Update Readme Files (#41)

* Update readme files * Update README.md * Unify the spelling * Prompt source code access * Update deepmodeling badge * re-organize paragraphs * Remove unidock-tools subtitles --------- Co-authored-by: Yuan Yannan <[email protected]>
dptech-corp · Feb 28, 2024 · f722245 · f722245
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -11,7 +11,7 @@ Even better, you can submit a Pull Request with a patch.
 ## Feature requests
 
 We highly appreciate your contributions, and would like to help you crafting the changes and making contributions to the community.
-If you would like to implement a new feature, please **submit a feature requesting issue with a proposal for your work first**. 
+If you would like to implement a new feature, please **submit a feature requesting issue with a proposal for your work first**.
 This help fitting your ideas and work with the development road map well, coordinating our efforts, and avoiding duplication of work.
 
 ## Submitting a Pull Request
@@ -35,7 +35,7 @@ This help fitting your ideas and work with the development road map well, coordi
     ```
 
 5. On GitHub, create a pull request (PR) from your bug-fix branch targeting `dptech-corp/Uni-Dock`.
- 
+
 6. After your pull request is merged, you can safely delete your branch and sync the changes from the main (upstream) repository:
 
 - Delete the remote branch on GitHub either [through the GitHub web UI](https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/managing-branches-in-your-repository/deleting-and-restoring-branches-in-a-pull-request#deleting-a-branch-used-for-a-pull-request) or your local shell as follows:

diff --git a/README.md b/README.md
@@ -3,28 +3,26 @@
 <picture><source media="(prefers-color-scheme: dark)" srcset="./unidock/assets/logo-dark.svg"><source media="(prefers-color-scheme: light)" srcset="./unidock/assets/logo.svg"><img alt="Uni-Dock logo" src="./unidock/assets/logo.svg"></picture>
 
 [![DeepModeling](https://img.shields.io/badge/DeepModeling-Incubating_Project-blue)](https://github.com/deepmodeling)
-## Introduction
 
 **Uni-Dock** is a GPU-accelerated molecular docking program developed by DP Technology.
 It supports various scoring functions including vina, vinardo, and ad4. Uni-Dock achieves more than 1000-fold speed-up on V100 GPU with high-accuracy compared with the AutoDock Vina running in single CPU core.
 The [paper](https://pubs.acs.org/doi/10.1021/acs.jctc.2c01145) has been accepted by JCTC (doi: 10.1021/acs.jctc.2c01145).
 
-![Runtime performance of Uni-Dock on different GPUs in three modes](./unidock/assets/gpu_speeds.png)
+**Uni-Dock** joins the DeepModeling community, a community devoted of AI for science, as an incubating level project. [Learn more about DeepModeling](https://github.com/deepmodeling/community)
 
-Check this [subfolder](./unidock/) for instructions on installing Uni-Dock.
+![Runtime performance of Uni-Dock on different GPUs in three modes](./unidock/assets/gpu_speeds.png)
 
-**Uni-Dock** joins the DeepModeling community, a community devoted of AI for science, as an incubating level project. To learn more about the DeepModeling community, see the [introduction of community](https://github.com/deepmodeling/community).
-## UniDockTools
+Please check [`unidock` folder](./unidock/) for installing instructions, source codes, and usage.
 
-**UniDockTools** is a python package developed to handle the inputs and outputs of Uni-Dock.
-In the future, UniDockTools will support more input formats and scoring functions. We hope it could be an easy-to-use virtual screening workflow for all users.
+**Uni-Dock Tools** is a Python package developed to handle the inputs and outputs of Uni-Dock.
+It is committed to support more input formats and scoring functions. We hope it could be an easy-to-use virtual screening workflow for users with diversed backgrounds.
 
-Check this [subfolder](./unidock_tools/) for more details.
+Please check [`unidock_tools` folder](./unidock_tools/) for installing instructions, source codes, and usage.
 
 ## Changelog
 
 - 2023-08-21: Upload source codes of Uni-Dock.
-- 2023-08-14: Add unidock_tools to support SDF format input for vina and vinardo scoring functions.
+- 2023-08-14: Add Uni-Dock Tools to support SDF format input for vina and vinardo scoring functions.
 
 ## Citation
 
@@ -34,18 +32,3 @@ Yu, Y., Cai, C., Wang, J., Bo, Z., Zhu, Z., & Zheng, H. (2023).
 Uni-Dock: GPU-Accelerated Docking Enables Ultralarge Virtual Screening.
 Journal of Chemical Theory and Computation.
 https://doi.org/10.1021/acs.jctc.2c01145
-
-Tang, S., Chen, R., Lin, M., Lin, Q., Zhu, Y., Ding, J., ... & Wu, J. (2022).
-Accelerating autodock vina with gpus. Molecules, 27(9), 3041.
-DOI 10.3390/molecules27093041
-
-J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli
-AutoDock Vina 1.2.0: New Docking Methods, Expanded Force
-Field, and Python Bindings, J. Chem. Inf. Model. (2021)
-DOI 10.1021/acs.jcim.1c00203
-
-O. Trott, A. J. Olson,
-AutoDock Vina: improving the speed and accuracy of docking
-with a new scoring function, efficient optimization and
-multithreading, J. Comp. Chem. (2010)
-DOI 10.1002/jcc.21334
diff --git a/unidock/README.md b/unidock/README.md
@@ -7,20 +7,6 @@ The [paper](https://pubs.acs.org/doi/10.1021/acs.jctc.2c01145) has been accepted
 
 ![Runtime performance of Uni-Dock on different GPUs in three modes](assets/gpu_speeds.png)
 
-## Changelog
-
-- 2023-08-14: Add `unidock_tools` to support SDF format input for vina and vinardo scoring functions.
-
-## License
-
-This project is licensed under the terms of the GNU Lesser General Public License v3.0. See [LICENSE](./LICENSE) for details.
-
-Developed by [DP Technology](https://dp.tech/en), [Hermite®](https://dp.tech/en/product/hermite) is a new-generation drug computing design platform which integrates artificial intelligence, physical modeling and high-performance computing to provide a one-stop computing solution for preclinical drug research and development. It integrates the features of Uni-Dock, along with virtual screening workflow for an efficient drug discovery process.
-
-Uni-Dock is now available on the new-generation drug computing design platform [Hermite®](https://dp.tech/en/product/hermite) for ultralarge virtual screening.
-
-For further cooperations on developing Uni-Dock and trying out Hermite®, please contact us at <[email protected]> .
-
 ## Installation
 
 Uni-Dock officially supports NVIDIA GPUs with [compute capability](https://en.wikipedia.org/wiki/CUDA#GPUs_supported) >= 7.0 on Linux platform.
@@ -57,7 +43,7 @@ The performance is not guaranteed on legacy GPU models. To build Uni-Dock with a
                            # Otherwise, prepend the building directory to your `PATH` environment variable.
      ```
 
-code foramt
+To format codes if changes are made:
 
 ```shell
 cd ./build/
@@ -195,9 +181,33 @@ python run_dock.py
 
 If you want to use search mode presets, specify the parameter `search_mode` in `config.json` and delete `nt` and `ns` in `config.json`.
 
-## Bug Report
+## Contributing
+
+We warmly welcome contributions from the open source community. Your bug reports, feature requests, and pull requests helps Uni-Dock improve.
+
+Please submit bug reports and feature requests to the Github [issue tracker](https://github.com/dptech-corp/Uni-Dock/issues/new/choose).
 
-Please report bugs to [Issues](https://github.com/dptech-corp/Uni-Dock/issues) page.
+If you would like to improve the codes, please refer to the [contributing guide](../.github/CONTRIBUTING.md) for details.
+
+## Changelog
+
+Major changes are documented. For the detailed changes, please refer to the commit history.
+
+### v1.1
+
+- Optimize 1:1 ligand docking.
+- Optimize Monte-Carlo simulation speed.
+- Generate compute kernels for various ligands sizes.
+
+## License
+
+This project is licensed under the terms of the GNU Lesser General Public License v3.0. See [LICENSE](./LICENSE) for details.
+
+Developed by [DP Technology](https://dp.tech/en), [Hermite®](https://dp.tech/en/product/hermite) is a new-generation drug computing design platform which integrates artificial intelligence, physical modeling and high-performance computing to provide a one-stop computing solution for preclinical drug research and development. It integrates the features of Uni-Dock, along with virtual screening workflow for an efficient drug discovery process.
+
+Uni-Dock is now available on the new-generation drug computing design platform [Hermite®](https://dp.tech/en/product/hermite) for ultralarge virtual screening.
+
+For further cooperations on developing Uni-Dock and trying out Hermite®, please contact us at <[email protected]> .
 
 ## Ackowledgement
 

diff --git a/unidock_tools/README.md b/unidock_tools/README.md
@@ -13,7 +13,7 @@ Main features are:
 
 ## Dependency
 
-- Uni-Dock
+- [Uni-Dock](../unidock/README.md#installation)
 - Python >= 3.6
 - RDKit
 - networkx
@@ -92,4 +92,4 @@ See [MCDock Usage](./MCDOCK.md#usage)
 
 # License
 
-This project is licensed under the terms of Apache license 2.0. See [LICENSE](./LICENSE) for additional details.
+This project is licensed under the terms of Apache license 2.0. See [LICENSE](./LICENSE) for additional details.
diff --git a/unidock_tools/tests/applications/test_ligprep.py b/unidock_tools/tests/applications/test_ligprep.py
@@ -12,7 +12,7 @@ def input_ligand():
 
 def test_ligprep_app_ligand_file(input_ligand):
     results_dir = "prepared_ligands"
-    cmd = f"unidocktools ligprep -l {input_ligand} -sd {results_dir}"
+    cmd = f"unidocktools ligandprep -l {input_ligand} -sd {results_dir}"
     print(cmd)
     resp = subprocess.run(cmd, shell=True, capture_output=True, encoding="utf-8")
     print(resp.stdout)
@@ -25,7 +25,7 @@ def test_ligprep_app_ligand_index(input_ligand):
     with open(index_file, "w") as f:
         f.write(input_ligand)
     results_dir = "prepared_ligands"
-    cmd = f"unidocktools ligprep -i {index_file} -sd {results_dir}"
+    cmd = f"unidocktools ligandprep -i {index_file} -sd {results_dir}"
     print(cmd)
     resp = subprocess.run(cmd, shell=True, capture_output=True, encoding="utf-8")
     print(resp.stdout)

diff --git a/...ools/tests/applications/test_pdb2pdbqt.py → ..._tools/tests/applications/test_proprep.py b/...ools/tests/applications/test_pdb2pdbqt.py → ..._tools/tests/applications/test_proprep.py
@@ -11,9 +11,9 @@ def pdb_file():
 
 def test_pdb2pdbqt_app(pdb_file):
     pdbqt_file = "protein.pdbqt"
-    cmd = f"unidocktools pdb2pdbqt -r {pdb_file} -o {pdbqt_file}"
+    cmd = f"unidocktools proteinprep -r {pdb_file} -o {pdbqt_file}"
     print(cmd)
     resp = subprocess.run(cmd, shell=True, capture_output=True, encoding="utf-8")
     print(resp.stdout)
-    assert resp.returncode==0, f"run pdb2pdbqt app err:\n{resp.stderr}"
+    assert resp.returncode==0, f"run proteinprep app err:\n{resp.stderr}"
     Path(pdbqt_file).unlink(missing_ok=True)
diff --git a/unidock_tools/tests/applications/test_unidock.py b/unidock_tools/tests/applications/test_unidock.py
@@ -33,7 +33,7 @@ def read_scores(sdf_file, score_name):
 
 def test_unidock_pipeline_default(receptor, ligand, pocket):
     results_dir = "unidock_results"
-    cmd = f"unidocktools unidock -r {receptor} -l {ligand} -sd {results_dir} \
+    cmd = f"unidocktools unidock_pipeline -r {receptor} -l {ligand} -sd {results_dir} \
         -cx {pocket[0]} -cy {pocket[1]} -cz {pocket[2]} -sx {pocket[3]} -sy {pocket[4]} -sz {pocket[5]} \
         -sf vina -nm 1"
     print(cmd)
@@ -55,7 +55,7 @@ def test_unidock_pipeline_ligand_index(receptor, ligand, pocket):
     with open(index_file, "w") as f:
         f.write(str(ligand))
     results_dir = "unidock_results_input_index"
-    cmd = f"unidocktools unidock -r {receptor} -i {index_file} -sd {results_dir} \
+    cmd = f"unidocktools unidock_pipeline -r {receptor} -i {index_file} -sd {results_dir} \
         -cx {pocket[0]} -cy {pocket[1]} -cz {pocket[2]} -sx {pocket[3]} -sy {pocket[4]} -sz {pocket[5]} \
         -sf vina -nm 1"
     print(cmd)
@@ -95,7 +95,7 @@ def test_unidock_pipeline_ligand_index(receptor, ligand, pocket):
 
 def test_unidock_pipeline_multi_pose(receptor, ligand, pocket):
     results_dir = "unidock_results_multi_pose"
-    cmd = f"unidocktools unidock -r {receptor} -l {ligand} -sd {results_dir} \
+    cmd = f"unidocktools unidock_pipeline -r {receptor} -l {ligand} -sd {results_dir} \
         -cx {pocket[0]} -cy {pocket[1]} -cz {pocket[2]} -sx {pocket[3]} -sy {pocket[4]} -sz {pocket[5]} \
         -sf vina -nm 4"
     print(cmd)