Codenano

Install

Don't forget to clone the content of the submodules as well git clone https://github.com/thenlevy/codenano.git --recursive.

Requirement

• You will need Docker to build the user space. This tutorial assumes that you know how to build a docker image from an existing Dockerfile
• The easiest way to install Codenano is to use the Nix package manager.

Run nix-shell at the root of the repository. Once you have a nix-shell running, run make. If everything goes well, this will display a generated .json file on stdout.

Build the docker image and tag it as codenano to prepare the user space docker build . -t codenano.

You are now ready to lanch the server cd to server and run cargo r -- --static ../static &. Codenano is now running on localhost:4000.

Designing Nanostructures

Getting started

You can copy and paste this code to generate a double cross-over

use codenano::*;


pub fn main() {
    let mut ori = Nanostructure::new();
    let id_0 = ori.add_grid_helix(0, 0);
    let id_1 = ori.add_grid_helix(1, 0);

    ori.draw_strand(id_0, false, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_0, true, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_1, false, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_1, true, 0, 20, AUTO_COLOR);

    ori.make_jump(ori.get_nucl(id_1, 11, false), ori.get_nucl(id_0, 11, true));
    ori.make_jump(ori.get_nucl(id_0, 12, true), ori.get_nucl(id_1, 12, false));


    ori.finish();
}

Helices, Strands and Nucleotides

In Codenano, designs are made by drawing strands on helices and making jumps between those strands. Helices can be seen as bi-infinite double axes with integers coordinates. Helices serves as support for the nucleotides. On each helix there is a "sense" axe on which strand go from 5' to 3' by increasing their coordinates, and an "antisense" axe on which strands go from 5' to 3' by decreasing their coordinates. Each nucleotide is identified by 3 values:

• The identifier of the helix it is on (an integer)
• Its coordinate on the axe (an integer)
• A boolean saying if the nucleotide is on the antisense axe (true) or on the sense axe (false)

Helices created by specifying a point in space that is their origin, and 3 angles specifing their roll, yaw, and pitch

There is also a simple version to create helices. The function add_grid_helix(i, j) create an helix whose origin is at the square (i,j) of a grid. All the helices created by this function are parallel, and have a pitch, yaw and roll of 0.

When they are created, helices have no nucleotides on them. To add nucleotides use the function draw_strand(id, antisense, begin, end, color) where

• id is an helix identifier
• antisense is a boolean saying on which axe of the helix we are drawing (false for sense, true for antisense)
• begin and end are the first and last (inclusive) coordinates of the axes on which nucleotides are to be added
• color is the color of the strand to be drawn. One can either specify a color using hexadecimal RGB or use AUTO_COLOR when feeling uninspired.

use codenano::*;


pub fn main() {
    let mut ori = Nanostructure::new();
    let id_0 = ori.add_grid_helix(0, 0);

    let id_1 = ori.add_helix(0., 0.2, 0., 0., 0., 0.); 
    // ^ This helix is parallel to id_0

    let id_2 = ori.add_helix(0., 0.5, -1., 0., 3.14/4., 3.14/6.);
    // ^ This helix has different orientation

    ori.draw_strand(id_0, false, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_0, true, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_1, false, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_1, true, 0, 20, AUTO_COLOR);

    // green strand
    ori.draw_strand(id_2, false, 0, 40, 0x00FF00);

    // blue strand
    ori.draw_strand(id_2, true, 0, 40, 0x0000FF);

    ori.finish();
}

Jumps

Strands determine where the covalent bounds between nucleotides are. There is a covalent bound between two adjacent nucleotides if they are on the same strand. It is also possible to create a covalent bound between two nucleotides by creating a jump between them. Doing the from one nucleotide on strand s1 to one other on strand s2 has the following effect

• The 5' end of s1 and the 3' end of s2 are merged into one strand
• The 3' end of s1 becomes a new independent strand
• The 5' end of s2 becomes a new independent strand

use codenano::*;

pub fn main() {
    let mut ori = Nanostructure::new();
    let id_0 = ori.add_grid_helix(0, 0);

    let id_1 = ori.add_helix(0., 0.2, 0., 0., 0., 0.); 
    // ^ This helix is parallel to id_0

    ori.draw_strand(id_0, false, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_0, true, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_1, false, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_1, true, 0, 20, AUTO_COLOR);

    ori.make_jump(ori.get_nucl(id_0, 11, false), ori.get_nucl(id_1, 11, false));
    ori.finish();
}

Example

Double cross-over

use codenano::*;


pub fn main() {
    let colors: Vec<u32> =vec![0x1f1f1f, 0xf81118,0xecba0f,0x2a84d2,
                               0x4e5ab7, 0xd6dbe5, 0x1dd361, 0x0f7ddb];


    let mut ori = Nanostructure::new();
    let id_0 = ori.add_grid_helix(0, 0);
    let id_1 = ori.add_grid_helix(1, 0);

    ori.draw_strand(id_0, false, 0, 20, colors[6]);
    ori.draw_strand(id_0, true, 0, 20, colors[1]);
    ori.draw_strand(id_1, false, 0, 20, colors[2]);
    ori.draw_strand(id_1, true, 0, 20, colors[3]);

    ori.make_jump(ori.get_nucl(id_1, 11, false), ori.get_nucl(id_0, 11, true));
    ori.make_jump(ori.get_nucl(id_0, 12, true), ori.get_nucl(id_1, 12, false));


    ori.finish();
}

single stranded tile

use codenano::*;

const tile_length:isize = 11; 



static mut colornum:usize = 0;

pub fn add_sst(ori: &mut Nanostructure, helix_id: usize, helix_pos: isize) {
        let colors: Vec<u32> =vec![0x1f1f1f, 0xf81118,0xecba0f,0x2a84d2,
                                   0x4e5ab7, 0xd6dbe5, 0x1dd361, 0x0f7ddb];
        let mut color = 0;
        unsafe {
        color = colors[ (1 * colornum) % colors.len()];
        colornum += 1; }
        ori.draw_strand(helix_id, false, helix_pos, helix_pos + tile_length, color);
        ori.draw_strand(helix_id + 1, true, helix_pos + tile_length, helix_pos, color);
        ori.make_jump(ori.get_nucl(helix_id, helix_pos +tile_length, false),
                      ori.get_nucl(helix_id + 1, helix_pos + tile_length, true));
}


pub fn main() {

    let mut ori = Nanostructure::new();
    let id_0 = ori.add_grid_helix(0, 0);
    let id_1 = ori.add_grid_helix(1, 0);
    let id_2 = ori.add_grid_helix(2, 0);
    let id_3 = ori.add_grid_helix(3, 0);
    let id_4 = ori.add_grid_helix(4, 0);
    let id_5 = ori.add_grid_helix(5, 0);
    let id_6 = ori.add_grid_helix(6, 0);

    for i in 0isize..5 {
        for j in 0usize..3 {
            add_sst(&mut ori, j * 2, i * tile_length + i);
            add_sst(&mut ori, j * 2 + 1, i * tile_length + i + tile_length/2);
        }
    }
    ori.finish();
}

Features for advanced users

Changing constants

There are two constants that can be changed. The first one is the number of base pair per turns, the second one is the angle between two opposite pairs.

By default the number of base pair per turn is 10.4, and the angle between two opposite pairs is 220 degree (and not 180 degree, this is why there is a major/minor groove). To change that you must create a DNAConst object, modify its value and pass it as an argument to the constructor of the Nanostructure object.

use codenano::*;


pub fn main() {

    let mut cst = DNAConst::default();
    cst.set_bpp(10.7); // number of base pair per turn
    cst.set_groove(3.14); // pi angle => no minor/major groove
    let mut ori = Nanostructure::with_constant(cst);
    let id_0 = ori.add_grid_helix(0, 0);
    let id_1 = ori.add_grid_helix(1, 0);

    ori.draw_strand(id_0, false, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_0, true, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_1, false, 0, 20, AUTO_COLOR);
    ori.draw_strand(id_1, true, 0, 20, AUTO_COLOR);

    ori.make_jump(ori.get_nucl(id_1, 11, false), ori.get_nucl(id_0, 11, true));
    ori.make_jump(ori.get_nucl(id_0, 12, true), ori.get_nucl(id_1, 12, false));


    ori.finish();
}

License

Codenano is distributed under the terms of both the MIT license and the Apache License (Version 2.0)

lib.rs:

Converter from the CaDNAno format to strands, and back.