The short story is that an AssemblyPlan contains Assemblies simulated using Mixes of DNA Fragments. Now for more details:
- An AssemblyPlan is mostly a list of Assembly instances
- A SequenceRepository provides parts sequences to simulate an Assembly.
- Simulating an Assembly results in an AssemblySimulation, which contains:
- Biopython SeqRecords of the predicted assembly constructs.
- The list of AssemblyMix instances created during the simulation.
- The list of AssemblyFlaw instances (errors and warnings) detected during the simulation.
- Simulating an AssemblyPlan results in an AssemblyPlanSimulation which is mostly a list of AssemblySimulation instances.
- An AssemblySimulation or AssemblyPlanSimulation can be written to a file using an AssemblyReportWriter
The biology of the different cloning techniques is implemented in the subclasses of Assembly and AssemblyMix.
An AssemblyMix contains a list of Fragment instances (which subclass BioPython's SeqRecord), and can be:
- A StickyEndFragmentMix:
- Such mixes contain a list of StickyEndFragment instances.
- A StickyEndFragment has a StickyEndSeq (subclass of BioPython's Seq with additional StickyEnd sequences on the left and right).
- Usable Subclasses include RestrictionLigationMix, Type2sRestrictionMix, BASICAssemblyMix. StickyEndFragments are generated by restriction mixes, for example by RestrictionLigationMix.
- An HomologousFragmentMix:
- Such mixes contain a list of HomologousFragment instances.
- Mixes also require a HomologyChecker to detect homologies.
- Subclasses include LCRAssemblyMix
