analyze_foldamers

analyze_foldamers is a Python package for structural analysis of coarse-grained oligomer molecular simulations.

• Identify native structures using RMSD or torsion-based clustering of trajectories

• Generate histograms of all bonded parameters (bonds, angles, torsions)

• Generate 2D histograms of any combination of bonded observables

• Determine helical parameters for folded oligomer structures

• Tools for automated rendering of molecular snapshots with VMD

Getting started

• Installation
  • Conda environment
• Examples
  • Clustering by RMSD
  • Bonded distributions

Bonded distributions

• Bond length distributions
• Bond angle distributions
• Torsion angle distributions
• 2D histograms

Clustering

• Clustering by particle coordinates RMSD
• Clustering by torsion angles

Helical fitting

• Helical parameter fitting

Visualization

• Visualizing molecular snapshots

Indices and tables

• Index

• Module Index

• Search Page