Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[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

[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)

[2.0.0] - 2023-02-27

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

Added

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

Changed

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

Removed

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

Deprecated

everything included in lower versions is now deprecated

[1.5] - 2023-02-27