Input Your DNA Origami Design
=============================

To get started, you need to input your origami design into the **scaffoldselector**.

The **scaffoldselector** works with origamis specified as a `contact map <https://contactmap.readthedocs.io>`_. This is a simple CSV format specifying how staple bases are hybridised with scaffold bases in the target origami design. 

Origami CAD designs in `scadnano <https://scadnano.org/>`_, `oxDNA <https://dna.physics.ox.ac.uk/index.php/Main_Page>`_ or `caDNAno <https://cadnano.org/>`_ can be easily converted to a contact map as described below.

scadnano to Contact Map
-----------------------

1. Move your scadnano design file to e.g. ``origami/contactmap/_assets/myorigami.sc``.

2. Run: ::

	cd origami
	source venv/bin/activate
	cd contactmap
	python3 scadnano2contact.py myorigami

3. The contact map is created at ``origami/contactmap/_assets/myorigami.csv``.

oxDNA to Contact Map
--------------------

1. Move your oxDNA topology and configuration files to the ``origami/contactmap/_assets/`` directory. For example ``myorigami.top`` and ``myorigami.dat`` (or ``myorigami.oxdna``). 

.. note:: The oxDNA files must be freshly-exported from a design tool and **they must not be relaxed**. Note that many oxDNA designs in `nanobase <https://nanobase.org/>`_ are already relaxed and thus are not suitable.

2. Run: ::

	cd origami
	source venv/bin/activate
	cd contactmap
	python3 oxdna2contact.py myorigami

3. The contact map is created at ``origami/contactmap/_assets/myorigami.csv``.

caDNAno to Contact Map
----------------------

Designs in caDNAno can either be imported into scadnano and exported as ``.sc`` files, or they can be converted to oxDNA files via `tacoxDNA <http://tacoxdna.sissa.it/>`_. Then the steps above can be applied.

.. note:: Conversion of designs via `tacoxDNA <http://tacoxdna.sissa.it/>`_. assigns **random sequences** to the scaffold and staples. When a contact map has been produced, its sequences can be changed by using utilities of the `contact map <https://contactmap.readthedocs.io>`_ module. 

Circularising Scaffold
----------------------

If an origami specified as a contact map has a linear scaffold strand which requires to be joined into a circle, this can be accomplished via the `contact map <https://contactmap.readthedocs.io>`_ module:

1. Move the contact map of your origami design to e.g. ``origami/contactmap/_assets/myorigami.csv``.

2. Run: ::

	cd origami
	source venv/bin/activate
	cd contactmap
	python3 contactutils.py circ myorigami

3. The contact map at ``origami/contactmap/_assets/myorigami.csv`` is **modified** to have a circular scaffold strand.

Many other operations on origami contact maps can also be performed: see the `contact map <https://contactmap.readthedocs.io>`_ module documentation.