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