2. Installation

The following is a brief guide to installing BpForms. The Dockerfile in the BpForms Git repository contains detailed instructions for how to install BpForms in Ubuntu Linux.

2.1. Prerequisites

First, install the third-party packages listed below.

To use ChemAxon Marvin to calculate major protonation and tautomerization states, set JAVA_HOME to the path to your Java virtual machine (JVM) and add Marvin to the Java class path:

export JAVA_HOME=/usr/lib/jvm/default-java
export CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar

2.2. Latest release From PyPI

Run the following command to install the latest release from PyPI.:

pip install bpforms

2.3. Latest revision from GitHub

Run the following command to install the latest version from GitHub.:

pip install git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils
pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[chem]
pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms

2.4. Installing the optional features

To calculate major protonation and tautomerization states, BpForms must be installed with the [protontation] option:

pip install bpforms[protontation]
pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[protontation]

To draw molecules, BpForms must be installed with the [draw] option:

pip install bpforms[draw]
pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[draw]

To export the alphabets in OBO format, BpForms must be installed with the [onto_export] option:

pip install bpforms[onto_export]
pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[onto_export]

To install the rest API, BpForms must be installed with the [rest_api] option:

pip install bpforms[rest_api]
pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[rest_api]