# parKVFinder-win **Repository Path**: william2015c/parKVFinder-win ## Basic Information - **Project Name**: parKVFinder-win - **Description**: No description available - **Primary Language**: Unknown - **License**: GPL-3.0 - **Default Branch**: master - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2025-11-07 - **Last Updated**: 2025-11-07 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README Welcome to the **parallel KVFinder for Windows (_parKVFinder-win_)** [repository](https://github.com/LBC-LNBio/parKVFinder-win), this page was built to help you get started with our cavity detection software. # Download & Installation Follow these steps to install parKVFinder-win on Windows 10: 1. Get the latest release from [here](https://github.com/LBC-LNBio/parKVFinder-win/archive/refs/tags/v1.0.2.zip). 2. Unzip the `parKVFinder-win-x.x.zip` on a preferred location. 3. Add KVFinder_PATH to your environment variables via Command Prompt: ```cmd :: KVFinder_PATH must be the location of your parKVFinder-win-x.x directory setx KVFinder_PATH C:\path\to\your\parKVFinder-win-x.x ``` or, open **Control Panel** > **System** > **Advanced system settings** > **Advanced** tab > **Enviroment Variables...** button > **User variables for \** panel > **New...** button. On the **Edit System Variable** windows, set `KVFinder_PATH` on **Variable name** and `C:\path\to\your\parKVFinder-win-x.x` on **Variable value**. # PyMOL Plug-in Installation First, you need to install PyMOL v2.x on your computer. If you do not have it installed, please refer to PyMOL [website](https://pymol.org/2/). `PyMOL2 parKVFinder Tools` is available to use `parKVFinder-win` with PyMOL v2.x, which has been developed using Qt interface and Python3. After installing PyMOL v2.x, plug-in requires the installation of [toml](https://pypi.org/project/toml/) module and PyMOL's native Python does not have it installed. So you need to install it: 1. Access PyMOL directory and open `Conda-Prompt.bat` file, which will open a Command Prompt with a conda environment. 2. On this Command Prompt, type: ```cmd pip3 install toml ``` Finally, to install the `PyMOL2 parKVFinder Tools` on PyMOL v2.x, download the latest `PyMOL2-parKVFinder-Tools.zip` from [here](https://github.com/LBC-LNBio/parKVFinder-win/releases/latest/download/PyMOL2-parKVFinder-Tools.zip) and follow these steps: 1. Open PyMOL. 2. Go to **Plugin** menu, click on **Plugin Manager**. 3. The **Plugin Manager** window will open, go to the **Install New Plugin** tab. 4. Under **Install from local file** panel, click on **Choose file...**. 5. The **Install Plugin** window will open, select the `PyMOL2-parKVFinder-Tools.zip` that you downloaded earliar. 6. The **Select plugin directory** window will open, select **C:\\\\\path\\to\\PyMOL\\lib\\site-packages\\pmg_tk\\startup** and click **OK**. 7. The **Confirm** window will open, click **OK**. 8. The **Sucess** window will appear, confirming that the plug-in has been installed. 9. Restart PyMOL. 10. `PyMOL2 parKVFinder Tools` is ready to use. Or, instead of selecting `PyMOL2-parKVFinder-Tools.zip` (Step 5), you can select `__init__.py` file on `parKVFinder-win-x.x\tools\PyMOL2-parKVFinder-Tools` directory tree. # Tutorial For an example of use, there is a comprehensive tutorial for `PyMOL2 parKVFinder Tools` and `parKVFinder-win` command line interface (CLI) [here](https://github.com/LBC-LNBio/parKVFinder/wiki/parKVFinder-Tutorial). _Note_: Instead of invoking the CLI using `parKVFinder` command, you must use `%KVFinder_PATH%\parKVFinder-win64.exe` command. # Manual A comprehensive list of all `PyMOL2 parKVFinder Tools` and `parKVFinder-win` CLI commands are provided in this [manual](https://github.com/LBC-LNBio/parKVFinder/wiki/parKVFinder-Manual). _Note_: Instead of invoking the CLI using `parKVFinder` command, you must use `%KVFinder_PATH%\parKVFinder-win64.exe` command. For more information, refer to parKVFinder [wiki](https://github.com/LBC-LNBio/parKVFinder/wiki). # About ## Issues parKVFinder software uses GitHub for project management. Please help us by reporting any problems or requests. On [Issues](https://github.com/LBC-LNBio/parKVFinder-win/issues) page, you can file a: - [Bug Report](https://github.com/LBC-LNBio/parKVFinder-win/issues/new?assignees=&labels=&template=bug_report.md&title=) - [Request a new feature](https://github.com/LBC-LNBio/parKVFinder-win/issues/new?assignees=&labels=&template=feature_request.md&title=) Only make sure the bug or request has not already been reported. Click on “Search” and enter some keywords to search. Thank you for helping us improve parKVFinder! ## Scientific team parKVFinder, parKVFinder-win, PyMOL2 parKVFinder Tools and PyMOL parKVFinder Tools were developed by: - João Victor da Silva Guerra - Helder Veras Ribeiro Filho - Leandro Oliveira Bortot - Rodrigo Vargas Honorato - José Geraldo de Carvalho Pereira - Paulo Sergio Lopes de Oliveira Computational Biology Laboratory ([LBC](https://github.com/LBC-LNBio)), Brazilian Biosciences National Laboratory ([LNBio](https://lnbio.cnpem.br/)), Brazilian Center for Research in Energy and Materials ([CNPEM](https://cnpem.br)). If you have any further questions, inquires or if you wish to contribute to parKVFinder project, please contact us at joao.guerra@lnbio.cnpem.br and paulo.oliveira@lnbio.cnpem.br. ## Citing parKVFinder João Victor da Silva Guerra, Helder Veras Ribeiro Filho, Leandro Oliveira Bortot, Rodrigo Vargas Honorato, José Geraldo de Carvalho Pereira, Paulo Sergio Lopes de Oliveira, ParKVFinder: A thread-level parallel approach in biomolecular cavity detection, SoftwareX, 2020, [https://doi.org/10.1016/j.softx.2020.100606](https://doi.org/10.1016/j.softx.2020.100606). ## Funding This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [Grant Number 350244/2020-0], and Brazilian Center for Research in Energy and Materials (CNPEM). ## License The software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.