shaileshp51/pycentre

pycentre

Installation

Supported platforms

• Linux
• macOS

Supported python versions

• python >= 3.6

Requires

• cython >= 0.18
• h5py>=2.6
• netCDF4 >=1.2.7
• numpy>=1.10
• pandas>=0.19
• networkx>=1.11
• pytraj >=1.0

Install

Step 1: Install requirements

Requirements for installation of pycentre can be installed using one of the follwoing options:

(a) Recommended: using anaconda or miniconda

The simplest way to install miniconda is as below, open terminal and run below commands.

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh

accept license and follow instructions.

Once anaconda/miniconda is successfully installed. Close and reopen terminal.

Its better to create a dedicated virtual environment to keep things clean. Now let's create a virtual environment say venv_pycentre as below.

conda create -n venv_pycentre python=3.7

Now let's install all required packages except pytraj.

conda install -n venv_pycentre h5py netcdf4 numpy pandas networkx

Now let's install pytraj

conda install -n venv_pycentre -c ambermd pytraj

First activate the virtual environment for pycentre, now we are ready to install pycentre

conda activate venv_pycentre

(b) Using pip3 for a working python3 >=3.6

Install packages required by pycentre setup

pip3 install python numpy

Step 2: Install pycentre from source code (for Linux and macOS)

Get pycentre source code from git

git clone https://github.com/shaileshp51/pycentre.git

cd pycentre

# Linux

python3 ./setup.py install

# macOS:

python3 setup.py install

Note: here python referes to python3, which may be accessible as python if its a conda virtual environment. If the python is system python3 you may have to use sudo to grant write permission for installation.

Usage

Now we are ready to start converting cartesian trajectories into BAT trajectory using cart2bat.py. All the options supported by cart2bat.py can be found in help message, which can be seen as: cart2bat.py --help