| Name | dockstring JSON |
| Version |
0.3.4
JSON |
| download |
| home_page | None |
| Summary | Package for easy ligand preparation and docking with AutoDock Vina against a highly-curated selection of 58 protein targets. One of the three components of the DOCKSTRING bundle (package, dataset, and benchmark tasks). |
| upload_time | 2024-10-25 14:04:18 |
| maintainer | None |
| docs_url | None |
| author | Miguel García-Ortegón, Gregor Simm, Austin Tripp |
| requires_python | >=3.7 |
| license | Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. "License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. "Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. "Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. "You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. "Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. "Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. "Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). "Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. "Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." "Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and (d) If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. 6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. 7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. 8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. 9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. END OF TERMS AND CONDITIONS APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets "[]" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same "printed page" as the copyright notice for easier identification within third-party archives. Copyright [yyyy] [name of copyright owner] Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. |
| keywords |
docking
ligand
protein
binding
benchmark
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# dockstring
A Python package for easy molecular docking and docking benchmarking.
We can dock molecules in a few lines of code from just a SMILES string!
For details, see [our paper](https://pubs.acs.org/doi/full/10.1021/acs.jcim.1c01334)
and our [website](https://dockstring.github.io/):
> García-Ortegón, Miguel, et al. "DOCKSTRING: easy molecular docking yields better benchmarks for ligand design." Journal of Chemical Information and Modeling (2021).
## Installation
**Supported platforms:**
This package is primarily intended for Linux, but we have some support for Mac.
Please note that the scores from the Mac version do not always perfectly match the Linux version,
so we encourage the use of the Linux version whenever possible.
**Package versions:**
When installing dockstring, please be mindful of which package versions you install.
The dockstring dataset was created using:
- `rdkit=2021.03.3`
- `openbabel=3.1.1`
- `python=3.7.10`
If you want to reproduce the calculations of the dockstring dataset exactly
(or calculate docking scores completely consistent with the dataset)
then ideally install these versions of the packages above.
However, python 3.7 has reached end of life, so we have tested higher versions of the packages:
It appears that `python<=3.10, openbabel=3.1.1, rdkit<=2022.03` will also work.
Ultimately we just suggest being mindful of which version you install,
and test whether it matches the dataset values after installation (instructions on this below).
If in doubt, use our `environment.yml` file.
Note that if you do not care about consistency with our pre-computed dataset then any package version is ok.
**Installation instructions:**
We recommend installing with `conda` using our package on [conda-forge](https://anaconda.org/conda-forge/dockstring):
this will automatically install the correct versions of `rdkit` and `openbabel` (which currently cannot be installed with pip).
To do this, run:
```bash
conda install -c conda-forge dockstring
```
It can alternatively be installed from [PyPI](https://pypi.org/project/dockstring/) by running:
```bash
python3 -m pip install dockstring
```
However, this will *not* install the dependencies because `openbabel` currently cannot be installed with pip.
If you want to use dockstring for benchmarking, we recommend installing the latest version by cloning this repo:
1. Clone this repository.
1. Choose whether to install into an existing environment or create a new environment.
- To install into a new environment, run:
```bash
conda env create -f environment.yml
conda activate dockstring
```
- To install into an existing environment, simply install the desired versions of `openbabel` and `rdkit`.
1. Install the dockstring package with `pip` from this repository:
```bash
pip install .
```
1. Check whether the installation was successful by running a test script.
Running without error indicates a successful install.
```bash
python tutorials/simple_example.py
```
1. *(optional)* Install [PyMol](https://pymol.org/) for target, search box and ligand visualization:
```bash
conda install -c conda-forge pymol-open-source
```
1. *(optional)* Check whether your local version of dockstring matches the dockstring dataset.
This is only necessary if you plan to mix pre-computed docking scores from the dockstring dataset
with locally-computed scores, or if you want to compare results with the dockstring paper.
We have created a `pytest` test which randomly docks `N` molecules from the dockstring dataset
and checks whether they match. The value of `N` can be changed by setting the environment variable
`num_dockstring_test_molecules`. We recommend starting with `N=50`, then progressing to `N=1000`
to do a full test. The test can be run with the following commands:
```bash
conda install -c conda-forge pytest # only if not installed already
num_dockstring_test_molecules=1000 python -m pytest tests/test_dataset_matching.py # change "1000" to the number you wish to dock
```
If the test passes then your local version of docktring matches the dataset exactly! 🥳
If the test does not pass, we encourage you to look how the error rate (this will be displayed in the error messages).
If 99%+ of scores match then it is probably ok to use dockstring in the benchmarks, but there will of course be some error
and this should be noted.
If this method of installation does not work for you, please raise a github issue and we will try to help.
## Tutorials
- See dockstring's basic usage [here](tutorials/1_docking_risperidone_against_DRD2.ipynb).
- Learn how to visualize docking poses [here](tutorials/2_visualizing_dataset_poses.ipynb)
See [our website](https://dockstring.github.io/) for links to tutorials for
our dataset and benchmarks.
## Development
See `DEVELOPMENT.md`
## Citation
If you use the dockstring package/dataset/benchmark in your work,
please use the following citation:
```tex
@article{garciaortegon2022dockstring,
author = {García-Ortegón, Miguel and Simm, Gregor N. C. and Tripp, Austin J. and Hernández-Lobato, José Miguel and Bender, Andreas and Bacallado, Sergio},
title = {DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design},
journal = {Journal of Chemical Information and Modeling},
volume = {62},
number = {15},
pages = {3486-3502},
year = {2022},
doi = {10.1021/acs.jcim.1c01334},
URL = {https://doi.org/10.1021/acs.jcim.1c01334}
}
```
Raw data
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"keywords": "docking, ligand, protein, binding, benchmark",
"author": "Miguel Garc\u00eda-Orteg\u00f3n, Gregor Simm, Austin Tripp",
"author_email": null,
"download_url": "https://files.pythonhosted.org/packages/88/c4/86069d6bea1d7bb430e929b02c45bc5e9c3a0d9426a53662a12fa50673ad/dockstring-0.3.4.tar.gz",
"platform": null,
"description": "# dockstring\n\n\n\n\nA Python package for easy molecular docking and docking benchmarking.\nWe can dock molecules in a few lines of code from just a SMILES string!\nFor details, see [our paper](https://pubs.acs.org/doi/full/10.1021/acs.jcim.1c01334)\nand our [website](https://dockstring.github.io/):\n\n> Garc\u00eda-Orteg\u00f3n, Miguel, et al. \"DOCKSTRING: easy molecular docking yields better benchmarks for ligand design.\" Journal of Chemical Information and Modeling (2021).\n\n## Installation\n\n**Supported platforms:**\nThis package is primarily intended for Linux, but we have some support for Mac.\nPlease note that the scores from the Mac version do not always perfectly match the Linux version,\nso we encourage the use of the Linux version whenever possible.\n\n**Package versions:**\n\nWhen installing dockstring, please be mindful of which package versions you install.\nThe dockstring dataset was created using:\n\n- `rdkit=2021.03.3`\n- `openbabel=3.1.1`\n- `python=3.7.10`\n\nIf you want to reproduce the calculations of the dockstring dataset exactly\n(or calculate docking scores completely consistent with the dataset)\nthen ideally install these versions of the packages above.\nHowever, python 3.7 has reached end of life, so we have tested higher versions of the packages:\nIt appears that `python<=3.10, openbabel=3.1.1, rdkit<=2022.03` will also work.\nUltimately we just suggest being mindful of which version you install,\nand test whether it matches the dataset values after installation (instructions on this below).\nIf in doubt, use our `environment.yml` file.\nNote that if you do not care about consistency with our pre-computed dataset then any package version is ok.\n\n**Installation instructions:**\n\nWe recommend installing with `conda` using our package on [conda-forge](https://anaconda.org/conda-forge/dockstring):\nthis will automatically install the correct versions of `rdkit` and `openbabel` (which currently cannot be installed with pip).\nTo do this, run:\n\n```bash\nconda install -c conda-forge dockstring\n```\n\nIt can alternatively be installed from [PyPI](https://pypi.org/project/dockstring/) by running:\n\n```bash\npython3 -m pip install dockstring\n```\n\nHowever, this will *not* install the dependencies because `openbabel` currently cannot be installed with pip.\n\nIf you want to use dockstring for benchmarking, we recommend installing the latest version by cloning this repo:\n\n1. Clone this repository.\n1. Choose whether to install into an existing environment or create a new environment.\n - To install into a new environment, run:\n ```bash\n conda env create -f environment.yml\n conda activate dockstring\n ```\n - To install into an existing environment, simply install the desired versions of `openbabel` and `rdkit`.\n1. Install the dockstring package with `pip` from this repository:\n ```bash\n pip install .\n ```\n1. Check whether the installation was successful by running a test script.\n Running without error indicates a successful install.\n ```bash\n python tutorials/simple_example.py\n ```\n1. *(optional)* Install [PyMol](https://pymol.org/) for target, search box and ligand visualization:\n ```bash\n conda install -c conda-forge pymol-open-source\n ```\n1. *(optional)* Check whether your local version of dockstring matches the dockstring dataset.\n This is only necessary if you plan to mix pre-computed docking scores from the dockstring dataset\n with locally-computed scores, or if you want to compare results with the dockstring paper.\n\n We have created a `pytest` test which randomly docks `N` molecules from the dockstring dataset\n and checks whether they match. The value of `N` can be changed by setting the environment variable\n `num_dockstring_test_molecules`. We recommend starting with `N=50`, then progressing to `N=1000`\n to do a full test. The test can be run with the following commands:\n ```bash\n conda install -c conda-forge pytest # only if not installed already\n num_dockstring_test_molecules=1000 python -m pytest tests/test_dataset_matching.py # change \"1000\" to the number you wish to dock\n ```\n If the test passes then your local version of docktring matches the dataset exactly! \ud83e\udd73\n If the test does not pass, we encourage you to look how the error rate (this will be displayed in the error messages).\n If 99%+ of scores match then it is probably ok to use dockstring in the benchmarks, but there will of course be some error\n and this should be noted.\n\nIf this method of installation does not work for you, please raise a github issue and we will try to help.\n\n## Tutorials\n\n- See dockstring's basic usage [here](tutorials/1_docking_risperidone_against_DRD2.ipynb).\n- Learn how to visualize docking poses [here](tutorials/2_visualizing_dataset_poses.ipynb)\n\nSee [our website](https://dockstring.github.io/) for links to tutorials for\nour dataset and benchmarks.\n\n## Development\n\nSee `DEVELOPMENT.md`\n\n## Citation\n\nIf you use the dockstring package/dataset/benchmark in your work,\nplease use the following citation:\n\n```tex\n@article{garciaortegon2022dockstring,\n author = {Garc\u00eda-Orteg\u00f3n, Miguel and Simm, Gregor N. C. and Tripp, Austin J. and Hern\u00e1ndez-Lobato, Jos\u00e9 Miguel and Bender, Andreas and Bacallado, Sergio},\n title = {DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design},\n journal = {Journal of Chemical Information and Modeling},\n volume = {62},\n number = {15},\n pages = {3486-3502},\n year = {2022},\n doi = {10.1021/acs.jcim.1c01334},\n URL = {https://doi.org/10.1021/acs.jcim.1c01334}\n}\n```\n",
"bugtrack_url": null,
"license": " Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. \"License\" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. \"Licensor\" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. \"Legal Entity\" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, \"control\" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. \"You\" (or \"Your\") shall mean an individual or Legal Entity exercising permissions granted by this License. \"Source\" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. \"Object\" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. \"Work\" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). \"Derivative Works\" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. \"Contribution\" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, \"submitted\" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as \"Not a Contribution.\" \"Contributor\" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. 4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: (a) You must give any other recipients of the Work or Derivative Works a copy of this License; and (b) You must cause any modified files to carry prominent notices stating that You changed the files; and (c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and (d) If the Work includes a \"NOTICE\" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. 5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. 6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. 7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. 8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. 9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. END OF TERMS AND CONDITIONS APPENDIX: How to apply the Apache License to your work. To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets \"[]\" replaced with your own identifying information. (Don't include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same \"printed page\" as the copyright notice for easier identification within third-party archives. Copyright [yyyy] [name of copyright owner] Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. ",
"summary": "Package for easy ligand preparation and docking with AutoDock Vina against a highly-curated selection of 58 protein targets. One of the three components of the DOCKSTRING bundle (package, dataset, and benchmark tasks).",
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