# 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

## 0.6.0 - 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 a 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.

### 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

- PR #419: Fixes Issue #417 and Issue #418, where `RDKitToolkitWrapper.from_file` would disregard the `allow_undefined_stereo` kwarg and skip the first molecule when reading a SMILES file.

### 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

- PR #329: `ParameterType` was refactored to improve its extensibility. It is now possible to create new parameter types by using the new descriptors `ParameterAttribute` and `IndexedParameterAttribute`.

- PR #357: Addresses Issue #356 by raising an informative error message if a user attempts to load an OpenMM topology which is probably missing connectivity information.

### 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 forcefield 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 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.