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Update index.rst
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dave-doty committed Oct 26, 2024
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Expand Up @@ -31,14 +31,19 @@ Scadnano provides function to convert design to and from cadnano v2:
**Important**

All ``cadnanov2`` designs can be imported to scadnano. However **not all scadnano designs can be imported
to cadnanov2**, to be exportable to ``cadnanov2`` a scadnano design need to comply with the following points:

* The design cannot feature any :class:`Loopout` or :class:`Extension`, since these are not concepts that exist in ``cadnanov2``.
* Following ``cadnanov2`` conventions, helices with **even** number must have their scaffold going **forward** and helices with **odd** number **backward**.
* If you use paranemic crossovers (i.e. crossovers where the domains before and after the crossover are in the same direction), the helices' row number (i.e. not the helices' indexes but their y coordinate) of the domains must have the same parity e.g. rows 0 and 2, or 1 and 3, but not 0 and 1.

Also note that maximum helices offsets can be altered in a ``scadnano`` to ``cadnanov2`` conversion as ``cadnanov2`` needs max offsets to be a multiple of 21 in the hex grid and 32 in the rectangular grid.
The conversion algorithm will choose the lowest multiple of 21 or 32 which fits the entire design.
to cadnanov2**; to be exportable to ``cadnanov2`` a scadnano design need to comply with the following constraints:

* The design cannot feature any :class:`Loopout` or :class:`Extension`, since these are not concepts that exist in
``cadnanov2``.
* Following ``cadnanov2`` conventions, helices with **even** number must have their scaffold going **forward** and
helices with **odd** number **backward**.
* If you use paranemic crossovers (i.e. crossovers where the domains before and after the crossover are in the same
direction), the helices' row number (i.e. not the helices' indexes but their y coordinate) of the domains must have
the same parity, meaning both even or both odd, for example rows 0 and 2, or 1 and 3, but not 0 and 1.

Also note that maximum helices offsets can be altered in a ``scadnano`` to ``cadnanov2`` conversion as ``cadnanov2``
needs max offsets to be a multiple of 21 in the hex grid and 32 in the rectangular grid. The conversion algorithm will
choose the lowest multiple of 21 or 32 which fits the entire design.

The ``cadnanov2`` json format does not embed sequences hence they will be lost after conversion.

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