Installation

Quick Installation (Recommended)

The easiest way to install HIPPOS is using Conda, you can choose either Anaconda or Miniconda. If you never used Conda before then most likely Miniconda is more suitable for you.

After you installed Conda in your machine, it is highly recommended to create new environment and activate it first:

conda create -n hippos-env

conda activate hippos-env

then install HIPPOS using the following command:

conda install -c conda-forge pyplif-hippos

Conda will deal with the dependencies like Open Babel, Bitarray, and Numpy libraries. Therefore you won’t need the extra step below.

To check if HIPPOS installed correctly try these commands:

hippos

hippos-genref

If HIPPOS installed correctly you should get a message that inform you the configuration file not found. Next, you can just jump to Getting Started with PLANTS or Vina tutorial. But if you prefer not to use Conda then you can install HIPPOS using the instructions below.

Installing Latest Update In Conda Environment

Sometimes the changes (or new feature) in the code is not yet released and therefore not available in conda-forge repository, therefore the easiest way to use this latest update is by creating new conda environment then activate it like mentioned above.

The next step is to install all the PyPLIF-HIPPOS requirements using Conda:

conda install -c conda-forge openbabel numpy bitarray

Then you can download the code from https://github.com/radifar/PyPLIF-HIPPOS, extract the zip file, then run the setup.sh. See the Installing on Linux instruction below for more details about setup.sh script.

Manual Installation

The following instruction is for manual installation step which is more tedious, but you can use it in case you would like to use the latest feature PyPLIF-HIPPOS by installing the newest code from Github. Another advantage of manual installation is the visibility of PyPLIF-HIPPOS which makes it easier to find, in case you would like to do some modification to PyPLIF-HIPPOS code.

Requirement

• python >= 3.5

• python3-openbabel >= 2.1

• python3-bitarray

• python3-numpy >= 1.3

Getting HIPPOS

You can get HIPPOS at Github by cloning the repository or download the code here.

Installing on Linux

The following instructions were tested and work well on Ubuntu 20.04, Debian 11 and Fedora 30, so they will most likely work in newer version too.

First make sure that you have Python 3 installed, and it is your default when you run python command. If it is not then you can install python-is-python3 package or use update-alternatives command:

sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 1

The next step is to install the requirements for PyPLIF-HIPPOS. And depending on your OS or package manager that you use, the command could be different.

In Ubuntu or Debian you can simply enter these commands to install the requirements above:

sudo apt install python3-openbabel

sudo apt install python3-bitarray

sudo apt install python3-numpy

In Fedora you can enter these commands instead:

sudo dnf install python3-openbabel

sudo dnf install python3-bitarray

sudo dnf install python3-numpy

After all of the dependencies installed, you can install HIPPOS by opening the terminal and enter the PyPLIF-HIPPOS directory and run setup.sh:

./setup.sh

This will run the script that will create an alias for the PyPLIF-HIPPOS program in this directory. So every time you call hippos or hippos-genref it will refer to this directory. Therefore it is advised not to delete this directory.

Notice that this process does not add anything to your machine, so this step is just registering a shortcut to your command line environment.

If HIPPOS installed successfully then a message like ‘PyPLIF HIPPOS is ready for service’ should appear.

If you would like to install newer version of HIPPOS and overwrite the old one then all you need to do is to run the setup.sh script again.

To test if HIPPOS had been installed, open new command line window and type the following:

hippos

Then press enter. Please note that it is imperative to open the new command line window right after the installation to allow the alias in your system get updated. Next type the following:

hippos-genref

Then press enter

If there are no error message then the installation is success.

Uninstalling

To uninstall PyPLIF-HIPPOS you can simply run setup.sh script with uninstall option

./setup.sh uninstall

And a message ‘PyPLIF HIPPOS has been successfully uninstalled’ will appear.

Notice that as the installation process is just registering alias for hippos and hippos-genref, the uninstallation process is actually just removing those alias and therefore nothing is really removed from your machine. If you would like to remove PyPLIF-HIPPOS you need to manually remove the PyPLIF-HIPPOS from the directory where you install it.

Installing on MacOS

To install PyPLIF-HIPPOS on MacOS it is highly recommended that you use Conda virtual environment. There are two ways to install PyPLIF-HIPPOS using Conda. First you can simply install PyPLIF-HIPPOS using the following command:

conda install -c conda-forge pyplif-hippos

Or, if you would like to use the latest update from PyPLIF-HIPPOS you can follow the installation process for Latest Update In Conda Environment above.

Installing on Windows

Unfortunately, the only way to use PyPLIF-HIPPOS in Windows is by adding a layer of virtualization and simulate Linux on top of it, which can be done by installing WSL (Windows Subsystem for Linux). You can use Ubuntu, Fedora, or Debian inside your WSL, then use any installation method that suitable for you.