diff --git a/doc/index.rst b/doc/index.rst index 2cde220..7e6a7f1 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -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.