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25 changes: 12 additions & 13 deletions README.md
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| **Latest release** | ![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/openforcefield/openff-interchange?include_prereleases) | |
| **User support** | [![Documentation Status](https://readthedocs.org/projects/openff-interchange/badge/?version=latest)](https://openff-interchange.readthedocs.io/en/latest/?badge=latest) | [![Discussions](https://img.shields.io/badge/Discussions-GitHub-blue?logo=github)](https://github.com/openforcefield/discussions/discussions) |

A project (and object) for storing, manipulating, and converting molecular mechanics data.
A project (and object) for storing, manipulating, and converting parametrized chemical systems.

## Documentation

Documentation for Interchange, including examples, a brief user guide, release history, and API docs, is available [on the OpenFF website](https://docs.openforcefield.org/projects/interchange/en/stable). Example notebooks are rendered online among examples from other projects in the [OpenFF ecosysytem docs](https://docs.openforcefield.org/en/latest/examples.html)
Documentation for Interchange, including examples, a brief user guide, release history, and API docs, is available [on the OpenFF website](https://docs.openforcefield.org/projects/interchange/en/stable). Example notebooks are rendered online among examples from other projects in the [OpenFF ecosysytem docs](https://docs.openforcefield.org/en/latest/examples.html).

## How to cite

Please cite Interchange using the [Zenodo record](https://doi.org/10.5281/zenodo.10068101) of the [latest release](https://zenodo.org/doi/10.5281/zenodo.8147764) or the version that was used. The BibTeX reference of the latest release can be found [at this link](https://zenodo.org/record/8147764/export/hx).
Please cite Interchange using the [Zenodo record](https://doi.org/10.5281/zenodo.10068101) of the [latest release](https://zenodo.org/doi/10.5281/zenodo.8147764) or the version that was used. The BibTeX reference of the latest release can be found at [this link](https://zenodo.org/record/8147764/export/hx).

## Installation

Recent versions of the OpenFF Toolkit (0.11.0+, released August 2022) install Interchange by default through its `conda` package.
Recent versions of the OpenFF Toolkit (0.11.0+, released August 2022) install Interchange by default through its Conda package.

Interchange can also be installed manually via `conda` (or `mamba`):
Interchange can also be installed manually via `mamba` (or `conda`, etc.):

```shell
conda install openff-interchange -c conda-forge
mamba install openff-interchange -c conda-forge
```

## Getting started

The `Interchange` object serves primarily as a container object for parametrized data. It can currently take in [SMIRNOFF](https://openforcefield.github.io/standards/standards/smirnoff/) or [Foyer](https://foyer.mosdef.org/en/stable/) force fields
and [chemical topologies](https://docs.openforcefield.org/projects/toolkit/en/stable/topology.html) prepared via the [OpenFF Toolkit](https://open-forcefield-toolkit.readthedocs.io/). The resulting object stores parametrized data and provides APIs for export to common formats.
The `Interchange` object serves primarily as a container object for parametrized chemical systems. Its key use case involves [SMIRNOFF](https://openforcefield.github.io/standards/standards/smirnoff/) force fields and [chemical topologies](https://docs.openforcefield.org/projects/toolkit/en/stable/topology.html) prepared via the [OpenFF Toolkit](https://open-forcefield-toolkit.readthedocs.io/). The resulting object stores parametrized chemical systems and provides APIs for export to common formats.

```python3
from openff.toolkit import ForceField, Molecule, Quantity
Expand All @@ -56,16 +55,16 @@ out = sage.create_interchange(force_field=sage, topology=topology)
system = out.to_openmm()

# or write to GROMACS files
out.to_gro("out.gro")
out.to_top("out.top")
out.to_gromacs(prefix="out")

# or write to Amber files
out.to_amber(prefix="out")

# or store as JSON
json_blob = out.json()
```

For more information, please consult the [full documentation](https://openff-interchange.readthedocs.io/).

For more examples specific to Interchange, navigate to the `examples/` directory.
For more functionality, usage guidelines, and examples, please consult the [full documentation](https://docs.openforcefield.org/projects/interchange/en/stable/)

## Developing

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Please note that all releases prior to a version 1.0.0 are considered pre-releases and many API changes will come before a stable release.

## Current development
## 0.5.0 - 2025-01-08

* #1332 Introduces the following behavior changes to the private Packmol wrappers:
* Packmol version 20.15.0 or newer is recommended.
* Periodic boundary conditions are accounted for when placing molecules if the box is orthorhombic and Packmol version 20.15.0 or newer is installed; this is the minimum version supporting this feature.
* This is functionally the same as the previous behavior, so no workaround is needed to recover it.
* The `tolerance` parameter is subtracted from computed box lengths when placing molecules if a Packmol version older than 20.15.0 is installed; this is the previous behavior.
* The `target_density` is used in box size calculations without modification; previously, box volumes were scaled up by a factor of 1.1.
* The previous behavior can be restored by passing scaling the `target_density` argument down by a factor of 1.1.
* The `target_density` is used in box size calculations without modification; previously, box volumes were scaled up by a factor of 1.331.
* The previous behavior can be restored by scaling the `target_density` argument down by a factor of 1.331.

* #1376 Makes `Interchange.topology` not store positions. Use `Interchange.positions` instead.
* #1387 Migrates version handling to `setuptools-scm`.
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