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doc/index.rst

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@@ -31,14 +31,19 @@ Scadnano provides function to convert design to and from cadnano v2:
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**Important**
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All ``cadnanov2`` designs can be imported to scadnano. However **not all scadnano designs can be imported
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to cadnanov2**, to be exportable to ``cadnanov2`` a scadnano design need to comply with the following points:
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* The design cannot feature any :class:`Loopout` or :class:`Extension`, since these are not concepts that exist in ``cadnanov2``.
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* Following ``cadnanov2`` conventions, helices with **even** number must have their scaffold going **forward** and helices with **odd** number **backward**.
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* 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.
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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.
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The conversion algorithm will choose the lowest multiple of 21 or 32 which fits the entire design.
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to cadnanov2**; to be exportable to ``cadnanov2`` a scadnano design need to comply with the following constraints:
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* The design cannot feature any :class:`Loopout` or :class:`Extension`, since these are not concepts that exist in
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``cadnanov2``.
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* Following ``cadnanov2`` conventions, helices with **even** number must have their scaffold going **forward** and
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helices with **odd** number **backward**.
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* If you use paranemic crossovers (i.e. crossovers where the domains before and after the crossover are in the same
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direction), the helices' row number (i.e. not the helices' indexes but their y coordinate) of the domains must have
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the same parity, meaning both even or both odd, for example rows 0 and 2, or 1 and 3, but not 0 and 1.
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Also note that maximum helices offsets can be altered in a ``scadnano`` to ``cadnanov2`` conversion as ``cadnanov2``
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needs max offsets to be a multiple of 21 in the hex grid and 32 in the rectangular grid. The conversion algorithm will
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choose the lowest multiple of 21 or 32 which fits the entire design.
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The ``cadnanov2`` json format does not embed sequences hence they will be lost after conversion.
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