This module allows to parse existing data for qualifying a protein sequence in order to assess the sequence knowledge available in various databases.
Project description
Libprotein For Pypi
This module allows to analyze existing data to qualify a protein sequence in order to evaluate the sequence knowledge available in various databases.
⚠️ All this tutorial is made for Ubuntu User for now!
Compile and Install the project
This guide provides compilation and installation instructions only for Ubuntu for now.
- First, start by installing github if it's not already installed
sudo apt install git
- Then, clone the repository to the destination you want.
(We will call this destination: <...>)
- Then install all dependencies:
⚠️ This step can take several minutes...
sudo apt-get install libcurl4-openssl-dev -y && sudo apt install make -y && sudo apt install libboost-all-dev -y && sudo apt install cmake -y && sudo apt install swig3.0 && sudo apt upgrade -y && sudo apt install -y
- Open your command prompt at <...>/libprotein/build
If the build location doesn't exist, create it at <...>/libprotein with:
mkdir build && cd build
- To compile and install Libprotein, use this command
cmake .. && make install
- To test if the project is working, you can run the command:
./src/mainlibprotein P08493
pfam file empty
--------------------------------------
YOUR PROTEIN PTMs
--------------------------------------
Pos Name
21 4-carboxyglutamate
22 Phosphoserine
25 Phosphoserine
28 Phosphoserine
56 4-carboxyglutamate
60 4-carboxyglutamate
67 4-carboxyglutamate
71 4-carboxyglutamate
------------------------------------------
there are no PFAM domains for your protein
-------------------------------------------
there are no SCOP domains for your protein
- You can now test Librprotein for the Uniprot IDs you want using :
./src/mainlibprotein <your uniprot ID>
Install Pymol from source
We will install Pymol from source to be able to use the latest version of Pymol because many Ubuntu distributions provide binary packages for open-source PyMOLbut hey often do not provide the latest version.
⚠️ If you encounter any problems during the installation, you can refer to the official documentation: Pymol Install on Ubuntu
- Start by installing all the dependencies needed for the installation of Pymol:
apt-get install git build-essential python3-dev libglew-dev \
libpng-dev libfreetype6-dev libxml2-dev \
libmsgpack-dev python3-pyqt5.qtopengl libglm-dev libnetcdf-dev
- Get the latest version of Pymol from the official repository:
git clone https://github.com/schrodinger/pymol-open-source.git
git clone https://github.com/rcsb/mmtf-cpp.git
mv mmtf-cpp/include/mmtf* pymol-open-source/include/
And go to the directory /pymol-open-source
cd pymol-open-source
- Now, we will compile and install Pymol:
Here i use $HOME, but you can use the directory you want by replacing the prefix command
prefix=$HOME/pymol-open-source-build
# Example for dependencies in non-standard places
# export PREFIX_PATH="$HOME/extra/glew-2.0.0:$HOME/extra/libpng-1.6.5:/opt/local"
python3 setup.py build install \
--home=$prefix
- Finally, you can now run Pymol with the command:
$HOME/pymol-open-source-build/bin/pymol
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