Crate codenano

Expand description

This crate (codenano) allows one to design DNA molecules.

The following creates a strand zig-zagging between three helices, and outputs it to a file:

use codenano::*;
let mut design: Design<(), ()> = Design::new();
for i in 0..3 {
   design.add_grid_helix(i, 0);
}
// Let's first design a strand.
design.strand(0, 0).to(31)
  .cross(1).to(10)
  .cross(2).to(21);
// Now its reverse complement:
design.strand(2, 21).to(10)
   .cross(1).to(31)
   .cross(0).to(0);
design.write_to("my_design.json").unwrap()

This library is compatible with the codenano-server crate, which watches changes made to a file and shows the result in 3D in a web browser. Additionally, the client part (also called codenano) of the the codenano-servercrate can run finite element simulations and display the secondary structure.

Re-exports§

pub use autoroll::RollSystem;
pub use autoroll::SpringSystem;

Modules§

autoroll: Automatic roll adjustment of helices
cadnano: Conversion to Cadnano format.
geometry: 3D points and vectors
guess3d: Guess of the 3D structure
mrdna: Conversion to Mrdna
opengl: Utilities for drawing a design in OpenGL.
patch: Modification of an existing design
sequences: Extra tools for sequences (random completions, etc.)
transforms: Common geometric transforms on domains (most useful when working on grids or partial grids).

Structs§

Design: The main type of this crate, describing a DNA design.
Domain: A domain, i.e. an interval of a helix.
DomainIter: An iterator over all positions of a domain.
Error: The Error type, a wrapper around a dynamic error type.
Helix: A DNA helix. All bases of all strands must be on a helix.
HelixId: Identity of a helix, useful for referring to it.
Parameters: DNA geometric parameters.
Plate96: Representation of a 96-well plate being filled. Plates are filled from top to bottom (i.e. rows are incremented first), then from left to forward (columns are incremented).
Strand: A DNA strand.
StrandId: Identity of a strand, useful for referring to it.
StrandRef: A pointer to a strand being built, containing a current domain and position.

Enums§

Color: Colors

Constants§