- py-cpuinfo <= 5 # Needed until https://github.com/MolSSI/QCEngine/issues/252 is resolved+released

- openmmforcefields >=0.7.2

- qcengine <= 0.14 # Remove this and py-cpuinfo pin above when there's a new release of QCEngine

:py:meth:`temporary_cd <openforcefield.utils.utils.temporary_cd>` and replaced their behavoir with

Behavior changed

- `PR #558 <https://github.com/openforcefield/openforcefield/pull/558>`_: The

:py:class`Topology <openforcefield.topology.Topology>`

particle indexing system now orders :py:class`TopologyVirtualSites <openforcefield.topology.TopologyVirtualSite>`

after all atoms.

- `PR #469 <https://github.com/openforcefield/openforcefield/pull/469>`_:

When running :py:meth:`Topology.to_openmm <openforcefield.topology.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 <https://github.com/openforcefield/openforcefield/pull/472>`_:

The :py:meth:`Molecule.__eq__ <openforcefield.topology.Molecule.__eq__>` now uses the new

:py:meth:`Molecule.are_isomorphic <openforcefield.topology.Molecule.are_isomorphic>` to perform the

similarity checking.

- `PR #472 <https://github.com/openforcefield/openforcefield/pull/472>`_:

The :py:meth:`Topology.from_openmm <openforcefield.topology.Topology.from_openmm>` and

:py:meth:`Topology.add_molecule <openforcefield.topology.Topology.add_molecule>` now use the

:py:meth:`Molecule.are_isomorphic <openforcefield.topology.Molecule.are_isomorphic>` to match

molecules.

- `PR #508 <https://github.com/openforcefield/openforcefield/pull/508>`_:

In order to provide the same results for the same chemical species, regardless of input

conformation, fractional bond order calculation methods now default to ignore input conformers

and generate a new conformer of the molecule before running semiempirical calculations.

Users can override this behavior by specifying the keyword argument

``use_conformers=molecule.conformers``

- `PR #544 <https://github.com/openforcefield/openforcefield/pull/544>`_: Raises

``NotImplementedError`` when calling

:py:meth:`ParameterHandler.get_parameter <openforcefield.typing.engines.smirnoff.parameters.ParameterHandler.get_parameter>`,

which is not yet implemented, but would previously silently return ``None``.

- `PR #551 <https://github.com/openforcefield/openforcefield/pull/551>`_: Implemented the

:py:meth:`ParameterHandler.get_parameter <openforcefield.typing.engines.smirnoff.parameters.ParameterHandler.get_parameter>` function.

* [`swap_existing_ligand_parameters.ipynb`](swap_existing_ligand_parameters.ipynb) contains an example illustrating taking a fully parameterized BRD4 protein-ligand system, with an AMBER protein force field and GAFF ligand parameters, and replacing the ligand parameters with OpenFF parameters from SMIRNOFF format. The BRD4:inhibitor complex is taken from the [free energy benchmark systems living review](https://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-070816-033654) [GitHub repo](https://github.com/MobleyLab/benchmarksets/tree/master/input_files/BRD4).

* [`swap_existing_ligand_parameters_with_openmmforcefields.ipynb`](swap_existing_ligand_parameters_with_openmmforcefields.ipynb) contains an example that uses the [`openmm-forcefields`](http://github.com/openmm/openmm-forcefields) package to take a fully parameterized BRD4 protein-ligand system, with an AMBER protein force field and GAFF ligand parameters, and replacing the ligand parameters with OpenFF parameters from SMIRNOFF format. The BRD4:inhibitor complex is taken from the [free energy benchmark systems living review](https://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-070816-033654) [GitHub repo](https://github.com/MobleyLab/benchmarksets/tree/master/input_files/BRD4).