iPHASimulator v2

Start here

Installation
Quick-start: construct, validate and export P3HB_4
Current capabilities and limitations

Workflow tutorials

Polymer design
GAFF2 parameterisation
OpenMM and GROMACS preparation
Optional enzyme–PHA in water with OpenMM (06C)
HPC execution
Trajectory preprocessing
Standalone enzyme–PHA trajectory preparation
Analysis
Docking preparation
Notebook catalogue

Reference and contributing

Python API reference
PHA–enzyme distance and contact workflow
iPHASimulator v2 Design
Repository README
Edit, preview and publish documentation

iPHASimulator v2

Python API reference
iphasimulator
iphasimulator.exceptions
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iphasimulator.exceptions

Dan comments:

Why does this empty file exist?

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