Tutorial

Before you use any scripts or modules, please put this line in your .bashrc file, and put in the path to your oxDNA UTILS:

export PYTHONPATH="$PYTHONPATH:/path/to/your/oxDNA/UTILS/"

Remember to do

. ~/.bashrc

Throughout the documentation, you will often see something called vh and vb. These are the virtual helix index and virtual base index in cadnano. You can get these numbers by hovering your mouse over a nucleotide in cadnano, and the two indices will show up at the lower left corner.

To use the scripts, simply follow the instructions given in their respective documentation pages. Note that some scripts are new and not included in the oxDNA package. You can download the missing scripts here.

To use the modules, here is an example code:

import origami_utils as oru
import readers

# Read the configuration file 'prova.conf' and topology file 'prova.top'
l = readers.LorenzoReader('prova.conf', 'prova.top')

# Get a base.System object from the reader
s = l.get_system()

# Initialise an Origami object from the System
# The 'virt2nuc' file can be generated from cadnano_interface.py with a cadnano json file
o = oru.Origami(system = s, cad2cuda_file = 'virt2nuc')

"""All code below are optional"""

"""
If you need to know which nucleotides are interacting with which...
Note: you don't have to run this unless you want to use class methods which require this list.
"""
# Get a list of interactions between nucleotides
# 'input' is a normal simulation input file, but it's only for the DNAnalysis program and it won't run a simulation
o.get_h_bond_list('input')

"""
If you want to get the oxDNA nucleotide index from the virtual helix and virtual base in cadnano...
"""
vh = 1       # virtual helix index (just an example)
vb = 2       # virtual base index (just an example)
scaf_id = o.get_nucleotides(vh, vb, type = "scaf")   # get the scaffold nucleotide id
stap_id = o.get_nucleotides(vh, vb, type = "stap")   # get the staple nucleotide id