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Virtual Cell Framework
http://vcell.org/
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SBML export/import for CSG Geometry not working #423

Open jcschaff opened 1 year ago

jcschaff commented 1 year ago

SBML export/import for CSG Geometry not working. An NullPointerException exception is thrown when trying to round-trip to SBML with a CSG (Constructive Solid Geometry) geometry. (see biomodel_124562627.vcml)

After looking at the SBMLExporter and Importer, it is clear that the typical implementation within vcell (an analytic background subvolume with one or more CSG objects) is not supported at all.

The strategy is to translate the background into an oversized CUBE to form the "background" - so that all of the SubVolumes can be exported as CSGObjects (rather than a mixture of CSGObjects and AnalyticSubVolumes) and will translate well to SBML. The SBMLImporter likely needs some work as well with respect to CSG Geometries.

moraru commented 1 year ago

This affects 3 simcontexts in published models and 16 simcontexts in public models