jdna.reaction

Simulate molecular reactions.

Classes

Assembly(templates, junctions, cyclic)	Stores a DNA assembly.
BindingEvent(template, primer, position)	Create new instance of BindingEvent(template, primer, position)
Reaction

Exceptions

PCRException	Exception with pcr.
ReactionException	Generic reaction exception.

class jdna.reaction.Assembly(templates, junctions, cyclic)

Bases: object

Stores a DNA assembly.

Assembly can be printed to display relevant assembly information:

assembly.print()

> "Unnamed" (320bp)
  Cyclic: True
  Num Fragments: 4
  Overhang Tms (°C): 53.65, 53.79, 54.96, 56.37
  Junction Lengths (bp): 20, 20, 20, 20
  Junction ΔG: -1.91e+4, -1.93e+4, -1.98e+4, -2.05e+4
  Junction ΔG (hairpin): (0.0, 232.50050218543765), (203.8205043739763,
  -84.3344956260189), (0.0, -60.91449781456504),
  (-1026.7134934374844, -622.0224934343823)
  Competing ΔG: -2.18e+4, -2.11e+4, -1.92e+4, -2.01e+4
  Product length (bp): 300

          -----Tm: 53.7°C-----
(0) 0     TTGACGACAGTGGCTATCCCCTGTTGCTAGGCACGGTGATATATCAGCCC
(1) 0     --------------------------------------------------
(2) 0     --------------------------------------------------
(3) 0     --------------------------------------------------

                                   -----Tm: 53.8°C-----
(0) 50    ATAGGGCCGGATCAACGTAGTTTGATCGTAGCTGTTCCGTCAGTC-----
(1) 50    -------------------------TCGTAGCTGTTCCGTCAGTCAGTGC
(2) 50    --------------------------------------------------
(3) 50    --------------------------------------------------

(0) 100   --------------------------------------------------
(1) 100   CGATGCCAGTCTACTGCTTTTCGCCCAGGGGGACACCTGACACTATGTTA
(2) 100   --------------------------------------------------
(3) 100   --------------------------------------------------

          -----Tm: 55.0°C-----
(0) 150   --------------------------------------------------
(1) 150   TGCCAAGCTCACGTTTCACA------------------------------
(2) 150   TGCCAAGCTCACGTTTCACAAGGCAGATTAAATAAGACTGAAACATTTGG
(3) 150   --------------------------------------------------

                                   -----Tm: 56.4°C-----
(0) 200   --------------------------------------------------
(1) 200   --------------------------------------------------
(2) 200   TGGAGGCGCGAGTCTTGCCCTTAGGCAGACCTGTTCGAGGGCGAA-----
(3) 200   -------------------------CAGACCTGTTCGAGGGCGAAAAACG

(0) 250   --------------------------------------------------
(1) 250   --------------------------------------------------
(2) 250   --------------------------------------------------
(3) 250   CCGAAGTCACATAGCGGCATGTTAGGTAGCTGTACACCCGTACTGCTACA

Assembly constructor.

Parameters

• templates (list) – list of templates

• junctions (list) – list of junctions

• cyclic (bool) – whether assembly is cyclic

print(*args, **kwargs)

Print the assembly.

> "Unnamed" (320bp)
      Num Fragments: 4
      Overhang Tms (°C): 61.49, 58.37, 54.72, 45.91
      Junction Lengths (bp): 20, 20, 20, 20
      Junction ΔG: -2.30e+4, -2.18e+4, -1.97e+4, -1.54e+4
      Junction ΔG (hairpin): (-1542.5069956260231, -1787.4319956260224),
      (-1832.7404978145642, -708.4919956260237), (0.0, 0.0), (0.0, 0.0)
      Competing ΔG: -3.39e+4, -2.43e+4, -2.19e+4, -1.33e+4
      Length: 300bp

                                                                                         |<Tm: 58.4°C
              -----Tm: 61.5°C-----                                                       ----------
    (0) 0     TGCTCGGCGAAGGGCCTGACAAGACCACTTCGTACCCTTTGTAACGTGACTTCTGTGAATCGATGGCGGATGTTGCTTGTGACGC
    (1) 0     ---------------------------------------------------------------------------CTTGTGACGC
    (2) 0     -------------------------------------------------------------------------------------
    (3) 0     -------------------------------------------------------------------------------------

              |<Tm: 58.4°C
              ----------                                                       -----Tm: 54.7°C-----
    (0) 85    ACCCGTAGCG---------------------------------------------------------------------------
    (1) 85    ACCCGTAGCGACATAACCGCCTTATTCCCACTTGTTTGGGGAGGCAAGTTTTGTAGTAGCCATTCTAATCCCGTTTTCTCCGCCG
    (2) 85    -----------------------------------------------------------------TAATCCCGTTTTCTCCGCCG
    (3) 85    -------------------------------------------------------------------------------------

                                                                     -----Tm: 45.9°C-----
    (0) 170   -------------------------------------------------------------------------------------
    (1) 170   -------------------------------------------------------------------------------------
    (2) 170   CTTGTTCAGCTTGATGTGTTGGAACAGCAAGTTTATTTTAGGGTGTCAGGAGGGGGAGGTCCTCTAGTATTAAGC----------
    (3) 170   -------------------------------------------------------GAGGTCCTCTAGTATTAAGCACCGGCCAAG

                                                           -----Tm: 61.5°C-----
    (0) 255   -----------------------------------------------------------------
    (1) 255   -----------------------------------------------------------------
    (2) 255   -----------------------------------------------------------------
    (3) 255   GCGGCACGGACGCCACTAGAAGGGAGGCGTTCATAGCGAGTCCTTTGCTCGGCGAAGGGCCTGAC

tms()

Return the tms of the junctions.

class jdna.reaction.BindingEvent(template, primer, position)

Bases: tuple

Create new instance of BindingEvent(template, primer, position)

_asdict()

Return a new OrderedDict which maps field names to their values.

classmethod _make(iterable)

Make a new BindingEvent object from a sequence or iterable

_replace(**kwds)

Return a new BindingEvent object replacing specified fields with new values

count()

Return number of occurrences of value.

index()

Return first index of value.

Raises ValueError if the value is not present.

property position

Alias for field number 2

property primer

Alias for field number 1

property template

Alias for field number 0

exception jdna.reaction.PCRException

Bases: jdna.reaction.ReactionException

Exception with pcr.

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception jdna.reaction.ReactionException

Bases: Exception

Generic reaction exception.

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.