libprotein 0.0.5

This module allows to parse existing data for qualifying a protein sequence in order to assess the sequence knowledge available in various databases.

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