Changelog
Changelog#
Dev
Fix issue in PDB writer (wrong column for element symbol)
1.6.1
Add option –ignore-CH3s (-igch3) which ignore CH pairs when they belongs to a CH3 group.
Update doc and notebook04 with option -igch3
Fix beta H reconstruction for Berger and GROMOSCPK POPS
Update .readthedocs.yml
1.6.0
Avoid output trajectory rewind when writing box dimensions
Switch to MDAnalysis 2.0
Add support of Python 3.9
Improve docstrings
1.5.0
Write box dimensions in the requested trajectory output
Fix write duplicate 1st frame when a trajectory output is requested
Avoid using universe.trajectory.time on a single pdb
Limit Python version >= 3.6 <=3.8 (for MDAnalysis compatibility)
Add support for: Berger DOPC/DPPC/POPS, GROMOS-CKP POPC/POPS, GROMOS-53A6L DPPC, CHARMM36UA
Force Python 3.8 for doc building
1.4.0
Add -v / –version option
Reorganize doc
Add Notebook04 (launch buildH as a module)
Support Berger cholesterol
Add Notebook05 (mixture POPC / cholesterol)
Create buildH logo and add it to doc
Add paper for JOSS
Add community guidelines
1.3.1
Fix setup.cfg to include json files in python package archive
1.3.0
Complete documentation
Accelerate functions within geometry.py with Numba
Implement the use of buildH as a module
Simplify calculation of CH on an sp3 carbon
Use MyST parser for documentation (handles latex equations)
Clarify some error messages
Fix residue number exceeding 9999
Add POPE def and json files
Add Notebook01 (basic buildH analysis on a Berger traj)
Add Notebook02 (+trajectory output)
Add Notebook03 (analysis on a mixture POPC/POPE)
Move CHARMM36 POPC validation to Zenodo
1.2.0
Build docs
Rename ‘-x/–xtc’ flag to -t/–traj’ one to be more generic
Replace mandatory topology argument to ‘-c/–coord’ flag
Improve performance of control functions.
Move misc functions to a module utils.py
Improve Exception handling & add proper exits
Improve PEP8 & PEP257 compliance
Improve test coverage
Fix bug when a trajectory was written when only a pdb was provided.
Add sanity checks for the various input files
Use json files instead of python module to read lipid topologies.
Optimize package for better performance
1.1.0
Create Python package structure
Create conda environment
Fix tests
Separate entry point
Update README for dev version installation
Handle version with bump2version