enzymes

type AssemblyLevel struct {
	//Enzyme used for assembly
	Enzyme wtype.TypeIIs
	// map of part labels to standard overhangs.
	PartOverhangs map[string]StandardOverhangs
	// Expected overhangs in the entry vector.
	EntryVectorEnds StandardOverhangs // Vector 5prime can also be found in Endstable position 0
}

type AssemblyStandard struct {
	// Name of the Assembly Standard.
	Name string
	// The AssemblyStandard may consist of a number of assembly levels which may use a different enzyme, set of standard overhangs or both.
	// The name of the level is used as the key to calling an AssemblyLevel object.
	Levels map[string]AssemblyLevel
}

type Assemblyparameters struct {
	Constructname string              `json:"construct_name"`
	Enzymename    string              `json:"enzyme_name"`
	Vector        wtype.DNASequence   `json:"vector"`
	Partsinorder  []wtype.DNASequence `json:"parts_in_order"`
}

type DigestedFragment struct {

	// Sequence of top strand
	TopStrand string

	// Sequence of bottom strand
	BottomStrand string

	// FivePrimeTopStrandStickyend is any over hang at the 5' end of the coding strand
	// This will be greater than "" if the fragment was generated by cutting with an enzyme which leaves a 5' overhang.
	// The complementary sticky end will be on the FivePrimeBottomStrandStickyend.
	// If this is not "" this will be the first part of the TopStrand sequence.
	FivePrimeTopStrandStickyend string

	// FivePrimeBottomStrandStickyend is any over hang at the 5' end of the complementary strand
	// This may be referred to as an underhang.
	// This will be greater than "" if the fragment was generated by cutting with an enzyme which leaves a 5' overhang.
	// The complementary sticky end will be on the FivePrimeTopStrandStickyend.
	// This sequence or it's reverse complement will not be present on the end of the Top strand.
	FivePrimeBottomStrandStickyend string

	// TopStickyend_3prime is any over hang at the 3' end of the coding strand.
	// This may be referred to as an underhang.
	// This will be greater than "" if the fragment was generated by cutting with an enzyme which leaves a 3' overhang.
	// The complementary sticky end will be on the BottomStickyend_3prime.
	// This sequence will be present on the end of the Top strand.
	ThreePrimeTopStrandStickyend string

	// BottomStickyend_3prime is any over hang at the 3' end of the complementary strand.
	// This may be referred to as an underhang.
	// This will be greater than "" if the fragment was generated by cutting with an enzyme which leaves a 3' overhang.
	// The complementary sticky end will be on the TopStickyend_3prime.
	// This sequence or it's reverse complement will not be present at the front of the Top strand.
	ThreePrimeBottomStrandStickyEnd string
}

type RestrictionSites struct {
	Enzyme    wtype.RestrictionEnzyme
	Positions []sequences.PositionPair
}

type StandardOverhangs struct {
	// Overhang expected to be left at the upstream end of a part after typeIIs digestion.
	Upstream string
	// Overhang expected to be left at the downstream end of a part after typeIIs digestion.
	Downstream string
}