bdb

If protein engineers, homology modellers, biologists, or bioinformaticians need B-factors from a PDB file, they normally want full isotropic B-factors. Normally it is indeed the full B-factor that is stored in the B-factor field in the ATOM records of a PDB file. However, sometimes the field contains "residual" B-factors or atomic mean-square displacements instead of B-factors. The BDB contains PDB files with full isotropic B-factors in the B-factor field if the original PDB file contains enough information to determine the content of the B-factor field and calculate the full B-factor if necessary.

BDB files can be viewed and downloaded here. More information on BDB entries, their construction, their web page, how to download the entire BDB databank, and how to cite the BDB can be found here.

License

GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007

Installation

From source

Download the source code and run the python installer:

• wget https://github.com/cmbi/bdb/releases/bdb-<version>.tar.gz
• tar -zxvf bdb-<version>.tar.gz
• cd bdb-<version>
• sudo python setup.py install

Development

If you'd like to contribute by adding features or fixing bugs, follow the steps in this section to setup a development environment.

Pre-requisites

The following pre-requisites are required by bdb and must be installed manually:

• virtualenv
• virtualenvwrapper
• ccp4 software suite

Setup

• Run mkvirtualenv --no-site-packages bdb to create a virtual environment, and switch to that environment with workon bdb.
• Run git clone https://github.com/cmbi/bdb.git to obtain the latest source code.
• Run git checkout develop to switch to the development branch. It's also recommended that you create a feature branch off develop.
• Run pip install -r requirements to install the module dependencies.

The last command installs the required module dependencies into the virtual environment you've created, isolating the development environment from the rest of your system.

Tests

The following command will run all the unit tests for bdb:

nosetests

To see the code coverage of the unit tests, run:

nosetests --with-coverage --cover-package=pdbb