being in a different order).

Ultimately, the ChargeIncrement contributions from parameters 2, 3, and 5 would be summed and applied.

It’s also important to identify a behavior that these rules were written to avoid: if not for the “regardless of order” clause in the second rule, parameters 4 and 5 could actually have been applied six and two times, respectively (due to symmetry in the SMIRKS and the use of wildcards). This situation could also arise as a result of molecular symmetry. For example, a methyl group could match the SMIRKS [C:1]([H:2])([H:3])([H:4]) six ways (with different orderings of the three hydrogen atoms), but the user would almost certainly not intend for the charge increments to be applied six times. The “regardless of order” clause was added specifically to address this.

In short, the first time a group of atoms becomes involved in a ChargeIncrement together, the OpenMM System gains a new parameter “slot”. Only another ChargeIncrement which applies to the exact same group of atoms (in any order) can take over the “slot”, pushing the original ChargeIncrement out.

Major Feature: Support for ProperTorsion k value interpolation

Chaya Stern’s work showed that we may be able to produce higher-quality proper torsion parameters by taking into account the “partial bond order” of the torsion’s central bond. We now have the machinery to compute AM1-Wiberg partial bond orders for entire molecules using the assign_fractional_bond_orders methods of either OpenEyeToolkitWrapper or AmberToolsToolkitWrapper. The thought is that, if some simple electron population analysis shows that a certain aromatic bond’s order is 1.53, maybe rotations about that bond can be described well by interpolating 53% of the way between the single and double bond k values.

Full details of how to define a torsion-interpolating SMIRNOFF force fields are available in the ProperTorsions section of the SMIRNOFF specification.

Behavior changed

  • PR #508: In order to provide the same results for the same chemical species, regardless of input conformation, Molecule assign_partial_charges, compute_partial_charges_am1bcc, and assign_fractional_bond_orders methods now default to ignore input conformers and generate new conformer(s) of the molecule before running semiempirical calculations. Users can override this behavior by specifying the keyword argument use_conformers=molecule.conformers.

  • PR #281: Closes Issue #250 by adding support for partial charge I/O in SDF. The partial charges are stored as a property in the SDF molecule block under the tag <atom.dprop.PartialCharge>.

  • PR #281: If a Molecule’s partial_charges attribute is set to None (the default value), calling to_openeye will now produce a OE molecule with partial charges set to nan. This would previously produce an OE molecule with partial charges of 0.0, which was a loss of information, since it wouldn’t be clear whether the original OFFMol’s partial charges were REALLY all-zero as opposed to None. OpenEye toolkit wrapper methods such as from_smiles and from_file now produce OFFMols with partial_charges = None when appropriate (previously these would produce OFFMols with all-zero charges, for the same reasoning as above).

  • PR #281: Molecule to_rdkit now sets partial charges on the RDAtom’s PartialCharges property (this was previously set on the partial_charges property). If the Molecule’s partial_charges attribute is None, this property will not be defined on the RDAtoms.

  • PR #281: Enforce the behavior during SDF I/O that a SDF may contain multiple molecules, but that the OFF Toolkit does not assume that it contains multiple conformers of the same molecule. This is an important distinction, since otherwise there is ambiguity around whether properties of one entry in a SDF are shared among several molecule blocks or not, or how to resolve conflicts if properties are defined differently for several “conformers” of chemically-identical species (More info here). If the user requests the OFF Toolkit to write a multi-conformer Molecule to SDF, only the first conformer will be written. For more fine-grained control of writing properties, conformers, and partial charges, consider using Molecule.to_rdkit or Molecule.to_openeye and using the functionality offered by those packages.

  • PR #281: Due to different constraints placed on the data types allowed by external toolkits, we make our best effort to preserve Molecule properties when converting molecules to other packages, but users should be aware that no guarantee of data integrity is made. The only data format for keys and values in the property dict that we will try to support through a roundtrip to another toolkit’s Molecule object is string.

  • PR #574: Removed check that all partial charges are zero after assignment by quacpac when AM1BCC used for charge assignment. This check fails erroneously for cases in which the partial charge assignments are correctly all zero, such as for N#N. It is also an unnecessary check given that quacpac will reliably indicate when it has failed to assign charges.

  • PR #597: Energy-minimized sample systems with Parsley 1.1.0.

  • PR #558: The Topology particle indexing system now orders TopologyVirtualSites after all atoms.

  • PR #469: When running Topology.to_openmm, unique atom names are generated if the provided atom names are not unique (overriding any existing atom names). This uniqueness extends only to atoms in the same molecule. To disable this behavior, set the kwarg ensure_unique_atom_names=False.

  • PR #472: Molecule.__eq__ now uses the new Molecule.are_isomorphic to perform the similarity checking.

  • PR #472: The Topology.from_openmm and Topology.add_molecule methods now use the Molecule.are_isomorphic method to match molecules.

  • PR #551: Implemented the ParameterHandler.get_parameter function (would previously return None).

API-breaking changes

  • PR #471: Closes Issue #465. atom.formal_charge and molecule.total_charge now return simtk.unit.Quantity objects instead of integers. To preserve backward compatibility, the setter for atom.formal_charge can accept either a simtk.unit.Quantity or an integer.

  • PR #601: Removes almost all of the previous ChemicalEnvironment API, since this entire module was simply copied from Chemper several years ago and has fallen behind on updates. Currently only ChemicalEnvironment.get_type, ChemicalEnvironment.validate, and an equivalent classmethod ChemicalEnvironment.validate_smirks remain. Also, please comment on this GitHub issue if you HAVE been using the previous extra functionality in this module and would like us to prioritize creation of a Chemper conda package.

  • PR #558: Removes TopologyMolecule.topology_particle_start_index, since the Topology particle indexing system now orders TopologyVirtualSites after all atoms. TopologyMolecule.atom_start_topology_index and TopologyMolecule.virtual_particle_start_topology_index are still available to access the appropriate values in the respective topology indexing systems.

  • PR #508: OpenEyeToolkitWrapper.compute_wiberg_bond_orders is now OpenEyeToolkitWrapper.assign_fractional_bond_orders. The charge_model keyword is now bond_order_model. The allowed values of this keyword have changed from am1 and pm3 to am1-wiberg and pm3-wiberg, respectively.

  • PR #508: Molecule.compute_wiberg_bond_orders is now Molecule.assign_fractional_bond_orders.

  • PR #595: Removed functions openforcefield.utils.utils.temporary_directory and openforcefield.utils.utils.temporary_cd and replaced their behavior with tempfile.TemporaryDirectory().

New features

  • PR #471: Closes Issue #208 by implementing support for the ChargeIncrementModel tag in the SMIRNOFF specification.

  • PR #471: Implements Molecule.assign_partial_charges, which calls one of the newly-implemented OpenEyeToolkitWrapper.assign_partial_charges, and AmberToolsToolkitWrapper.assign_partial_charges. strict_n_conformers is a optional boolean keyword argument indicating whether an IncorrectNumConformersError should be raised if an invalid number of conformers is supplied during partial charge calculation. For example, if two conformers are supplied, but partial_charge_method="AM1BCC" is also set, then there is no clear use for the second conformer. The previous behavior in this case was to raise a warning, and to preserve that behavior, strict_n_conformers defaults to a value of False.

  • PR #471: Adds keyword argument raise_exception_types (default: [Exception]) to ToolkitRegistry.call. The default value will provide the previous OpenFF Toolkit behavior, which is that the first ToolkitWrapper that can provide the requested method is called, and it either returns on success or raises an exception. This new keyword argument allows the ToolkitRegistry to ignore certain exceptions, but treat others as fatal. If raise_exception_types = [], the ToolkitRegistry will attempt to call each ToolkitWrapper that provides the requested method and if none succeeds, a single ValueError will be raised, with text listing the errors that were raised by each ToolkitWrapper.

  • PR #601: Adds RDKitToolkitWrapper.get_tagged_smarts_connectivity and OpenEyeToolkitWrapper.get_tagged_smarts_connectivity, which allow the use of either toolkit for smirks/tagged smarts validation.

  • PR #600: Adds ForceField.__getitem__ to look up ParameterHandler objects based on their string names.

  • PR #508: Adds AmberToolsToolkitWrapper.assign_fractional_bond_orders.

  • PR #469: The Molecule class adds Molecule.has_unique_atom_names and Molecule.has_unique_atom_names.

  • PR #472: Adds to the Molecule class Molecule.are_isomorphic and Molecule.is_isomorphic_with and Molecule.hill_formula and Molecule.to_hill_formula and Molecule.to_qcschema and Molecule.from_qcschema and Molecule.from_mapped_smiles and Molecule.from_pdb_and_smiles and Molecule.canonical_order_atoms and Molecule.remap

    … note:: The to_qcschema method accepts an extras dictionary which is passed into the validated qcelemental.models.Molecule object.

  • PR #506: The Molecule class adds Molecule.find_rotatable_bonds

  • PR #521: Adds Molecule.to_inchi and Molecule.to_inchikey and Molecule.from_inchi

    … warning:: InChI was not designed as an molecule interchange format and using it as one is not recommended. Many round trip tests will fail when using this format due to a loss of information. We have also added support for fixed hydrogen layer nonstandard InChI which can help in the case of tautomers, but overall creating molecules from InChI should be avoided.

  • PR #529: Adds the ability to write out to XYZ files via Molecule.to_file Both single frame and multiframe XYZ files are supported. Note reading from XYZ files will not be supported due to the lack of connectivity information.

  • PR #535: Extends the the API for the Molecule.to_smiles to allow for the creation of cmiles identifiers through combinations of isomeric, explicit hydrogen and mapped smiles, the default settings will return isomeric explicit hydrogen smiles as expected.

      .. warning::
     Atom maps can be supplied to the properties dictionary to modify which atoms have their map index included,
     if no map is supplied all atoms will be mapped in the order they appear in the
     [`Molecule`](openff.toolkit.topology.Molecule).

  • PR #563: Adds test_forcefields/ion_charges.offxml, giving LibraryCharges for monatomic ions.

  • PR #543: Adds 3 new methods to the Molecule class which allow the enumeration of molecule states. These are Molecule.enumerate_tautomers, Molecule.enumerate_stereoisomers, Molecule.enumerate_protomers

    .. warning::
   Enumerate protomers is currently only available through the OpenEye toolkit.

  • PR #573: Adds quacpac error output to quacpac failure in Molecule.compute_partial_charges_am1bcc.

  • PR #560: Added visualization method to the the Molecule class.

  • PR #620: Added the ability to register parameter handlers via entry point plugins. This functionality is accessible by initializing a ForceField with the load_plugins=True keyword argument.

  • PR #582: Added fractional bond order interpolation Adds return_topology kwarg to Forcefield.create_openmm_system, which returns the processed topology along with the OpenMM System when True (default False).

Tests added

Bugfixes

  • PR #558: Fixes a bug where TopologyVirtualSite.atoms would not correctly apply TopologyMolecule atom ordering on top of the reference molecule ordering, in cases where the same molecule appears multiple times, but in a different order, in the same Topology.

  • Issue #460: Creates unique atom names in Topology.to_openmm if the existing ones are not unique. The lack of unique atom names had been causing problems in workflows involving downstream tools that expect unique atom names.

  • Issue #448: We can now make molecules from mapped smiles using Molecule.from_mapped_smiles where the order will correspond to the indeing used in the smiles. Molecules can also be re-indexed at any time using the Molecule.remap.

  • Issue #462: We can now instance the Molecule from a QCArchive entry record instance or dictionary representation.

  • Issue #412: We can now instance the Molecule using Molecule.from_mapped_smiles. This resolves an issue caused by RDKit considering atom map indices to be a distinguishing feature of an atom, which led to erroneous definition of chirality (as otherwise symmetric substituents would be seen as different). We anticipate that this will reduce the number of times you need to type allow_undefined_stereo=True when processing molecules that do not actually contain stereochemistrty.

  • Issue #513: The Molecule.to_rdkit now re-sets the aromaticity model after sanitizing the molecule.

  • Issue #500: The Molecule.find_rotatable_bonds has been added which returns a list of rotatable Bond instances for the molecule.

  • Issue #491: We can now parse large molecules without hitting a match limit cap.

  • Issue #474: We can now convert molecules to InChI and InChIKey and from InChI.

  • Issue #523: The Molecule.to_file method can now correctly write to MOL files, in line with the supported file type list.

  • Issue #568: The Molecule.to_file can now correctly write multi-model PDB files when using the RDKit backend toolkit.

Examples added

0.6.0 - Library Charges

This release adds support for a new SMIRKS-based charge assignment method, Library Charges. The addition of more charge assignment methods opens the door for new types of experimentation, but also introduces several complex behaviors and failure modes. Accordingly, we have made changes to the charge assignment infrastructure to check for cases when partial charges do not sum to the formal charge of the molecule, or when no charge assignment method is able to generate charges for a molecule. More detailed explanation of the new errors that may be raised and keywords for overriding them are in the “Behavior Changed” section below.

With this release, we update test_forcefields/tip3p.offxml to be a working example of assigning LibraryCharges. However, we do not provide any force field files to assign protein residue LibraryCharges. If you are interested in translating an existing protein FF to SMIRNOFF format or developing a new one, please feel free to contact us on the Issue tracker or open a Pull Request.

New features

  • PR #433: Closes Issue #25 by adding initial support for the LibraryCharges tag in the SMIRNOFF specification using LibraryChargeHandler. For a molecule to have charges assigned using Library Charges, all of its atoms must be covered by at least one LibraryCharge. If an atom is covered by multiple LibraryCharge s, then the last LibraryCharge matched will be applied (per the hierarchy rules in the SMIRNOFF format).

    This functionality is thus able to apply per-residue charges similar to those in traditional protein force fields. At this time, there is no concept of “residues” or “fragments” during parametrization, so it is not possible to assign charges to some atoms in a molecule using LibraryCharge s, but calculate charges for other atoms in the same molecule using a different method. To assign charges to a protein, LibraryCharges SMARTS must be provided for the residues and protonation states in the molecule, as well as for any capping groups and post-translational modifications that are present.

    It is valid for LibraryCharge SMARTS to partially overlap one another. For example, a molecule consisting of atoms A-B-C connected by single bonds could be matched by a SMIRNOFF LibraryCharges section containing two LibraryCharge SMARTS: A-B and B-C. If listed in that order, the molecule would be assigned the A charge from the A-B LibraryCharge element and the B and C charges from the B-C element. In testing, these types of partial overlaps were found to frequently be sources of undesired behavior, so it is recommended that users define whole-molecule LibraryCharge SMARTS whenever possible.

  • PR #455: Addresses Issue #393 by adding ParameterHandler.attribute_is_cosmetic and ParameterType.attribute_is_cosmetic, which return True if the provided attribute name is defined for the queried object but does not correspond to an allowed value in the SMIRNOFF spec.

Behavior changed

  • PR #433: If a molecule can not be assigned charges by any charge-assignment method, an openforcefield.typing.engines.smirnoff.parameters.UnassignedMoleculeChargeException will be raised. Previously, creating a system without either ToolkitAM1BCCHandler or the charge_from_molecules keyword argument to ForceField.create_openmm_system would produce an OpenMM System where the molecule has zero charge on all atoms. However, given that we will soon be adding more options for charge assignment, it is important that failures not be silent. Molecules with zero charge can still be produced by setting the Molecule.partial_charges array to be all zeroes, and including the molecule in the charge_from_molecules keyword argument to create_openmm_system.

  • PR #433: Due to risks introduced by permitting charge assignment using partially-overlapping LibraryCharge s, the toolkit will now raise a openforcefield.typing.engines.smirnoff.parameters.NonIntegralMoleculeChargeException if the sum of partial charges on a molecule are found to be more than 0.01 elementary charge units different than the molecule’s formal charge. This exception can be overridden by providing the allow_nonintegral_charges=True keyword argument to ForceField.create_openmm_system.

Tests added

  • PR #430: Added test for Wiberg Bond Order implemented in OpenEye Toolkits. Molecules taken from DOI:10.5281/zenodo.3405489 . Added by Sukanya Sasmal.

  • PR #569: Added round-trip tests for more serialization formats (dict, YAML, TOML, JSON, BSON, messagepack, pickle). Note that some are unsupported, but the tests raise the appropriate error.

Bugfixes

  • PR #431: Fixes an issue where ToolkitWrapper objects would improperly search for functionality in the GLOBAL_TOOLKIT_REGISTRY, even though a specific ToolkitRegistry was requested for an operation.

  • PR #439: Fixes Issue #438, by replacing call to NetworkX Graph.node with call to Graph.nodes, per 2.4 migration guide.

Files modified

  • PR #433: Updates the previously-nonfunctional test_forcefields/tip3p.offxml to a functional state by updating it to the SMIRNOFF 0.3 specification, and specifying atomic charges using the LibraryCharges tag.

0.5.1 - Adding the parameter coverage example notebook

This release contains a new notebook example, check_parameter_coverage.ipynb, which loads sets of molecules, checks whether they are parameterizable, and generates reports of chemical motifs that are not. It also fixes several simple issues, improves warnings and docstring text, and removes unused files.

The parameter coverage example notebook goes hand-in-hand with the release candidate of our initial force field, openff-1.0.0-RC1.offxml , which will be temporarily available until the official force field release is made in October. Our goal in publishing this notebook alongside our first major refitting is to allow interested users to check whether there is parameter coverage for their molecules of interest. If the force field is unable to parameterize a molecule, this notebook will generate reports of the specific chemistry that is not covered. We understand that many organizations in our field have restrictions about sharing specific molecules, and the outputs from this notebook can easily be cropped to communicate unparameterizable chemistry without revealing the full structure.

The force field release candidate is in our new refit force field package, openforcefields. This package is now a part of the Open Force Field Toolkit conda recipe, along with the original smirnoff99Frosst line of force fields.

Once the openforcefields conda package is installed, you can load the release candidate using:

ff = ForceField('openff-1.0.0-RC1.offxml')

The release candidate will be removed when the official force field, openff-1.0.0.offxml, is released in early October.

Complete details about this release are below.

Example added

  • PR #419: Adds an example notebook check_parameter_coverage.ipynb which shows how to use the toolkit to check a molecule dataset for missing parameter coverage, and provides functionality to output tagged SMILES and 2D drawings of the unparameterizable chemistry.

New features

  • PR #419: Unassigned valence parameter exceptions now include a list of tuples of TopologyAtom which were unable to be parameterized (exception.unassigned_topology_atom_tuples) and the class of the ParameterHandler that raised the exception (exception.handler_class).

  • PR #425: Implements Trevor Gokey’s suggestion from Issue #411, which enables pickling of ForceFields and ParameterHandlers. Note that, while XML representations of ForceField\ s are stable and conform to the SMIRNOFF specification, the pickled ForceField\ s that this functionality enables are not guaranteed to be compatible with future toolkit versions.

Improved documentation and warnings

  • PR #425: Addresses Issue #410, by explicitly having toolkit warnings print Warning: at the beginning of each warning, and adding clearer language to the warning produced when the OpenEye Toolkits can not be loaded.

  • PR #425: Addresses Issue #421 by adding type/shape information to all Molecule partial charge and conformer docstrings.

  • PR #425: Addresses Issue #407 by providing a more extensive explanation of why we don’t use RDKit’s mol2 parser for molecule input.

Bugfixes

Files removed

  • PR #425: Addresses Issue #424 by deleting the unused files openforcefield/typing/engines/smirnoff/gbsaforces.py and openforcefield/tests/test_smirnoff.py. gbsaforces.py was only used internally and test_smirnoff.py tested unsupported functionality from before the 0.2.0 release.

0.5.0 - GBSA support and quality-of-life improvements

This release adds support for the GBSA tag in the SMIRNOFF specification. Currently, the HCT, OBC1, and OBC2 models (corresponding to AMBER keywords igb=1, 2, and 5, respectively) are supported, with the OBC2 implementation being the most flexible. Unfortunately, systems produced using these keywords are not yet transferable to other simulation packages via ParmEd, so users are restricted to using OpenMM to simulate systems with GBSA.

OFFXML files containing GBSA parameter definitions are available, and can be loaded in addition to existing parameter sets (for example, with the command ForceField('test_forcefields/smirnoff99Frosst.offxml', 'test_forcefields/GBSA_OBC1-1.0.offxml')). A manifest of new SMIRNOFF-format GBSA files is below.

Several other user-facing improvements have been added, including easier access to indexed attributes, which are now accessible as torsion.k1, torsion.k2, etc. (the previous access method torsion.k still works as well). More details of the new features and several bugfixes are listed below.

New features

  • PR #363: Implements GBSAHandler, which supports the GBSA tag in the SMIRNOFF specification. Currently, only GBSAHandlers with gb_model="OBC2" support setting non-default values for the surface_area_penalty term (default 5.4*calories/mole/angstroms**2), though users can zero the SA term for OBC1 and HCT models by setting sa_model="None". No model currently supports setting solvent_radius to any value other than 1.4*angstroms. Files containing experimental SMIRNOFF-format implementations of HCT, OBC1, and OBC2 are included with this release (see below). Additional details of these models, including literature references, are available on the SMIRNOFF specification page.

    … warning :: The current release of ParmEd can not transfer GBSA models produced by the Open Force Field Toolkit to other simulation packages . These GBSA forces are currently only computable using OpenMM.

  • PR #363: When using Topology.to_openmm(), periodic box vectors are now transferred from the Open Force Field Toolkit Topology into the newly-created OpenMM Topology.

  • PR #377: Single indexed parameters in ParameterHandler and ParameterType can now be get/set through normal attribute syntax in addition to the list syntax.

  • PR #394: Include element and atom name in error output when there are missing valence parameters during molecule parameterization.

Bugfixes

  • PR #385: Fixes Issue #346 by having OpenEyeToolkitWrapper.compute_partial_charges_am1bcc fall back to using standard AM1-BCC if AM1-BCC ELF10 charge generation raises an error about “trans COOH conformers”

  • PR #399: Fixes issue where ForceField constructor would ignore parameter_handler_classes kwarg.

  • PR #400: Makes link-checking tests retry three times before failing.

Files added

  • PR #363: Adds test_forcefields/GBSA_HCT-1.0.offxml, test_forcefields/GBSA_OBC1-1.0.offxml, and test_forcefields/GBSA_OBC2-1.0.offxml, which are experimental implementations of GBSA models. These are primarily used in validation tests against OpenMM’s models, and their version numbers will increment if bugfixes are necessary.

0.4.1 - Bugfix Release

This update fixes several toolkit bugs that have been reported by the community. Details of these bugfixes are provided below.

It also refactors how ParameterType and ParameterHandler store their attributes, by introducing ParameterAttribute and IndexedParameterAttribute. These new attribute-handling classes provide a consistent backend which should simplify manipulation of parameters and implementation of new handlers.

Bug fixes

  • PR #329: Fixed a bug where the two BondType parameter attributes k and length were treated as indexed attributes. (k and length values that correspond to specific bond orders will be indexed under k_bondorder1, k_bondorder2, etc when implemented in the future)

  • PR #329: Fixed a bug that allowed setting indexed attributes to single values instead of strictly lists.

  • PR #370: Fixed a bug in the API where BondHandler, ProperTorsionHandler , and ImproperTorsionHandler exposed non-functional indexed parameters.

  • PR #351: Fixes Issue #344, in which the main FrozenMolecule constructor and several other Molecule-construction functions ignored or did not expose the allow_undefined_stereo keyword argument.

  • PR #351: Fixes a bug where a molecule which previously generated a SMILES using one cheminformatics toolkit returns the same SMILES, even though a different toolkit (which would generate a different SMILES for the molecule) is explicitly called.

  • PR #354: Fixes the error message that is printed if an unexpected parameter attribute is found while loading data into a ForceField (now instructs users to specify allow_cosmetic_attributes instead of permit_cosmetic_attributes)

  • PR #364: Fixes Issue #362 by modifying OpenEyeToolkitWrapper.from_smiles and RDKitToolkitWrapper.from_smiles to make implicit hydrogens explicit before molecule creation. These functions also now raise an error if the optional keyword hydrogens_are_explicit=True but the SMILES are interpreted by the backend cheminformatic toolkit as having implicit hydrogens.

  • PR #371: Fixes error when reading early SMIRNOFF 0.1 spec files enclosed by a top-level SMIRFF tag.

… note :: The enclosing SMIRFF tag is present only in legacy files. Since developing a formal specification, the only acceptable top-level tag value in a SMIRNOFF data structure is SMIRNOFF.

Code enhancements

Force fields added

  • PR #368: Temporarily adds test_forcefields/smirnoff99frosst_experimental.offxml to address hierarchy problems, redundancies, SMIRKS pattern typos etc., as documented in issue #367. Will ultimately be propagated to an updated force field in the openforcefield/smirnoff99frosst repo.

  • PR #371: Adds test_forcefields/smirff99Frosst_reference_0_1_spec.offxml, a SMIRNOFF 0.1 spec file enclosed by the legacy SMIRFF tag. This file is used in backwards-compatibility testing.

0.4.0 - Performance optimizations and support for SMIRNOFF 0.3 specification

This update contains performance enhancements that significantly reduce the time to create OpenMM systems for topologies containing many molecules via ForceField.create_openmm_system.

This update also introduces the SMIRNOFF 0.3 specification. The spec update is the result of discussions about how to handle the evolution of data and parameter types as further functional forms are added to the SMIRNOFF spec.

We provide methods to convert SMIRNOFF 0.1 and 0.2 force fields written with the XML serialization (.offxml) to the SMIRNOFF 0.3 specification. These methods are called automatically when loading a serialized SMIRNOFF data representation written in the 0.1 or 0.2 specification. This functionality allows the toolkit to continue to read files containing SMIRNOFF 0.2 spec force fields, and also implements backwards-compatibility for SMIRNOFF 0.1 spec force fields.

… warning :: The SMIRNOFF 0.1 spec did not contain fields for several energy-determining parameters that are exposed in later SMIRNOFF specs. Thus, when reading SMIRNOFF 0.1 spec data, the toolkit must make assumptions about the values that should be added for the newly-required fields. The values that are added include 1-2, 1-3 and 1-5 scaling factors, cutoffs, and long-range treatments for nonbonded interactions. Each assumption is printed as a warning during the conversion process. Please carefully review the warning messages to ensure that the conversion is providing your desired behavior.

SMIRNOFF 0.3 specification updates

  • The SMIRNOFF 0.3 spec introduces versioning for each individual parameter section, allowing asynchronous updates to the features of each parameter class. The top-level SMIRNOFF tag, containing information like aromaticity_model, Author, and Date, still has a version (currently 0.3). But, to allow for independent development of individual parameter types, each section (such as Bonds, Angles, etc) now has its own version as well (currently all 0.3).

  • All units are now stored in expressions with their corresponding values. For example, distances are now stored as 1.526*angstrom, instead of storing the unit separately in the section header.

  • The current allowed value of the potential field for ProperTorsions and ImproperTorsions tags is no longer charmm, but is rather k*(1+cos(periodicity*theta-phase)). It was pointed out to us that CHARMM-style torsions deviate from this formula when the periodicity of a torsion term is 0, and we do not intend to reproduce that behavior.

  • SMIRNOFF spec documentation has been updated with tables of keywords and their defaults for each parameter section and parameter type. These tables will track the allowed keywords and default behavior as updated versions of individual parameter sections are released.

Performance improvements and bugfixes

  • PR #329: Performance improvements when creating systems for topologies with many atoms.

  • PR #347: Fixes bug in charge assignment that occurs when charges are read from file, and reference and charge molecules have different atom orderings.

New features

  • PR #311: Several new experimental functions.

    • Adds convert_0_2_smirnoff_to_0_3, which takes a SMIRNOFF 0.2-spec data dict, and updates it to 0.3. This function is called automatically when creating a ForceField from a SMIRNOFF 0.2 spec OFFXML file.

    • Adds convert_0_1_smirnoff_to_0_2, which takes a SMIRNOFF 0.1-spec data dict, and updates it to 0.2. This function is called automatically when creating a ForceField from a SMIRNOFF 0.1 spec OFFXML file.

    • NOTE: The format of the “SMIRNOFF data dict” above is likely to change significantly in the future. Users that require a stable serialized ForceField object should use the output of ForceField.to_string('XML') instead.

    • Adds ParameterHandler and ParameterType add_cosmetic_attribute and delete_cosmetic_attribute functions. Once created, cosmetic attributes can be accessed and modified as attributes of the underlying object (eg. ParameterType.my_cosmetic_attrib = 'blue') These functions are experimental, and we are interested in feedback on how cosmetic attribute handling could be improved. (See Issue #338) Note that if a new cosmetic attribute is added to an object without using these functions, it will not be recognized by the toolkit and will not be written out during serialization.

    • Values for the top-level Author and Date tags are now kept during SMIRNOFF data I/O. If multiple data sources containing these fields are read, the values are concatenated using “AND” as a separator.

API-breaking changes

  • ForceField.to_string and ForceField.to_file have had the default value of their discard_cosmetic_attributes kwarg set to False.

  • ParameterHandler and ParameterType constructors now expect the version kwarg (per the SMIRNOFF spec change above) This requirement can be skipped by providing the kwarg skip_version_check=True

  • ParameterHandler and ParameterType functions no longer handle X_unit attributes in SMIRNOFF data (per the SMIRNOFF spec change above).

  • The scripts in utilities/convert_frosst are now deprecated. This functionality is important for provenance and will be migrated to the openforcefield/smirnoff99Frosst repository in the coming weeks.

  • ParameterType ._SMIRNOFF_ATTRIBS is now ParameterType ._REQUIRED_SPEC_ATTRIBS, to better parallel the structure of the ParameterHandler class.

  • ParameterType ._OPTIONAL_ATTRIBS is now ParameterType ._OPTIONAL_SPEC_ATTRIBS, to better parallel the structure of the ParameterHandler class.

  • Added class-level dictionaries ParameterHandler ._DEFAULT_SPEC_ATTRIBS and ParameterType ._DEFAULT_SPEC_ATTRIBS.

0.3.0 - API Improvements

Several improvements and changes to public API.

New features

  • PR #292: Implement Topology.to_openmm and remove ToolkitRegistry.toolkit_is_available

  • PR #322: Install directories for the lookup of OFFXML files through the entry point group openforcefield.smirnoff_forcefield_directory. The ForceField class doesn’t search in the data/forcefield/ folder anymore (now renamed data/test_forcefields/), but only in data/.

API-breaking Changes

  • PR #278: Standardize variable/method names

  • PR #291: Remove ForceField.load/to_smirnoff_data, add ForceField.to_file/string and ParameterHandler.add_parameters. Change behavior of ForceField.register_X_handler functions.

Bugfixes

  • PR #327: Fix units in tip3p.offxml (note that this file is still not loadable by current toolkit)

  • PR #325: Fix solvent box for provided test system to resolve periodic clashes.

  • PR #325: Add informative message containing Hill formula when a molecule can’t be matched in Topology.from_openmm.

  • PR #325: Provide warning or error message as appropriate when a molecule is missing stereochemistry.

  • PR #316: Fix formatting issues in GBSA section of SMIRNOFF spec

  • PR #308: Cache molecule SMILES to improve system creation speed

  • PR #306: Allow single-atom molecules with all zero coordinates to be converted to OE/RDK mols

  • PR #313: Fix issue where constraints are applied twice to constrained bonds

0.2.2 - Bugfix release

This release modifies an example to show how to parameterize a solvated system, cleans up backend code, and makes several improvements to the README.

Bugfixes

  • PR #279: Cleanup of unused code/warnings in main package __init__

  • PR #259: Update T4 Lysozyme + toluene example to show how to set up solvated systems

  • PR #256 and PR #274: Add functionality to ensure that links in READMEs resolve successfully

0.2.1 - Bugfix release

This release features various documentation fixes, minor bugfixes, and code cleanup.

Bugfixes

  • PR #267: Add neglected <ToolkitAM1BCC> documentation to the SMIRNOFF 0.2 spec

  • PR #258: General cleanup and removal of unused/inaccessible code.

  • PR #244: Improvements and typo fixes for BRD4:inhibitor benchmark

0.2.0 - Initial RDKit support

This version of the toolkit introduces many new features on the way to a 1.0.0 release.

New features

  • Major overhaul, resulting in the creation of the SMIRNOFF 0.2 specification and its XML representation

  • Updated API and infrastructure for reference SMIRNOFF ForceField implementation

  • Implementation of modular ParameterHandler classes which process the topology to add all necessary forces to the system.

  • Implementation of modular ParameterIOHandler classes for reading/writing different serialized SMIRNOFF force field representations

  • Introduction of Molecule and Topology classes for representing molecules and biomolecular systems

  • New ToolkitWrapper interface to RDKit, OpenEye, and AmberTools toolkits, managed by ToolkitRegistry

  • API improvements to more closely follow PEP8 guidelines

  • Improved documentation and examples

0.1.0

This is an early preview release of the toolkit that matches the functionality described in the preprint describing the SMIRNOFF v0.1 force field format: [DOI].

New features

This release features additional documentation, code comments, and support for automated testing.

Bugfixes

Treatment of improper torsions

A significant (though currently unused) problem in handling of improper torsions was corrected. Previously, non-planar impropers did not behave correctly, as six-fold impropers have two potential chiralities. To remedy this, SMIRNOFF impropers are now implemented as three-fold impropers with consistent chirality. However, current force fields in the SMIRNOFF format had no non-planar impropers, so this change is mainly aimed at future work.