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

Current development

  • 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).

New features

  • 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. See also an entry in the “Behavior changed” section.

  • 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 moldules.

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

Bugfixes

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

  • PR #1030: Fixes a bug in which capitalization of the bond_order_model sometimes matters.

Behavior changed

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

  • PR #1036: SMARTS matching logic for library charges was updated to use only one unique match. No adverse side effects were found in testing, but could bad behavior may possibly exist in some unknown caes. Note that the default behavior for other parameter handlers was not updated.

  • 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.

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

  • PR #1021: Renames openff.toolkit.utils.exceptions.ParseError to openff.toolkit.utils.exceptions.SMILESParseError to avoid a conflict with an identically-named exception in the SMIRNOFF XML parsing code.

  • PR #1021: Renames and moves openff.toolkit.typing.engines.smirnoff.forcefield.ParseError to openff.toolkit.utils.exceptions.SMIRNOFFParseError. This ParseError is deprecated and will be removed in a future release.

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

  • PR #762: Molecule.from_rdkit now converts implicit hydrogens into explicit hydrogens by default. This change may affect RDKitToolkitWrapper/Molecule.from_smiles, from_mapped_smiles, from_file, from_file_obj, from_inchi, and from_qcschema. This new behavior can be disabled using the hydrogens_are_explicit=True keyword argument to from_smiles, or loading the molecule into the desired explicit protonation state in RDKit, then calling from_rdkit on the RDKit molecule with hydrogens_are_explicit=True.

  • PR #894: Calls to Molecule.from_openeye, Molecule.from_rdkit, Molecule.from_smiles, OpenEyeToolkitWrapper.from_smiles, and RDKitToolkitWrapper.from_smiles will now load atom maps into the the resulting Molecule's offmol.properties['atom_map'] field, even if not all atoms have map indices assigned.

  • PR #904: TopologyAtom objects now have an element getter TopologyAtom.element.

Bugfixes

  • PR #891: Calls to Molecule/OpenEyeToolkitWrapper.from_openeye no longer mutate the input OE molecule.

  • PR #897: Fixes enumeration of stereoisomers for molecules with already defined stereochemistry using RDKitToolkitWrapper.enumerate_stereoisomers.

  • PR #859: Makes RDKitToolkitWrapper.enumerate_tautomers actually use the max_states keyword argument during tautomer generation, which will reduce resource use in some cases.

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

  • PR #839: Add support for computing WBOs from multiple conformers using the AmberTools and OpenEye toolkits, and from ELF10 conformers using the OpenEye toolkit wrapper.

  • PR #832: Expose ELF conformer selection through the Molecule API via a new apply_elf_conformer_selection function.

  • PR #831: Expose ELF conformer selection through the OpenEye wrapper.

  • PR #790: Fixes Issue #720 where qcschema roundtrip to/from results in an error due to missing cmiles entry in attributes.

  • PR #793: Add an initial ELF conformer selection implementation which uses RDKit.

  • PR #799: Closes Issue #746 by adding Molecule.smirnoff_impropers, Molecule.amber_impropers, TopologyMolecule.smirnoff_impropers, TopologyMolecule.amber_impropers, Topology.smirnoff_impropers, and Topology.amber_impropers.

  • PR #847: Instances of ParameterAttribute documentation can now specify their docstrings with the optional docstring argument to the __init__() method.

  • PR #827: The setter for Topology.box_vectors now infers box vectors when box lengths are pass as a list of length 3.

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

  • PR #583: Methods such as Molecule.from_rdkit and Molecule.from_openeye, which delegate their internal logic to ToolkitRegistry functions, now guarantee that they will return an object of the correct type when being called on Molecule-derived classes. Previously, running these constructors using subclasses of FrozenMolecule would not return an instance of that subclass, but rather just an instance of a Molecule.

  • PR #753: ParameterLookupError is now raised when passing to ParameterList.index a SMIRKS pattern not found in the parameter list.

New features

  • PR #751: Adds LicenseError, a subclass of ToolkitUnavailableException which is raised when attempting to add a cheminformatics ToolkitWrapper for a toolkit that is installed but unlicensed.

  • PR #678: Adds ForceField.deregister_parameter_handler.

  • PR #730: Adds Topology.is_periodic.

  • PR #753: Adds ParameterHandler.__getitem__ to look up individual ParameterType objects.

Bugfixes

  • PR #745: Fixes bug when serializing molecule with conformers to JSON.

  • PR #750: Fixes a bug causing either sigma or rmin_half to sometimes be missing on vdWHandler.vdWType objects.

  • PR #756: Fixes bug when running vdWHandler.create_force using a vdWHandler that was initialized using the API.

  • PR #776: Fixes a bug in which the Topology.from_openmm and Topology.from_mdtraj methods would dangerously allow unique_molecules=None.

  • PR #777: RDKitToolkitWrapper now outputs the full warning message when allow_undefined_stereo=True (previously the description of which stereo was undefined was squelched)

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

    • VirtualParticle

    • TopologyVirtualParticle

    • BondChargeVirtualSite.get_openmm_virtual_site

    • MonovalentLonePairVirtualSite.get_openmm_virtual_site

    • DivalentLonePairVirtualSite.get_openmm_virtual_site

    • TrivalentLonePairVirtualSite.get_openmm_virtual_site

    • ValenceDict.key_transform

    • ValenceDict.index_of

    • ImproperDict.key_transform

    • ImproperDict.index_of

  • 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

  • PR #682: Catches failures in Molecule.from_iupac instead of silently failing.

  • PR #743: Prevents the non-bonded (vdW) cutoff from silently falling back to the OpenMM default of 1 nm in Forcefield.create_openmm_system and instead sets its to the value specified by the force field.

  • PR #737: Prevents OpenEye from incidentally being used in the conformer generation step of AmberToolsToolkitWrapper.assign_fractional_bond_orders.

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

  • PR #662: Adds .aromaticity_model of ForceField and .TAGNAME of ParameterHandler as public attributes.

  • PR #667 and PR #681 linted the codebase with black and isort, respectively.

  • PR #675 adds .toolkit_version to ToolkitWrapper and .registered_toolkit_versions to ToolkitRegistry.

  • PR #696 Exposes a setter for ForceField.aromaticity_model

  • PR #685 Adds a custom __hash__ function to ForceField

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

  • PR #647: Updates OpenEyeToolkitWrapper for 2020.0.4 OpenEye Toolkit behavior/API changes.

  • PR #646: Fixes a bug where Molecule.chemical_environment_matches was not able to accept a ChemicalEnvironment object as a query.

  • PR #634: Fixes a bug in which calling RDKitToolkitWrapper.from_file directly would not load files correctly if passed lowercase file_format. Note that this bug did not occur when calling Molecule.from_file.

  • PR #631: Fixes a bug in which calling unit_to_string returned None when the unit is dimensionless. Now "dimensionless" is returned.

  • PR #630: Closes issue Issue #629 in which the wrong exception is raised when attempting to instantiate a ForceField from an unparsable string.

New features

  • PR #632: Adds ForceField.registered_parameter_handlers

  • PR #614: Adds ToolkitRegistry.deregister_toolkit to de-register registered toolkits, which can include toolkit wrappers loaded into GLOBAL_TOOLKIT_REGISTRY by default.

  • PR #656: Adds a new allowed am1elf10 option to the OpenEye implementation of assign_partial_charges which calculates the average partial charges at the AM1 level of theory using conformers selected using the ELF10 method.

  • PR #643: Adds openforcefield.typing.engines.smirnoff.forcefield.get_available_force_fields, which returns paths to the files of force fields available through entry point plugins.

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.

  • 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

  • PR #558: Adds tests ensuring that the new Topology particle indexing system are properly implemented, and that TopologyVirtualSites reference the correct TopologyAtoms.

  • PR #469: Added round-trip SMILES test to add coverage for Molecule.from_smiles.

  • PR #469: Added tests for unique atom naming behavior in Topology.to_openmm, as well as tests of the ensure_unique_atom_names=False kwarg disabling this behavior.

  • PR #472: Added tests for Molecule.hill_formula and Molecule.to_hill_formula for the various supported input types.

  • PR #472: Added round-trip test for Molecule.from_qcschema and Molecule.to_qcschema.

  • PR #472: Added tests for Molecule.is_isomorphic_with and Molecule.are_isomorphic with various levels of isomorphic graph matching.

  • PR #472: Added toolkit dependent tests for Molecule.canonical_order_atoms due to differences in the algorithms used.

  • PR #472: Added a test for Molecule.from_mapped_smiles using the molecule from issue #412 to ensure it is now fixed.

  • PR #472: Added a test for Molecule.remap, this also checks for expected error when the mapping is not complete.

  • PR #472: Added tests for Molecule.from_pdb_and_smiles to check for a correct combination of smiles and PDB and incorrect combinations.

  • PR #509: Added test for Molecule.chemical_environment_matches to check that the complete set of matches is returned.

  • PR #509: Added test for Forcefield.create_openmm_system to check that a protein system can be created.

  • PR #506: Added a test for the molecule identified in issue #513 as losing aromaticity when converted to rdkit.

  • PR #506: Added a verity of toolkit dependent tests for identifying rotatable bonds while ignoring the user requested types.

  • PR #521: Added toolkit independent round-trip InChI tests which add coverage for Molecule.to_inchi and Molecule.from_inchi. Also added coverage for bad inputs and Molecule.to_inchikey.

  • PR #529: Added to XYZ file coverage tests.

  • PR #563: Added LibraryCharges parameterization test for monatomic ions in test_forcefields/ion_charges.offxml.

  • PR #543: Added tests to assure that state enumeration can correctly find molecules tautomers, stereoisomers and protomers when possible.

  • PR #573: Added test for quacpac error output for quacpac failure in Molecule.compute_partial_charges_am1bcc.

  • PR #579: Adds regression tests to ensure RDKit can be be used to write multi-model PDB files.

  • PR #582: Added fractional bond order interpolation tests, tests for ValidatedDict.

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 ForceFields are stable and conform to the SMIRNOFF specification, the pickled ForceFields 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 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.