1. Installation

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

1.1. 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

1.2. Latest release From PyPI

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

pip install bcforms[all]

1.3. 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, protonation]
pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms
pip install git+https://github.com/KarrLab/bcforms.git#egg=bcforms[all]

1.4. Installing the optional features

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

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

To install the REST API, BcForms must be installed with the [rest_api option]::

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