Version 2.0

RABDAM version 2:

• Calculates Bnet-percentile values.
• Introduces the filter flag to allow users to check their input models meet the requirements for Bnet and Bnet-percentile calculation set out in Shelley & Garman, 2022.
• Switches over from using PDBCUR to using cctbx to generate a copy of the unit cell. Due to small rounding differences in the xyz coordinates output by the two programs, occasionally this affects the BDamage packing density calculation, and so for some models there are slight differences in the Bnet values output from RABDAM version 2 as compared to RABDAM version 1.

Adds zenodo doi

Adds zenodo doi as required for Nat Comms publication; no changes to the code itself.

Release v1.6.4

Updates setup.py and requirements.txt to list minimum package requirements to ensure RABDAM runs as expected.

Release v1.6.3

Updates Bnet calculation to use scipy rather than seaborn when calculating the kernel density estimate

Release v1.6.2

Updates previous release to fix imports so that RABDAM can be run as a package in Python 3 as well as Python 2.

Release v1.6.1

Several changes to the program workflow, including:

• By default now parses mmCIF instead of PDB files (although PDB parsing function is retained)
• Removes the BDB accession code check (since goes out of date very quickly)
• Improved atom filtering
• Updates the web addresses from which mmCIF/PDB files are downloaded
• Includes unit tests (FYI test_bnet_calculation needs to be run on your local machine since requires PDBCUR (not available in circleci))

Release v1.5.1

Updates list of PDB accession codes deposited with full isotropic B-factor values as calculated by the B-factor Data Bank (BDB)

Release v1.4.1

Updates list of PDB accession codes deposited with full isotropic B-factor values as calculated by the B-factor Data Bank (BDB)

Release v1.3.1

Updates package version number (I accidentally forgot to do this in the previous release (v1.3.0))

Release v1.3.0

• Increases speed of unit cell 3x3x3 translation (now runs to completion on the ribosome in approx. 20 mins on my laptop, previously the calculation took hours and consumed all available RAM)
• Updates list of BDB codes
• Fixes bug in output PDB file (previously chains were not separated by TER cards)