API Reference¶
Complete reference for all public classes and functions in the mdna package.
Top-Level Functions¶
These are available directly via import mdna:
| Function | Description |
|---|---|
make() |
Generate DNA from sequence and/or shape |
load() |
Load DNA from trajectory, frames, or sequence |
connect() |
Join two DNA structures |
compute_rigid_parameters() |
Compute rigid base parameters from a trajectory |
sequence_to_pdb() |
Generate PDB file directly from sequence |
sequence_to_md() |
Generate and simulate DNA with OpenMM |
Core Classes¶
| Class | Description |
|---|---|
Nucleic |
Central DNA structure object (sequence + frames + trajectory) |
Shapes |
Factory for predefined DNA shape control points |
Geometry & Analysis¶
| Class | Description |
|---|---|
NucleicFrames |
Rigid base parameter computation from trajectories |
ReferenceBase |
Single nucleobase reference frame fitting |
GrooveAnalysis |
DNA groove width computation |
TorsionAnalysis |
Backbone torsion angle computation |
Build Internals¶
| Class | Description |
|---|---|
SplineFrames |
Spline interpolation and frame generation |
SequenceGenerator |
DNA topology construction from sequence |
StructureGenerator |
Atomic coordinate placement into frames |
Relaxation¶
| Class | Description |
|---|---|
Minimizer |
Monte Carlo energy minimization |