lbc-lnbio / pymol-kvfinder-web-tools

PyMOL KVFinder-web Tools: a PyMOL v2 plugin for interacting with KVFinder-web service

PyMOL KVFinder-web Tools

Welcome to the PyMOL KVFinder-web Tools, this page was built to help you get started with our graphical PyMOL plugin for KVFinder-web service.

KVFinder-web

KVFinder-web is an open-source web-based application of an updated version of parKVFinder software (v1.2.0) cavity detection and characterization of any type of biomolecular structure. The characterization includes spatial, depth, constitutional and hydropathy characterization.

The KVFinder-web has two independent components:

• a RESTful web service: KVFinder-web service;
• a graphical web portal: KVFinder-web portal

To broaden the range of possibilities for user interaction, we also provide additional client-side applications, that are:

• a graphical PyMOL plugin: PyMOL KVFinder-web Tools;
• an example of a Python HTTP client: http-client.py

The full KVFinder-web documentation can be found here: http://lbc-lnbio.github.io/KVFinder-web.

PyMOL KVFinder-web Tools

The PyMOL KVFinder-web Tools, written in Python and Qt, is a PyMOL v2.x plugin for detecting and characterizing biomolecular cavities at a KVFinder-web service with functionalities similar to PyMOL parKVFinder Tools, which is natively configured to our publicly available web service (http://kvfinder-web.cnpem.br).

Installation

PyMOL v2 is required if you wish to use PyMOL KVFinder-web Tools.

To install the Python dependencies from requirements.txt, run:

pip3 install -r requirements.txt

To install PyMOL KVFinder-web Tools, download the latest version of PyMOL KVFinder-web Tools from here. Now, follow these steps:

1. Open PyMOL;
2. Go to Plugin menu and select Plugin Manager option;
3. The Plugin Manager window will open, go to the Install New Plugin tab;
4. Under Install from local file group, click on Choose file...;
5. The Install Plugin window will open, select the PyMOL-KVFinder-web-Tools.zip;
6. The Select plugin directory window will open, select /home/user/.pymol/startup and click OK;
7. The Confirm window will open, click on OK;
8. The Sucess window will open, confirming that the plugin has been installed;
9. Restart PyMOL;
10. PyMOL KVFinder-web Tools is ready to use under Plugin menu.

Or, if you clone this repository, instead of selecting PyMOL-KVFinder-web-Tools.zip (Step 5), user must select __init__.py of PyMOL-KVFinder-web-Tools directory.

To use the PyMOL KVFinder-web Tools in a locally configured KVFinder-web service, users must change the server url and port hardcoded on the __init__.py file and reinstall the client plugin on PyMOL.

From:

    # Server                                 #
    server = "http://kvfinder-web.cnpem.br"  #
    # Path                                   #
    port = "/api"                            #

to:

    # Server                                 #
    server = "http://localhost:8081"         #
    # Path                                   #
    path = ""                                #

If the KVFinder-web service is on another computer on your network, you must provide the IP Address instead of localhost.

Troubleshooting

Recently, an issue arose from Qt missing OpenSSL 3.x support on Linux distributions, so a workaround is available here. If you have any other issues, please check our Issues section.

KVFinder-web portal

The KVFinder-web portal, written in R and Shiny, is a graphical web application for detecting and characterizing biomolecular cavities at a KVFinder-web service, natively configured in our publicly available web service (http://kvfinder-web.cnpem.br).

KVFinder-web service

KVFinder-web service, written in Rust language, has a robust web-queue-worker architecture that processes HTTP requests and responses from the interface, manages jobs, and executes parKVFinder for accepted jobs.

Funding

KVFinder-web interface was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Brazilian Biosciences National Laboratory (LNBio) and Brazilian Center for Research in Energy and Materials (CNPEM).

License

The software is licensed under the terms of the Apache-2.0 License 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 Apache-2.0 License for more details.

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pymol-kvfinder-web-tools's Issues

Qt missing OpenSSL 3.x support on Linux distributions

Summary

Error submitting a job to the PyMOL KVFinder-web Tools KVFinder-web service.

Setup

• OS: Pop!_OS 22.04 LTS
• PyMOL Version: v2.5.0
• Python Version: 3.10.6

Steps to reproduce

1. Load a structure in pymol
2. Submit a job to KVFinder-web service

What is the current bug behavior?

When submitting a job to our public KVFinder-web service (http://kvfinder-web.cnpem.br/api) from PyMOL KVFinder-web Tools, the network reply fails and comes back empty.

Relevant logs and/or screenshots

Incompatible version of OpenSSL (built with OpenSSL 1.x, runtime version is >= 3.x)
The backend "cert-only" does not support QSslKey
Active TLS backend does not support key creation
The backend "cert-only" does not support QSslKey
Active TLS backend does not support key creation
The backend "cert-only" does not support QSslKey
Active TLS backend does not support key creation
The backend "cert-only" does not support QSslKey
Active TLS backend does not support key creation
The backend "cert-only" does not support QSslKey
Active TLS backend does not support key creation
The backend "cert-only" does not support QSslKey
Active TLS backend does not support key creation
The backend "cert-only" does not support QSslSocket
The backend named "cert-only" does not support TLS
QSslSocket::connectToHostEncrypted: TLS initialization failed
QSslSocket::connectToHostEncrypted: TLS initialization failed