Contents

Welcome to buildH’s documentation!

Version 1.3.0

Build hydrogen atoms from a united-atom MD of lipids and calculate the order parameters.

Index

Changelog

Dev

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

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