Version 2.2.0

[2.2.0] - 2024-05-14

MINOR release of SURFMAP - minor breaking changes

Added

• command line option to set min/max values for the bfactor color scale (--bfactor-min-value, --bfactor-max-value)

Changed

• change command line option to set max absolute value for electrostatics color scale [BREAKING CHANGE]
  • from --color-max-val to --elec-max-value

Version 2.1.0

[2.1.0] - 2023-12-27

MINOR release of SURFMAP - no breaking changes

Added

• command line option to set min/max values for the electrostatics color scale

Patched

• change the Proline value in the Kyte and Doolittle scale (from 1.6 to -1.6)

Major release version 2.0.0 - 2023-02-28

[2.0.0] - 2023-02-28

MAJOR release where SURFMAP has been completely restructured as a python package.

Added

• added a new docker CLI handler
• added surfmap options -pqr and -ff
• added surfmap executable command
• added extract_interface utility script
• added write_pdb_bs utility script
• added MANIFEST.in
• added examples for new utility scripts
• added setup.py
• added Dockerfile
• added check for surfmap requirements (apbs, r)
• added optional environment variable for surfmap image version
• added logging with 3 verbose levels
• added surfmap.log file as output
• added multival_csv2pdb as binary

Changed

• changed README
• changed LICENCE from GPL to MIT
• changed install process
• changed docker repository name
• changed pdb_to_xyzr from awk to python3
• changed copyright notices
• changed path-related instructions in R scripts
• changed compute_shell.sh from bash to a python function
• changed electrostatics computation as a python function
• changed version format

Removed

• removed use of surfmap.py
• removed use of run_surfmap.py
• removed electrostatics computation from shell computation
• removed awk/nawk dependency
• removed unused JS scripts/packages

Deprecated

• everything included in lower versions is now deprecated

Version 1.5

CHANGE

• fix a bug occurring for pdb files with more than 999 residues (appeared only for circular variance property mapping)