Welcome to hoobas’s documentation!

Hoobas is a Python package designed for building molecular topologies for molecular dynamics simulations. It is compatible for use with packages such as HOOMD-blue, EspresSo, and OpenMM.

Introduction

• Getting started
• Composite objects in hoobas
• Tutorial and examples
  • Crystallization of DNA-Grafted Janus Particles
  • Hexagonal Crystal Surface
  • Generating Hyperbranched Polymers
  • Polyethylenimine
  • Random Ionomers
  • Rigid Bottlebrush
  • Lipid Bilayers

Python Documentation

• hoobas package
  • Build
  • Composite
  • Simulation Domains
  • Colloids
  • Linear chains
  • Layers
  • Colloid shapes
  • Martini handlers
  • Beads

Extending hoobas

• New Composite Objects
• New colloid shapes

Hoobas is a highly object-oriented molecular builder. It enables to user to build complex, polydisperse topologies for molecular dynamics simulation. Hoobas can generate an initial system of colloids coated with arbitrary ligands and place them on either random positions or lattice sites defined by arbitrary lattice (supports triclinic boxes). Functions are built-in to add other particles, such as salts, and free chains floating.

Indices

• Index
• Module Index

Source code

The hoobas git repository is on bitbucket

hoobas overview

This section will review basic features of hoobas. For detailed examples, please see the examples directory in the hoobas git repository. If hoobas is installed or if the path to hoobas has been added to PYTHONPATH, these should work independently.

Here is where a basic overview of the code goes. For example:

The basic objects of hoobas are CompositeObjects