How To Install concavity on Debian 10
Introduction
In this tutorial we learn how to install concavity on Debian 10.
What is concavity
concavity is:
ConCavity predicts protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
ConCavity takes as input a PDB format protein structure and optionally files that characterize the evolutionary sequence conservation of the chains in the structure file.
The following result files are produced by default:
- Residue ligand binding predictions for each chain (*.scores).
- Residue ligand binding predictions in a PDB format file (residue scores placed in the temp. factor field, *_residue.pdb).
- Pocket prediction locations in a DX format file (*.dx).
- PyMOL script to visualize the predictions (*.pml).
There are three methods to install concavity on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install concavity Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install concavity using apt-get by running the following command:
sudo apt-get -y install concavity
Install concavity Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install concavity using apt by running the following command:
sudo apt -y install concavity
Install concavity Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install concavity using aptitude by running the following command:
sudo aptitude -y install concavity
How To Uninstall concavity on Debian 10
To uninstall only the concavity package we can use the following command:
sudo apt-get remove concavity
Uninstall concavity And Its Dependencies
To uninstall concavity and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove concavity
Remove concavity Configurations and Data
To remove concavity configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge concavity
Remove concavity configuration, data, and all of its dependencies
We can use the following command to remove concavity configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge concavity
Dependencies
concavity have the following dependencies:
References
Summary
In this tutorial we learn how to install concavity package on Debian 10 using different package management tools: apt, apt-get and aptitude.
