User Guide Overview¶

The User Guide walks you through MDNA's three core workflows: Build, Modify, and Analyse. Each section contains task-oriented examples showing how to use the toolkit in practice.

graph LR
    B[Build] --> M[Modify] --> A[Analyse]
    B --> A

Build¶

Create DNA structures from sequence, shape, or both. Generate linear strands, circular minicircles, custom-shaped DNA, and multi-segment assemblies.

Building DNA →

Modify¶

Edit existing structures: mutate bases (canonical and non-canonical), add methylation, flip nucleobases into Hoogsteen configuration.

Modifying DNA →

Analyse¶

Load MD trajectories and compute rigid base parameters, linking numbers, groove widths, and torsion angles.

Analyzing DNA →

Non-Canonical Bases¶

Work with fluorescent, hachimoji, and hydrophobic base pairs beyond the standard A/T/G/C alphabet.

Non-Canonical Bases →

Key Entry Points¶

All high-level functions are available directly from import mdna:

Function	Purpose
`mdna.make()`	Generate DNA from sequence and/or shape
`mdna.load()`	Load DNA from MDTraj trajectory or frames
`mdna.connect()`	Join two DNA structures
`mdna.compute_rigid_parameters()`	Compute rigid base parameters from a trajectory
`mdna.sequence_to_pdb()`	Generate PDB file from sequence
`mdna.Shapes`	Library of predefined DNA shapes