Welcome to the parallel KVFinder for Windows (parKVFinder-win) repository, 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.

2. Unzip the parKVFinder-win-x.x.zip on a preferred location.

3. Add KVFinder_PATH to your environment variables via Command Prompt:

:: 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 <user> 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.

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 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:

pip3 install toml

Finally, to install the PyMOL2 parKVFinder Tools on PyMOL v2.x, download the latest PyMOL2-parKVFinder-Tools.zip from here 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:\<user>\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.

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.

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.

About

Issues

parKVFinder software uses GitHub for project management. Please help us by reporting any problems or requests.

On Issues page, you can file a:

• Bug Report
• Request a new feature

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), Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM).

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.

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.