acellera-openff-toolkit 0.18.0__tar.gz

acellera_openff_toolkit-0.18.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2016-2019 Open Force Field Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

acellera_openff_toolkit-0.18.0/MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE
+include MANIFEST.in
+
+graft openff
+global-exclude *.py[cod] __pycache__ *.so

acellera_openff_toolkit-0.18.0/PKG-INFO

@@ -0,0 +1,109 @@
+Metadata-Version: 2.4
+Name: acellera-openff-toolkit
+Version: 0.18.0
+Summary: openff-toolkit
+Author-email: Open Force Field Consortium <info@openforcefield.org>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/openforcefield/openff-toolkit
+Keywords: force field,molecular mechanics,parameterization
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Utilities
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: license-file
+
+| **Status** | [![GH Actions Status](https://github.com/openforcefield/openff-toolkit/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-toolkit/actions?query=branch%3Amain+workflow%3ACI)  [![Codecov coverage](https://img.shields.io/codecov/c/github/openforcefield/openff-toolkit.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/openforcefield/openff-toolkit) |
+| :------ |:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| **Latest Release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openff-toolkit.svg)](https://github.com/openforcefield/openff-toolkit/releases)  [![Commits since release](https://img.shields.io/github/commits-since/openforcefield/openff-toolkit/0.17.1.svg)](https://github.com/openforcefield/openff-toolkit/releases/tag/0.17.1)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17259324.svg)](https://doi.org/10.5281/zenodo.17259324)
+| **Communication** | [![docs stable](https://img.shields.io/badge/docs-stable-5077AB.svg?logo=read%20the%20docs)](https://open-forcefield-toolkit.readthedocs.io/) [![user & dev discussions](https://img.shields.io/badge/user%20%26%20dev%20discussions-GitHub-red?logo=github)](https://github.com/openforcefield/discussions/discussions) |
+| **Foundation** | [![license](https://img.shields.io/github/license/openforcefield/openff-toolkit.svg)](https://opensource.org/licenses/MIT) [![platforms](https://img.shields.io/badge/Platforms-Linux%2C%20MacOS-orange.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![python](https://img.shields.io/badge/python-3.11%2C%203.12%2C%203.13-blue.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![Funding](https://img.shields.io/badge/Funding-Open%20Force%20Field%20Consortium-brightgreen.svg)](http://openforcefield.org)        |
+| **Installation** | [![Releases](https://img.shields.io/badge/obtain-latest-green.svg)](https://github.com/openforcefield/openff-toolkit/releases) [![Conda](https://img.shields.io/conda/v/conda-forge/openff-toolkit.svg)](https://anaconda.org/conda-forge/openff-toolkit) [![Last updated](https://anaconda.org/conda-forge/openff-toolkit/badges/latest_release_relative_date.svg)](https://anaconda.org/conda-forge/openff-toolkit) [![Anaconda Cloud downloads](https://anaconda.org/conda-forge/openff-toolkit/badges/downloads.svg)](https://anaconda.org/conda-forge/openff-toolkit)          |
+
+# The Open Force Field toolkit
+
+The Open Force Field Toolkit, built by the [Open Force Field Initiative](http://openforcefield.org), is a Python toolkit for the development and application of modern molecular mechanics force fields based on direct chemical perception and rigorous statistical parameterization methods.
+
+The toolkit currently covers two main areas we have committed to stably maintain throughout their lifetimes:
+* Tools for using [SMIRKS Native Open Force Field (SMIRNOFF)](https://openforcefield.github.io/standards/standards/smirnoff/) force fields
+* Tools for [direct chemical environment perception](https://dx.doi.org/10.1021/acs.jctc.8b00640) and manipulation
+
+**Note**: Prior to version 0.9.0, this toolkit and its associated repository were named `openforcefield` and used different import paths. For details on this change and migration instructions, see the [release notes](https://open-forcefield-toolkit.readthedocs.io/en/stable/releasehistory.html#namespace-migration) of version 0.9.0.
+
+## Documentation
+
+[Documentation](https://open-forcefield-toolkit.readthedocs.io/en/stable/) for the Open Force Field Toolkit is hosted at [readthedocs](https://open-forcefield-toolkit.readthedocs.io/en/stable). Example notebooks are available in the `examples/` directory and also hosted on the [`Open Force Field`](https://docs.openforcefield.org/en/latest/examples.html) website.
+
+## How to cite
+
+Please cite the OpenFF Toolkit using the [Zenodo record](https://zenodo.org/record/13886754) of the [latest release](https://zenodo.org/record/13886754) or the version that was used. The BibTeX reference of the latest release can be found [here](https://zenodo.org/records/13886754/export/bibtex).
+
+## Installation
+
+The Open Force Field Toolkit (`openff-toolkit`) is a Python toolkit, and supports Python 3.9 through 3.11.
+
+### Installing via Mamba/Conda
+
+Detailed installation instructions can be found [here](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html).
+
+## Force Fields
+
+Two major force field development efforts have been undertaken by the Open Force Field Initiative, with results hosted in separate repositories.
+
+* The [Open Force Fields repository](https://github.com/openforcefield/openff-forcefields/), which features the [Parsley](https://openforcefield.org/community/news/general/introducing-openforcefield-1.0/) and [Sage](https://openforcefield.org/community/news/general/sage2.0.0-release/) force field lines. These are the Open Force Field Initiative's efforts toward building _new_ force fields. The initial parameters are taken from smirnoff99Frosst, but software and data produced by the Initiative's efforts have been used to refit parameter values and add new SMIRKS-based parameters.
+* The [smirnoff99Frosst repository](https://github.com/openforcefield/smirnoff99Frosst/), which is descended from AMBER's parm99 force field as well as Merck-Frosst's parm@frosst. This line of force fields does not aim to alter parameter values, but is instead a test of accurately converting an atom type-based force field to the SMIRNOFF format.
+
+Force fields from both of these packages are available in their respective GitHub repositories and also as conda packages. Tables detailing the individual file names/versions within these force field lines are in the README of each repository. By default, installing the Open Force Field toolkit using `conda` or the single-file toolkit installers will also install these conda packages. A [plugin architecture](https://github.com/openforcefield/openff-toolkit/blob/main/FAQ.md#how-can-i-distribute-my-own-force-fields-in-smirnoff-format) is provided for other force field developers to produce python/conda packages that can be imported by the Open Force Field Toolkit as well.
+
+# Toolkit features
+
+## The SMIRKS Native Open Force Field (SMIRNOFF) format
+
+This repository provides tools for using the [SMIRKS Native Open Force Field (SMIRNOFF) specification](https://openforcefield.github.io/standards/standards/smirnoff/), which currently supports an XML representation for force field definition files.
+
+By convention, files containing [XML representations](https://en.wikipedia.org/wiki/XML) of SMIRNOFF force fields carry `.offxml` extensions.
+
+Example SMIRNOFF `.offxml` force field definitions can be found in [`openff/toolkit/data/test_forcefields/`](https://github.com/openforcefield/openff-toolkit/tree/main/openff/toolkit/data/test_forcefields). These force fields are for testing only, and we neither record versions of these files, nor do we guarantee their correctness or completeness.
+
+### Working with SMIRNOFF parameter sets
+
+SMIRNOFF force fields can be parsed by the `ForceField` class, which offers methods including `create_openmm_system` for exporting to OpenMM and `create_interchange` for exporting to other formats (GROMACS, Amber, LAMMPS) via [Interchange](https://docs.openforcefield.org/projects/interchange).
+
+```python
+# Load a molecule into the OpenFF Molecule object
+from openff.toolkit import Molecule
+from openff.toolkit.utils import get_data_file_path
+sdf_file_path = get_data_file_path('molecules/ethanol.sdf')
+molecule = Molecule.from_file(sdf_file_path)
+
+# Create an OpenFF Topology object from the molecule
+from openff.toolkit import Topology
+topology = Topology.from_molecules(molecule)
+
+# Load the latest OpenFF force field release: version 2.1.0, codename "Sage"
+from openff.toolkit import ForceField
+forcefield = ForceField('openff-2.1.0.offxml')
+
+# Create an OpenMM system representing the molecule with SMIRNOFF-applied parameters
+openmm_system = forcefield.create_openmm_system(topology)
+
+# Create an Interchange object for representations in other formats
+interchange = forcefield.create_interchange(topology)
+```
+
+Detailed examples of using SMIRNOFF with the toolkit can be found [in the documentation](https://open-forcefield-toolkit.readthedocs.io/en/stable/examples.html).
+
+# Frequently asked questions (FAQ)
+
+See [`FAQ.md`](FAQ.md) for answers to a variety of common problems, such as:
+* Why do I need to provide molecules corresponding to the components of my system, or a `Topology` with bond orders?
+* Can I use an Amber, CHARMM, or GROMACS topology/coordinate file as a starting point for applying a SMIRNOFF force field?
+* What if I am starting from a PDB file?
+
+# Contributors
+
+For a partial list of contributors, see the [GitHub Contributors page](https://github.com/openforcefield/openff-toolkit/graphs/contributors). Others whose work constitutes significant contributions but did not make it into the `git` history include Shuzhe Wang.

acellera_openff_toolkit-0.18.0/README.md

@@ -0,0 +1,90 @@
+| **Status** | [![GH Actions Status](https://github.com/openforcefield/openff-toolkit/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-toolkit/actions?query=branch%3Amain+workflow%3ACI)  [![Codecov coverage](https://img.shields.io/codecov/c/github/openforcefield/openff-toolkit.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/openforcefield/openff-toolkit) |
+| :------ |:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| **Latest Release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openff-toolkit.svg)](https://github.com/openforcefield/openff-toolkit/releases)  [![Commits since release](https://img.shields.io/github/commits-since/openforcefield/openff-toolkit/0.17.1.svg)](https://github.com/openforcefield/openff-toolkit/releases/tag/0.17.1)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17259324.svg)](https://doi.org/10.5281/zenodo.17259324)
+| **Communication** | [![docs stable](https://img.shields.io/badge/docs-stable-5077AB.svg?logo=read%20the%20docs)](https://open-forcefield-toolkit.readthedocs.io/) [![user & dev discussions](https://img.shields.io/badge/user%20%26%20dev%20discussions-GitHub-red?logo=github)](https://github.com/openforcefield/discussions/discussions) |
+| **Foundation** | [![license](https://img.shields.io/github/license/openforcefield/openff-toolkit.svg)](https://opensource.org/licenses/MIT) [![platforms](https://img.shields.io/badge/Platforms-Linux%2C%20MacOS-orange.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![python](https://img.shields.io/badge/python-3.11%2C%203.12%2C%203.13-blue.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![Funding](https://img.shields.io/badge/Funding-Open%20Force%20Field%20Consortium-brightgreen.svg)](http://openforcefield.org)        |
+| **Installation** | [![Releases](https://img.shields.io/badge/obtain-latest-green.svg)](https://github.com/openforcefield/openff-toolkit/releases) [![Conda](https://img.shields.io/conda/v/conda-forge/openff-toolkit.svg)](https://anaconda.org/conda-forge/openff-toolkit) [![Last updated](https://anaconda.org/conda-forge/openff-toolkit/badges/latest_release_relative_date.svg)](https://anaconda.org/conda-forge/openff-toolkit) [![Anaconda Cloud downloads](https://anaconda.org/conda-forge/openff-toolkit/badges/downloads.svg)](https://anaconda.org/conda-forge/openff-toolkit)          |
+
+# The Open Force Field toolkit
+
+The Open Force Field Toolkit, built by the [Open Force Field Initiative](http://openforcefield.org), is a Python toolkit for the development and application of modern molecular mechanics force fields based on direct chemical perception and rigorous statistical parameterization methods.
+
+The toolkit currently covers two main areas we have committed to stably maintain throughout their lifetimes:
+* Tools for using [SMIRKS Native Open Force Field (SMIRNOFF)](https://openforcefield.github.io/standards/standards/smirnoff/) force fields
+* Tools for [direct chemical environment perception](https://dx.doi.org/10.1021/acs.jctc.8b00640) and manipulation
+
+**Note**: Prior to version 0.9.0, this toolkit and its associated repository were named `openforcefield` and used different import paths. For details on this change and migration instructions, see the [release notes](https://open-forcefield-toolkit.readthedocs.io/en/stable/releasehistory.html#namespace-migration) of version 0.9.0.
+
+## Documentation
+
+[Documentation](https://open-forcefield-toolkit.readthedocs.io/en/stable/) for the Open Force Field Toolkit is hosted at [readthedocs](https://open-forcefield-toolkit.readthedocs.io/en/stable). Example notebooks are available in the `examples/` directory and also hosted on the [`Open Force Field`](https://docs.openforcefield.org/en/latest/examples.html) website.
+
+## How to cite
+
+Please cite the OpenFF Toolkit using the [Zenodo record](https://zenodo.org/record/13886754) of the [latest release](https://zenodo.org/record/13886754) or the version that was used. The BibTeX reference of the latest release can be found [here](https://zenodo.org/records/13886754/export/bibtex).
+
+## Installation
+
+The Open Force Field Toolkit (`openff-toolkit`) is a Python toolkit, and supports Python 3.9 through 3.11.
+
+### Installing via Mamba/Conda
+
+Detailed installation instructions can be found [here](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html).
+
+## Force Fields
+
+Two major force field development efforts have been undertaken by the Open Force Field Initiative, with results hosted in separate repositories.
+
+* The [Open Force Fields repository](https://github.com/openforcefield/openff-forcefields/), which features the [Parsley](https://openforcefield.org/community/news/general/introducing-openforcefield-1.0/) and [Sage](https://openforcefield.org/community/news/general/sage2.0.0-release/) force field lines. These are the Open Force Field Initiative's efforts toward building _new_ force fields. The initial parameters are taken from smirnoff99Frosst, but software and data produced by the Initiative's efforts have been used to refit parameter values and add new SMIRKS-based parameters.
+* The [smirnoff99Frosst repository](https://github.com/openforcefield/smirnoff99Frosst/), which is descended from AMBER's parm99 force field as well as Merck-Frosst's parm@frosst. This line of force fields does not aim to alter parameter values, but is instead a test of accurately converting an atom type-based force field to the SMIRNOFF format.
+
+Force fields from both of these packages are available in their respective GitHub repositories and also as conda packages. Tables detailing the individual file names/versions within these force field lines are in the README of each repository. By default, installing the Open Force Field toolkit using `conda` or the single-file toolkit installers will also install these conda packages. A [plugin architecture](https://github.com/openforcefield/openff-toolkit/blob/main/FAQ.md#how-can-i-distribute-my-own-force-fields-in-smirnoff-format) is provided for other force field developers to produce python/conda packages that can be imported by the Open Force Field Toolkit as well.
+
+# Toolkit features
+
+## The SMIRKS Native Open Force Field (SMIRNOFF) format
+
+This repository provides tools for using the [SMIRKS Native Open Force Field (SMIRNOFF) specification](https://openforcefield.github.io/standards/standards/smirnoff/), which currently supports an XML representation for force field definition files.
+
+By convention, files containing [XML representations](https://en.wikipedia.org/wiki/XML) of SMIRNOFF force fields carry `.offxml` extensions.
+
+Example SMIRNOFF `.offxml` force field definitions can be found in [`openff/toolkit/data/test_forcefields/`](https://github.com/openforcefield/openff-toolkit/tree/main/openff/toolkit/data/test_forcefields). These force fields are for testing only, and we neither record versions of these files, nor do we guarantee their correctness or completeness.
+
+### Working with SMIRNOFF parameter sets
+
+SMIRNOFF force fields can be parsed by the `ForceField` class, which offers methods including `create_openmm_system` for exporting to OpenMM and `create_interchange` for exporting to other formats (GROMACS, Amber, LAMMPS) via [Interchange](https://docs.openforcefield.org/projects/interchange).
+
+```python
+# Load a molecule into the OpenFF Molecule object
+from openff.toolkit import Molecule
+from openff.toolkit.utils import get_data_file_path
+sdf_file_path = get_data_file_path('molecules/ethanol.sdf')
+molecule = Molecule.from_file(sdf_file_path)
+
+# Create an OpenFF Topology object from the molecule
+from openff.toolkit import Topology
+topology = Topology.from_molecules(molecule)
+
+# Load the latest OpenFF force field release: version 2.1.0, codename "Sage"
+from openff.toolkit import ForceField
+forcefield = ForceField('openff-2.1.0.offxml')
+
+# Create an OpenMM system representing the molecule with SMIRNOFF-applied parameters
+openmm_system = forcefield.create_openmm_system(topology)
+
+# Create an Interchange object for representations in other formats
+interchange = forcefield.create_interchange(topology)
+```
+
+Detailed examples of using SMIRNOFF with the toolkit can be found [in the documentation](https://open-forcefield-toolkit.readthedocs.io/en/stable/examples.html).
+
+# Frequently asked questions (FAQ)
+
+See [`FAQ.md`](FAQ.md) for answers to a variety of common problems, such as:
+* Why do I need to provide molecules corresponding to the components of my system, or a `Topology` with bond orders?
+* Can I use an Amber, CHARMM, or GROMACS topology/coordinate file as a starting point for applying a SMIRNOFF force field?
+* What if I am starting from a PDB file?
+
+# Contributors
+
+For a partial list of contributors, see the [GitHub Contributors page](https://github.com/openforcefield/openff-toolkit/graphs/contributors). Others whose work constitutes significant contributions but did not make it into the `git` history include Shuzhe Wang.

acellera_openff_toolkit-0.18.0/acellera_openff_toolkit.egg-info/PKG-INFO

@@ -0,0 +1,109 @@
+Metadata-Version: 2.4
+Name: acellera-openff-toolkit
+Version: 0.18.0
+Summary: openff-toolkit
+Author-email: Open Force Field Consortium <info@openforcefield.org>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/openforcefield/openff-toolkit
+Keywords: force field,molecular mechanics,parameterization
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Utilities
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: license-file
+
+| **Status** | [![GH Actions Status](https://github.com/openforcefield/openff-toolkit/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-toolkit/actions?query=branch%3Amain+workflow%3ACI)  [![Codecov coverage](https://img.shields.io/codecov/c/github/openforcefield/openff-toolkit.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/openforcefield/openff-toolkit) |
+| :------ |:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| **Latest Release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openff-toolkit.svg)](https://github.com/openforcefield/openff-toolkit/releases)  [![Commits since release](https://img.shields.io/github/commits-since/openforcefield/openff-toolkit/0.17.1.svg)](https://github.com/openforcefield/openff-toolkit/releases/tag/0.17.1)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17259324.svg)](https://doi.org/10.5281/zenodo.17259324)
+| **Communication** | [![docs stable](https://img.shields.io/badge/docs-stable-5077AB.svg?logo=read%20the%20docs)](https://open-forcefield-toolkit.readthedocs.io/) [![user & dev discussions](https://img.shields.io/badge/user%20%26%20dev%20discussions-GitHub-red?logo=github)](https://github.com/openforcefield/discussions/discussions) |
+| **Foundation** | [![license](https://img.shields.io/github/license/openforcefield/openff-toolkit.svg)](https://opensource.org/licenses/MIT) [![platforms](https://img.shields.io/badge/Platforms-Linux%2C%20MacOS-orange.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![python](https://img.shields.io/badge/python-3.11%2C%203.12%2C%203.13-blue.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![Funding](https://img.shields.io/badge/Funding-Open%20Force%20Field%20Consortium-brightgreen.svg)](http://openforcefield.org)        |
+| **Installation** | [![Releases](https://img.shields.io/badge/obtain-latest-green.svg)](https://github.com/openforcefield/openff-toolkit/releases) [![Conda](https://img.shields.io/conda/v/conda-forge/openff-toolkit.svg)](https://anaconda.org/conda-forge/openff-toolkit) [![Last updated](https://anaconda.org/conda-forge/openff-toolkit/badges/latest_release_relative_date.svg)](https://anaconda.org/conda-forge/openff-toolkit) [![Anaconda Cloud downloads](https://anaconda.org/conda-forge/openff-toolkit/badges/downloads.svg)](https://anaconda.org/conda-forge/openff-toolkit)          |
+
+# The Open Force Field toolkit
+
+The Open Force Field Toolkit, built by the [Open Force Field Initiative](http://openforcefield.org), is a Python toolkit for the development and application of modern molecular mechanics force fields based on direct chemical perception and rigorous statistical parameterization methods.
+
+The toolkit currently covers two main areas we have committed to stably maintain throughout their lifetimes:
+* Tools for using [SMIRKS Native Open Force Field (SMIRNOFF)](https://openforcefield.github.io/standards/standards/smirnoff/) force fields
+* Tools for [direct chemical environment perception](https://dx.doi.org/10.1021/acs.jctc.8b00640) and manipulation
+
+**Note**: Prior to version 0.9.0, this toolkit and its associated repository were named `openforcefield` and used different import paths. For details on this change and migration instructions, see the [release notes](https://open-forcefield-toolkit.readthedocs.io/en/stable/releasehistory.html#namespace-migration) of version 0.9.0.
+
+## Documentation
+
+[Documentation](https://open-forcefield-toolkit.readthedocs.io/en/stable/) for the Open Force Field Toolkit is hosted at [readthedocs](https://open-forcefield-toolkit.readthedocs.io/en/stable). Example notebooks are available in the `examples/` directory and also hosted on the [`Open Force Field`](https://docs.openforcefield.org/en/latest/examples.html) website.
+
+## How to cite
+
+Please cite the OpenFF Toolkit using the [Zenodo record](https://zenodo.org/record/13886754) of the [latest release](https://zenodo.org/record/13886754) or the version that was used. The BibTeX reference of the latest release can be found [here](https://zenodo.org/records/13886754/export/bibtex).
+
+## Installation
+
+The Open Force Field Toolkit (`openff-toolkit`) is a Python toolkit, and supports Python 3.9 through 3.11.
+
+### Installing via Mamba/Conda
+
+Detailed installation instructions can be found [here](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html).
+
+## Force Fields
+
+Two major force field development efforts have been undertaken by the Open Force Field Initiative, with results hosted in separate repositories.
+
+* The [Open Force Fields repository](https://github.com/openforcefield/openff-forcefields/), which features the [Parsley](https://openforcefield.org/community/news/general/introducing-openforcefield-1.0/) and [Sage](https://openforcefield.org/community/news/general/sage2.0.0-release/) force field lines. These are the Open Force Field Initiative's efforts toward building _new_ force fields. The initial parameters are taken from smirnoff99Frosst, but software and data produced by the Initiative's efforts have been used to refit parameter values and add new SMIRKS-based parameters.
+* The [smirnoff99Frosst repository](https://github.com/openforcefield/smirnoff99Frosst/), which is descended from AMBER's parm99 force field as well as Merck-Frosst's parm@frosst. This line of force fields does not aim to alter parameter values, but is instead a test of accurately converting an atom type-based force field to the SMIRNOFF format.
+
+Force fields from both of these packages are available in their respective GitHub repositories and also as conda packages. Tables detailing the individual file names/versions within these force field lines are in the README of each repository. By default, installing the Open Force Field toolkit using `conda` or the single-file toolkit installers will also install these conda packages. A [plugin architecture](https://github.com/openforcefield/openff-toolkit/blob/main/FAQ.md#how-can-i-distribute-my-own-force-fields-in-smirnoff-format) is provided for other force field developers to produce python/conda packages that can be imported by the Open Force Field Toolkit as well.
+
+# Toolkit features
+
+## The SMIRKS Native Open Force Field (SMIRNOFF) format
+
+This repository provides tools for using the [SMIRKS Native Open Force Field (SMIRNOFF) specification](https://openforcefield.github.io/standards/standards/smirnoff/), which currently supports an XML representation for force field definition files.
+
+By convention, files containing [XML representations](https://en.wikipedia.org/wiki/XML) of SMIRNOFF force fields carry `.offxml` extensions.
+
+Example SMIRNOFF `.offxml` force field definitions can be found in [`openff/toolkit/data/test_forcefields/`](https://github.com/openforcefield/openff-toolkit/tree/main/openff/toolkit/data/test_forcefields). These force fields are for testing only, and we neither record versions of these files, nor do we guarantee their correctness or completeness.
+
+### Working with SMIRNOFF parameter sets
+
+SMIRNOFF force fields can be parsed by the `ForceField` class, which offers methods including `create_openmm_system` for exporting to OpenMM and `create_interchange` for exporting to other formats (GROMACS, Amber, LAMMPS) via [Interchange](https://docs.openforcefield.org/projects/interchange).
+
+```python
+# Load a molecule into the OpenFF Molecule object
+from openff.toolkit import Molecule
+from openff.toolkit.utils import get_data_file_path
+sdf_file_path = get_data_file_path('molecules/ethanol.sdf')
+molecule = Molecule.from_file(sdf_file_path)
+
+# Create an OpenFF Topology object from the molecule
+from openff.toolkit import Topology
+topology = Topology.from_molecules(molecule)
+
+# Load the latest OpenFF force field release: version 2.1.0, codename "Sage"
+from openff.toolkit import ForceField
+forcefield = ForceField('openff-2.1.0.offxml')
+
+# Create an OpenMM system representing the molecule with SMIRNOFF-applied parameters
+openmm_system = forcefield.create_openmm_system(topology)
+
+# Create an Interchange object for representations in other formats
+interchange = forcefield.create_interchange(topology)
+```
+
+Detailed examples of using SMIRNOFF with the toolkit can be found [in the documentation](https://open-forcefield-toolkit.readthedocs.io/en/stable/examples.html).
+
+# Frequently asked questions (FAQ)
+
+See [`FAQ.md`](FAQ.md) for answers to a variety of common problems, such as:
+* Why do I need to provide molecules corresponding to the components of my system, or a `Topology` with bond orders?
+* Can I use an Amber, CHARMM, or GROMACS topology/coordinate file as a starting point for applying a SMIRNOFF force field?
+* What if I am starting from a PDB file?
+
+# Contributors
+
+For a partial list of contributors, see the [GitHub Contributors page](https://github.com/openforcefield/openff-toolkit/graphs/contributors). Others whose work constitutes significant contributions but did not make it into the `git` history include Shuzhe Wang.

acellera_openff_toolkit-0.18.0/acellera_openff_toolkit.egg-info/SOURCES.txt

@@ -0,0 +1,235 @@
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+setup.cfg
+acellera_openff_toolkit.egg-info/PKG-INFO
+acellera_openff_toolkit.egg-info/SOURCES.txt
+acellera_openff_toolkit.egg-info/dependency_links.txt
+acellera_openff_toolkit.egg-info/top_level.txt
+devtools/scripts/build_cookiecutter_json.py
+docs/conf.py
+docs/conftest.py
+examples/examples_helper.py
+examples/conformer_energies/conformer_energies.py
+examples/deprecated/SMIRNOFF_comparison/compare_molecule_energies.py
+examples/deprecated/SMIRNOFF_comparison/compare_set_energies.py
+examples/deprecated/liquid_box/openff_simulation.py
+examples/deprecated/liquid_box/create_mol2_pdb/create_mol2_pdb.py
+examples/deprecated/mixedFF_structure/generate_mixedFF_complex.py
+examples/deprecated/testing/test_impropers/tleap_tools.py
+openff/toolkit/__init__.py
+openff/toolkit/_tests/__init__.py
+openff/toolkit/_tests/_stale_tests.py
+openff/toolkit/_tests/conftest.py
+openff/toolkit/_tests/create_molecules.py
+openff/toolkit/_tests/mocking.py
+openff/toolkit/_tests/test_energies.py
+openff/toolkit/_tests/test_examples.py
+openff/toolkit/_tests/test_forcefield.py
+openff/toolkit/_tests/test_interchange.py
+openff/toolkit/_tests/test_io.py
+openff/toolkit/_tests/test_links.py
+openff/toolkit/_tests/test_mm_molecule.py
+openff/toolkit/_tests/test_molecule.py
+openff/toolkit/_tests/test_nagl.py
+openff/toolkit/_tests/test_parameter_plugins.py
+openff/toolkit/_tests/test_parameters.py
+openff/toolkit/_tests/test_toolkit_io.py
+openff/toolkit/_tests/test_toolkits.py
+openff/toolkit/_tests/test_topology.py
+openff/toolkit/_tests/test_utils.py
+openff/toolkit/_tests/test_utils_callback.py
+openff/toolkit/_tests/test_utils_collections.py
+openff/toolkit/_tests/test_utils_serialization.py
+openff/toolkit/_tests/utils.py
+openff/toolkit/_tests/molecule/__init__.py
+openff/toolkit/_tests/molecule/test_state_enumeration.py
+openff/toolkit/data/README.md
+openff/toolkit/data/molecules/AlkEthOH_test_filt1_ff.mol2
+openff/toolkit/data/molecules/AlkEthOH_test_filt1_tripos.mol2
+openff/toolkit/data/molecules/AlkEthOH_tripos.tar.gz
+openff/toolkit/data/molecules/CID20742535_anion.sdf
+openff/toolkit/data/molecules/CID20742535_neutral.sdf
+openff/toolkit/data/molecules/FreeSolv.tar.gz
+openff/toolkit/data/molecules/MiniDrugBank.sdf
+openff/toolkit/data/molecules/MiniDrugBank_tripos.mol2
+openff/toolkit/data/molecules/PT2385.sdf
+openff/toolkit/data/molecules/QL8.sdf
+openff/toolkit/data/molecules/README.md
+openff/toolkit/data/molecules/benzene.crd
+openff/toolkit/data/molecules/benzene.mol2
+openff/toolkit/data/molecules/benzene.top
+openff/toolkit/data/molecules/butane_multi.sdf
+openff/toolkit/data/molecules/cyclohexane.mol2
+openff/toolkit/data/molecules/ethanol.mol2
+openff/toolkit/data/molecules/ethanol.sdf
+openff/toolkit/data/molecules/ethanol_partial_charges.sdf
+openff/toolkit/data/molecules/ethanol_reordered.mol2
+openff/toolkit/data/molecules/ethanol_reordered.sdf
+openff/toolkit/data/molecules/ethene_rdkit.sdf
+openff/toolkit/data/molecules/laromustine_ff.mol2
+openff/toolkit/data/molecules/laromustine_tripos.mol2
+openff/toolkit/data/molecules/methane_multiconformer.sdf
+openff/toolkit/data/molecules/methane_multiconformer_properties.sdf
+openff/toolkit/data/molecules/nh4.pdb
+openff/toolkit/data/molecules/po4_phenylphosphate.pdb
+openff/toolkit/data/molecules/ruxolitinib_conformers.sdf
+openff/toolkit/data/molecules/toluene.mol2
+openff/toolkit/data/molecules/toluene.mol2.gz
+openff/toolkit/data/molecules/toluene.pdb
+openff/toolkit/data/molecules/toluene.sdf
+openff/toolkit/data/molecules/toluene_charged.mol2
+openff/toolkit/data/molecules/z_3_hydroxy_propenal.sdf
+openff/toolkit/data/proteins/5tbm_complex_solv.pdb
+openff/toolkit/data/proteins/5tbm_complex_solv_box.pdb
+openff/toolkit/data/proteins/CTerminal_ALA.pdb
+openff/toolkit/data/proteins/CTerminal_ALA.sdf
+openff/toolkit/data/proteins/CTerminal_ALA_ALA.pdb
+openff/toolkit/data/proteins/CTerminal_ALA_ALA_misnamedH.pdb
+openff/toolkit/data/proteins/CTerminal_ARG.pdb
+openff/toolkit/data/proteins/CTerminal_TRP.pdb
+openff/toolkit/data/proteins/MainChain_ALA.pdb
+openff/toolkit/data/proteins/MainChain_ALA.sdf
+openff/toolkit/data/proteins/MainChain_ALA_ALA.pdb
+openff/toolkit/data/proteins/MainChain_ALA_ALA.sdf
+openff/toolkit/data/proteins/MainChain_ALA_ALA_icodes.pdb
+openff/toolkit/data/proteins/MainChain_ALA_ALA_no_hydrogens.pdb
+openff/toolkit/data/proteins/MainChain_ARG.pdb
+openff/toolkit/data/proteins/MainChain_ARG.sdf
+openff/toolkit/data/proteins/MainChain_CYM.pdb
+openff/toolkit/data/proteins/MainChain_CYS.pdb
+openff/toolkit/data/proteins/MainChain_CYX.pdb
+openff/toolkit/data/proteins/MainChain_CYX.sdf
+openff/toolkit/data/proteins/MainChain_GLH.sdf
+openff/toolkit/data/proteins/MainChain_GLU.sdf
+openff/toolkit/data/proteins/MainChain_HID.pdb
+openff/toolkit/data/proteins/MainChain_HIE.pdb
+openff/toolkit/data/proteins/MainChain_HIE.sdf
+openff/toolkit/data/proteins/MainChain_HIP.pdb
+openff/toolkit/data/proteins/MainChain_HIP.sdf
+openff/toolkit/data/proteins/MainChain_PRO.pdb
+openff/toolkit/data/proteins/MainChain_TRP.pdb
+openff/toolkit/data/proteins/NTerminal_ALA.pdb
+openff/toolkit/data/proteins/NTerminal_ALA.sdf
+openff/toolkit/data/proteins/NTerminal_ALA_ALA.pdb
+openff/toolkit/data/proteins/NTerminal_ARG.pdb
+openff/toolkit/data/proteins/NTerminal_TRP.pdb
+openff/toolkit/data/proteins/T4-protein-unprocessed-4w51.pdb
+openff/toolkit/data/proteins/T4-protein.mol2
+openff/toolkit/data/proteins/T4-protein.pdb
+openff/toolkit/data/proteins/T4-protein.sdf
+openff/toolkit/data/proteins/T4_protein_waters.pdb
+openff/toolkit/data/proteins/TwoMol_SER_CYS.pdb
+openff/toolkit/data/proteins/aa_residues_substructures_explicit_bond_orders_with_caps.json
+openff/toolkit/data/proteins/aa_residues_substructures_explicit_bond_orders_with_caps_explicit_connectivity.json
+openff/toolkit/data/proteins/aa_residues_substructures_with_caps.json
+openff/toolkit/data/proteins/ace-ZZZ-gly-nme.pdb
+openff/toolkit/data/proteins/ace-ZZZ-gly-nme.sdf
+openff/toolkit/data/proteins/ace-a10-nme.sdf
+openff/toolkit/data/proteins/ace-ala-nh2.pdb
+openff/toolkit/data/proteins/fluoresceine_dyed_helix_capped.pdb
+openff/toolkit/data/proteins/neutral_arginine.pdb
+openff/toolkit/data/proteins/split_chain.pdb
+openff/toolkit/data/proteins/split_chain_reordered.pdb
+openff/toolkit/data/reference_energies/README.md
+openff/toolkit/data/reference_energies/reference_0.8.0.json
+openff/toolkit/data/reference_energies/reference_0.8.0.json.txt
+openff/toolkit/data/reference_energies/reference_after_1007.json
+openff/toolkit/data/reference_energies/reference_after_1007.json.txt
+openff/toolkit/data/reference_energies/reference_after_802.json
+openff/toolkit/data/reference_energies/reference_after_802.json.txt
+openff/toolkit/data/systems/README.md
+openff/toolkit/data/systems/amber/cyclohexane_ethanol_0.4_0.6.inpcrd
+openff/toolkit/data/systems/amber/cyclohexane_ethanol_0.4_0.6.prmtop
+openff/toolkit/data/systems/monomers/butanol.mol2
+openff/toolkit/data/systems/monomers/butanol.sdf
+openff/toolkit/data/systems/monomers/cyclohexane.mol2
+openff/toolkit/data/systems/monomers/cyclohexane.sdf
+openff/toolkit/data/systems/monomers/ethanol.mol2
+openff/toolkit/data/systems/monomers/ethanol.sdf
+openff/toolkit/data/systems/monomers/methane.mol2
+openff/toolkit/data/systems/monomers/methane.sdf
+openff/toolkit/data/systems/monomers/propane.mol2
+openff/toolkit/data/systems/monomers/propane.sdf
+openff/toolkit/data/systems/monomers/tip3p_water.mol2
+openff/toolkit/data/systems/monomers/water.mol2
+openff/toolkit/data/systems/monomers/water.sdf
+openff/toolkit/data/systems/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb
+openff/toolkit/data/systems/packmol_boxes/cyclohexane_water.pdb
+openff/toolkit/data/systems/packmol_boxes/ethanol_water.pdb
+openff/toolkit/data/systems/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb
+openff/toolkit/data/systems/test_systems/1_cyclohexane_1_ethanol.pdb
+openff/toolkit/data/systems/test_systems/1_ethanol.pdb
+openff/toolkit/data/systems/test_systems/1_ethanol_no_conect.pdb
+openff/toolkit/data/systems/test_systems/1_ethanol_reordered.pdb
+openff/toolkit/data/systems/test_systems/PE.pdb
+openff/toolkit/data/systems/test_systems/README.md
+openff/toolkit/data/systems/test_systems/T4_lysozyme_water_ions.pdb
+openff/toolkit/data/test_forcefields/Frosst_AlkEthOH.offxml
+openff/toolkit/data/test_forcefields/Frosst_AlkEthOH_GBSA.offxml
+openff/toolkit/data/test_forcefields/Frosst_AlkEthOH_MDL.offxml
+openff/toolkit/data/test_forcefields/Frosst_AlkEthOH_parmAtFrosst.offxml
+openff/toolkit/data/test_forcefields/GBSA_HCT-1.0.offxml
+openff/toolkit/data/test_forcefields/GBSA_OBC1-1.0.offxml
+openff/toolkit/data/test_forcefields/GBSA_OBC2-1.0.offxml
+openff/toolkit/data/test_forcefields/README.md
+openff/toolkit/data/test_forcefields/ammonia_minimal.offxml
+openff/toolkit/data/test_forcefields/benzene_minimal.offxml
+openff/toolkit/data/test_forcefields/chargeincrement-test.offxml
+openff/toolkit/data/test_forcefields/frcmod.Frosst_AlkEthOH_withIDs
+openff/toolkit/data/test_forcefields/ion_charges.offxml
+openff/toolkit/data/test_forcefields/mangled.offxml
+openff/toolkit/data/test_forcefields/smirff99Frosst_reference_0_1_spec.offxml
+openff/toolkit/data/test_forcefields/smirnoff99Frosst_experimental.offxml
+openff/toolkit/data/test_forcefields/smirnoff99Frosst_reference_0_1_spec.offxml
+openff/toolkit/data/test_forcefields/smirnoff99Frosst_reference_0_2_spec.offxml
+openff/toolkit/data/test_forcefields/test_forcefield.offxml
+openff/toolkit/data/test_forcefields/tip3p.offxml
+openff/toolkit/data/test_forcefields/unsupported_smirnoff_version.offxml
+openff/toolkit/data/test_forcefields/old/README.md
+openff/toolkit/data/test_forcefields/old/hbonds.offxml
+openff/toolkit/data/test_forcefields/old/test_ff_0_0_2_spec_0_1.offxml
+openff/toolkit/data/test_forcefields/old/test_ff_0_0_2_spec_0_2.offxml
+openff/toolkit/data/test_forcefields/old/test_ff_0_0_2_spec_0_3.offxml
+openff/toolkit/data/test_forcefields/old/test_ff_0_0_4_fixed_spec_0_1.offxml
+openff/toolkit/data/test_forcefields/old/test_ff_0_0_4_fixed_spec_0_2.offxml
+openff/toolkit/data/test_forcefields/old/test_ff_0_0_4_fixed_spec_0_3.offxml
+openff/toolkit/data/test_forcefields/old/test_ff_0_0_4_spec_0_1.offxml
+openff/toolkit/data/test_forcefields/old/test_ff_0_0_4_spec_0_2.offxml
+openff/toolkit/data/test_forcefields/old/test_ff_0_0_4_spec_0_3.offxml
+openff/toolkit/topology/__init__.py
+openff/toolkit/topology/_mm_molecule.py
+openff/toolkit/topology/molecule.py
+openff/toolkit/topology/topology.py
+openff/toolkit/typing/__init__.py
+openff/toolkit/typing/engines/__init__.py
+openff/toolkit/typing/engines/smirnoff/__init__.py
+openff/toolkit/typing/engines/smirnoff/forcefield.py
+openff/toolkit/typing/engines/smirnoff/io.py
+openff/toolkit/typing/engines/smirnoff/parameters.py
+openff/toolkit/typing/engines/smirnoff/plugins.py
+openff/toolkit/utils/__init__.py
+openff/toolkit/utils/_viz.py
+openff/toolkit/utils/ambertools_wrapper.py
+openff/toolkit/utils/base_wrapper.py
+openff/toolkit/utils/builtin_wrapper.py
+openff/toolkit/utils/callback.py
+openff/toolkit/utils/collections.py
+openff/toolkit/utils/constants.py
+openff/toolkit/utils/exceptions.py
+openff/toolkit/utils/nagl_wrapper.py
+openff/toolkit/utils/openeye_wrapper.py
+openff/toolkit/utils/rdkit_wrapper.py
+openff/toolkit/utils/serialization.py
+openff/toolkit/utils/toolkit_registry.py
+openff/toolkit/utils/toolkits.py
+openff/toolkit/utils/utils.py
+utilities/deprecated/convert_frosst/convert_frcmod_0.1.py
+utilities/deprecated/convert_frosst/convert_frcmod_0.2.py
+utilities/deprecated/convert_frosst/convert_frcmod_0.3.py
+utilities/make_substructure_dict/_cif_to_substructure_dict.py
+utilities/make_substructure_dict/_make_chemical_substructures.py
+utilities/make_substructure_dict/_make_metadata_assignment_substructures.py
+utilities/test_plugins/setup.py
+utilities/test_plugins/custom_plugins/handler_plugins.py

acellera_openff_toolkit-0.18.0/acellera_openff_toolkit.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

acellera_openff_toolkit-0.18.0/acellera_openff_toolkit.egg-info/top_level.txt

@@ -0,0 +1,5 @@
+devtools
+docs
+examples
+openff
+utilities

acellera_openff_toolkit-0.18.0/devtools/scripts/build_cookiecutter_json.py

@@ -0,0 +1,22 @@
+import json
+import sys
+
+release_tag = sys.argv[1]
+python_version = sys.argv[2]
+ci_os = sys.argv[3]
+
+platform_mapping = {
+    "ubuntu-latest": "linux-64",
+    "macOS-latest": "osx-64",
+}
+
+data = {
+    "name": "openff-toolkit",
+    "channel": "conda-forge",
+    "python": [python_version],
+    "platform": [platform_mapping[ci_os]],
+    "release": release_tag,
+}
+
+with open("new_cookiecutter.json", "w") as fp:
+    json.dump(data, fp)