Welcome to buildH’s documentation!

Version 1.2.0

Build hydrogens from a united-atom MD of lipids and calculate the order parameter.

Install buildH with pip:

$ python3 -m pip install buildh

User manual

• Motivation
• Features
• Usage
• Examples
• Validation of buildH
• Algorithm for building hydrogens
• TODO

Tutorial

• Report on buildH hydrogen rebuilding and order parameter calculation

Reference manual

• API reference for core submodule
• API reference for geometry submodule
• API reference for hydrogens submodule
• API reference for init_dics submodule
• API reference for lipids submodule
• API reference for utils submodule
• API reference for writers submodule

Index

• Index

Changelog

Dev

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