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README.md

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-# Uni-Dock
+# Uni-Dock
+
+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 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](assets/gpu_speeds.png)
+
+## Usage Guideline
+
+We offer the software **for academic purposes only**. By downloading and using Uni-Dock, you are agreeing to the usage guideline under our GitHub repository.
+
+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.
+
+For commercial usage and further cooperations, please contact us at [email protected] .
+
+## Online Access
+
+We provides an [online Uni-Dock service](https://labs.dp.tech/projects/uni-dock-serving/).
+
+## Installation
+
+For using Uni-Dock, an NVIDIA GPU with an appropriate CUDA runtime environment is required.
+Download the latest binary from [the Release page](https://github.com/dptech-corp/Uni-Dock/releases).
+
+## Examples
+
+## Bug Report
+
+Please report bugs to [Issues](https://github.com/dptech-corp/Uni-Dock/issues) page.
+
+## Ackowledgement
+
+If you used Uni-Dock in your work, please cite:
+
+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
+
+## FAQ
+
+1. The GPU encounters out-of-memory error.
+Uni-Dock estimates the number of ligands put into GPU memory in one pass based on the available GPU memory size. If it fails, please use `--max_gpu_memory` to limit the usage of GPU memory size by Uni-Dock.
+2. I want to put all my ligands in `--gpu_batch`, but it exceeds the maximum command line length that linux can accept.
+    - You can save your command in a shell script like `run.sh`, and run the command by `bash run.sh`.
+    - You can save your ligands path in a file (separated by spaces) by `ls *.pdbqt > index.txt`, and use `--ligand_index index.txt` in place of `--gpu_batch`.

license/usage-guidelines-en.md

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+# Uni-Dock Software Usage Guidelines
+These software usage guidelines (hereinafter referred to as "these guidelines") are intended to regulate the behavior and obligations of users during the use of Uni-Dock software (hereinafter referred to as "this software"). Before downloading, installing, using or accessing this software in any way, please read and understand the following terms and conditions carefully. If you do not agree with all or part of the content of these guidelines, please stop using this software immediately. Once you start accessing, downloading, installing, and using this software, it means you have read, understood, and agreed to be bound by these guidelines.
+## 1. Usage License
+1.1 The ownership and copyright of this software belong to Beijing DP Technology Co.,Ltd. (hereinafter referred to as "DP Technology"). Subject to compliance with these guidelines, DP Technology hereby grants academic users (hereinafter referred to as "you") a worldwide, non-exclusive, royalty-free usage license for academic purposes only.
+1.2 The license granted under these guidelines applies only to the object code version of this software. You have no rights to the source code of this software.
+## 2. Usage Restrictions
+2.1 These guidelines only grant academic users the right to use this software for academic purposes. Any commercial organization, commercial institution or other non-academic users are not allowed to use this software. If this provision is violated, DP Technology reserves the right to pursue all legal liabilities.
+2.2 You may not use this software or any derivative works thereof for any commercial purpose, nor sell, rent, transfer, distribute or otherwise make it available to any third party. You must ensure that the use of this software is limited to your personal academic research and prohibit the use of this software for the benefit of any other entity (whether charged or not).
+2.3 You may not modify or create any derivative, compilation or collective works involving this software.
+2.4 You may not modify, crack, decompile, disassemble, reverse engineer, isolate, separate or otherwise extract the source code or attempt to discover the source code of this software from any program or documentation in any way. You may not remove, modify or obscure any copyright, trademark or other proprietary rights notices in this software. You may not use this software for any illegal activities, including but not limited to infringing on the intellectual property rights, privacy rights of others, etc. 	2.5 You agree to use this software only for lawful academic purposes, comply with the laws and regulations of your country or region, and assume all legal liabilities arising from violations of laws and regulations.
+## 3. Software Ownership
+This software is provided here for use under these guidelines only, not for sale. The ownership and all other rights (including but not limited to intellectual property rights and trade secrets) of this software and all related documentation are and shall remain the exclusive property of DP Technology. You have no rights except for the limited usage license rights expressly granted under these guidelines.
+## 4.Suggestions
+You may make suggestions regarding this software, provided that:
+(i) You represent and warrant that the suggestion does not infringe any third party's intellectual property rights;
+(ii) You acknowledge that DP Technology has the right to use the suggestion, but is not obligated to do so;
+(iii) You grant DP Technology a non-exclusive, irrevocable, sublicensable, royalty-free, worldwide license to reproduce, distribute, transmit, publicly display, publicly perform, modify, translate, create derivative works based on, produce, manufacture, market, sell, offer for sale, and/or otherwise use, in whole or in part, the suggestion and any derivative works thereof, including but not limited to incorporating the suggestion, in whole or in part, into DP Technology's software and/or other software, and in any medium now or hereafter known or developed, and to grant multiple sublicenses for engaging in the foregoing activities;
+(iv) You waive any rights or claims to the suggestion, and DP Technology has no obligation, royalty or restriction based on intellectual property or other aspects (such as attribution in using the suggestion).
+## 5. Citation Requirements
+If the results obtained using this software are published in a publication, you should acknowledge the use of Uni-Dock software in the results and indicate the name of the rights holder. When citing Uni-Dock, please use the following content:
+- 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.
+## 6. Reservation of Rights
+You acknowledge that all rights to this software not expressly granted to you, whether existing now or in the future, are reserved by DP Technology. Any unauthorized use of this software will be considered an infringement, and DP Technology has the right to pursue all legal liabilities of the infringer.
+## 7. Confidential Information
+You agree to treat the code and related documentation of this software as confidential information of DP Technology, and not to provide the relevant code to any third party, and to take a reasonably prudent attitude to prevent the leakage of the code and related documentation of this software.
+## 8. No Warranty
+This software is provided "as is" without any express or implied warranty, including but not limited to warranties of non-infringement of any code or specification, merchantability, fitness for a particular purpose, or non-infringement of third party rights. You agree to assume all risks associated with the use of this software or these guidelines.
+## 9. Disclaimer
+To the maximum extent permitted by law, DP Technology shall not be liable for any damages related to this software or these guidelines, including any direct, indirect, special, consequential or incidental damages, regardless of the legal theory on which the liability is based. This software may not be used unless the user accepts the restrictions of this disclaimer.
+## 10. In the event that you breach these guidelines or fail to comply with any material term or condition of these guidelines in any way, all rights granted to you will automatically terminate.
+## 11. Reporting
+If you believe that someone has violated these guidelines, please report to DP Technology. DP Technology will strictly maintain the confidentiality of your identity. The reporting email address is [email protected].
+## 12. Legal Jurisdiction
+Nothing in these guidelines shall be construed as granting, by implication, estoppel or otherwise, any license or right other than those expressly granted under these guidelines. If any provision of these guidelines is deemed unenforceable, such provision shall be modified only to the extent necessary to make it enforceable. These guidelines shall be governed by the laws of the People's Republic of China, without regard to its conflict of laws provisions and the United Nations Convention on Contracts for the International Sale of Goods. All disputes arising from these guidelines shall be under the jurisdiction of the People's Court of Haidian District, Beijing.
+## 13. Future Versions
+DP Technology reserves the right to change or discontinue this software or these guidelines at any time without prior notice.
+## 14. These guidelines has both Chinese and English versions. In case of any conflict between the English and Chinese versions, the Chinese version shall prevail.

license/usage-guidelines-zh.md

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+# Uni-Dock软件使用准则
+本软件使用准则（以下简称“本准则”）旨在规范用户在使用Uni-Dock软件（以下简称“本软件”）过程中的行为和义务。在下载、安装、使用或以任何方式访问本软件之前，请务必仔细阅读并理解以下条款和条件。若您不同意本准则的全部或部分内容，请您立即停止使用本软件。一旦您开始访问、下载、安装、使用本软件，即表示您已阅读、理解并同意接受本准则的约束。
+## 1、使用许可
+1.1 本软件的所有权及版权归北京深势科技有限公司（以下简称“深势科技”）所有。在遵守本准则的前提下，深势科技特此授予学术用户（以下简称“您”）一个全球范围内的、非排他性的、免版权费用的使用许可，可为了满足学术目的而使用本软件。
+1.2 本准则下授予的许可仅适用于本软件的目标代码版本。您不对本软件源代码拥有任何权利。
+## 2、使用限制
+2.1 本准则仅授予学术用户出于学术目的使用本软件，任何商业组织、商业机构或其他非学术用户不得使用本软件，如果违反本条款，深势科技将保留一切追诉的权利。
+2.2 您不得将本软件或任何形式的衍生作品用于任何商业目的，也不得将其出售、出租、转让、分发或以其他方式提供给任何第三方。您必须确保本软件的使用仅限于您个人学术研究，禁止您为任何其他实体的利益使用本软件（无论是否收费）。
+2.3 您不得修改或创建任何涉及本软件的衍生、编译或集体作品。
+2.4 您不得以任何方式修改、破解、反编译、反汇编、反向工程、隔离、分离或以其他方式从任何程序或文档中提取源代码或试图发现本软件的源代码。您不得以任何方式去除、修改或屏蔽本软件中的任何版权、商标或其他专有权利声明。您不得使用本软件进行任何非法活动，包括但不限于侵犯他人的知识产权、隐私权等。
+2.5 您同意将本软件仅用于合法的学术目的，且遵守您所在国家或地区的法律法规，您将承担因违反法律法规而产生的一切法律责任。
+## 3、软件所有权
+本软件在此仅作使用许可，并非出售。本软件及与软件有关的全部文档的所有权及其他所有权利（包括但不限于知识产权和商业秘密），始终是深势科技的专有财产，您不拥有任何权利，但本准则下被明确授予的有限的使用许可权利除外。
+## 4、提出建议
+您可以对本软件提出建议，前提是：
+（i）您声明并保证，该建议未侵害任何第三方的任何知识产权；
+（ii）您承认，深势科技有权使用该建议，但无使用该建议的义务；
+（iii）您授予深势科技一项非独占的、不可撤销的、可分许可的、无版权费的、全球范围的免费许可，以复制、分发、传播、公开展示、公开表演、修改、翻译、基于其制作衍生作品、生产、制作、推销、销售、提供销售和/或以其他方式整体或部分地使用该建议和基于其的衍生作品，包括但不限于，通过将该建议整体或部分地纳入深势科技的软件和/或其他软件，以及在现存的或将来任何时候存在的任何媒介中或通过该媒介体现，以及为从事上述活动而授予多个分许可；
+（iv）您放弃对该建议的任何权利或主张，深势科技无需承担任何义务、版税或基于知识产权或其他方面的限制（例如在使用该建议时进行归属）。
+## 5、引用要求
+如您使用本软件获得的成果发表在出版物上，您应在成果中承认对Uni-Dock软件的使用并标注权利人名称。引用 Uni-Dock时请使用以下内容：
+- 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.
+## 6、保留权利
+您认可，所有未被明确授予您的本软件的权利，无论是当前或今后存在的，均由深势科技予以保留，任何未经深势科技明确授权而使用本软件的行为将被视为侵权，深势科技有权追究侵权者的一切法律责任。
+## 7、保密信息
+您同意将本软件代码及相关文档视为深势科技的机密信息，您不会向任何第三方提供相关代码，并将采取合理审慎的使用态度来防止本软件代码及相关文档被泄露。
+## 8、无保证
+该软件是“按原样”提供的，没有任何明示或暗示的保证，包括但不限于不包含任何代码或规范没有缺陷、适销性、适用于特定目的或不侵犯第三方权利的保证。您同意您自主承担使用本软件或与本准则有关的全部风险。
+## 9、免责条款
+在法律允许的最大范围内，无论基于何种法律理论，深势科技都不对与本软件或本准则相关的任何损害承担责任，包括任何直接的、间接的、特殊的、后果性或附带的损害。
+除非接受本免责条款的约束，否则不得使用本软件。
+## 10、如果您以任何方式违反本准则或未能遵守本准则的任何重要条款或条件，则您被授予的所有权利将自动终止。
+## 11、举报
+如果您认为有人违反了本准则，请向深势科技进行举报，深势科技将对您的身份进行严格保密，举报邮箱地址为 [email protected]。
+## 12、法律管辖
+本准则中的任何内容均不得解释为通过暗示、禁止反悔或其他方式授予本准则中授予的许可或权利以外的任何许可或权利。如果本准则的任何条款被认定为不可执行，则仅在必要的范围内对该条款进行修改，使其可执行。本准则应受中华人民共和国法律管辖，不适用法律冲突条款及《联合国国际货物销售合同公约》，因本准则产生的一切争议由北京市海淀区人民法院管辖。
+## 13、未来版本
+深势科技保留不经事先通知随时变更或停止本软件或本准则的权利。
+## 14、本准则同时具有中文版本和英文版本，如果英文版本和中文版本有冲突，以中文版本为准。