Sets new sequence provider to generate sequences of newly created DNA structures
Sequence provider currently used for generation of sequence of new DNA structures
Sets new sequence provider to generate sequences of newly created DNA structures
Sequence provider currently used for generation of sequence of new DNA structures
Builds complementary strand for the given single strand.
source single strand
new DNA single strand complementary to the provided one (both in sequence and position). The "pair" information is assigned by the function but it is up to the caller to add this new single strand to the corresponding structure.
Builds complementary nucleotide to the given nucleotide (both in nucleobase type and location).
nucleotide for which to create a complement
parent strand of the source nucleotide
strand of the newly created nucleotide
location in the newly created nucleotide's strand where it is supposed to be inserted
nucleotide proxy referencing newly created complementary nucleotide
Creates double strand going from point A to point B.
start position of the double strand
end position of the double strand
structure to which the double strand should be appended
tuple referencing two newly created strands
Builds a DNA helix of given length and directionality. The calling function must decide if the returing strand is supposed to be appended to an existing structure or serve as a basis for new separate structure/component.
length of the created strand
positon where the strand should start
direction of the strand's helical axis
hydrogen face direction of the first nucleotide of the strand
sequence provider to use instead of the default DNAFactory's one
new DNA single strand
Builds DNA single strand based on the data of provided nucleic acid strand creator.
strand creator carrying the data of the strand to be created
new DNA single strand
Builds new DNA single strand with the given sequence.
FASTA sequence storing the sequence of the new strand
new DNA single strand
Creates new nucleotide having the given parameters.
origin of the helical axis (location of the nucleotide)
normal of the nucleobase's plane
direction of the origin - C1' atom vector (similar to hydrogen face direction)
nucleobase type
parent strand of the new nucleotide
to which end to insert the new nucleotide
global ID of the new nucleotide
proxy referencing the newly created nucleotide
Extends given double helix if any exists. If not, the provided single strand will be extended.
strand to be extended (one of the double helice's strands)
where to perform the extension w.r.t provided primary strand
length of the extension
direction of the extension (if not provided, helical axis direction is used)
custom sequence provider for the extended part
array of up to two single single strand. First element is the extended primary strand, second is reference to extended complementary strand (if any exists).
Extends provided single strand in the designated direction.
strand to extend
which end of the strand to extend
length of the extension
direction of the extension (if not set, helical axis direction will be used)
custom sequence provider for the extended part
reference to the provided strand with the corresponding part extended
Generates given number of nucleotides starting at a template nucleotide.
number of nucleotides to generate
template nucleotide aka the basis of the newly created strand
parent strand of the nucleotides
end of strand to be extended
sequence provider to be used for generation of base types
custom DNA form
custom direction of the helical axis
reference to DNA strand with the newly created nucleotides appended
Generated using TypeDoc
Class serving for the creation of coarse-grained DNA structures