Open Force Field Toolkit 0.4.0

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

0.4.0 - 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 forcefields 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 forcefield 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.