primerize.thermo Module¶

class primerize.thermo.Nearest_Neighbor_Parameter(*args, **kwargs)¶

Bases: Singleton

Wrapper object of Nearest Neighbor parameters; for internal use.

T¶

float

delH_NN¶

numpy.array(float(4, 4))

delS_NN¶

numpy.array(float(4, 4))

delG_NN¶

numpy.array(float(4, 4))

delH_AT_closing_penalty¶

numpy.array(float(1, 4))

delS_AT_closing_penalty¶

numpy.array(float(1, 4))

delG_AT_closing_penalty¶

numpy.array(float(1, 4))

delH_mismatch¶

numpy.array(float(4, 4, 4))

delS_mismatch¶

numpy.array(float(4, 4, 4))

delG_mismatch¶

numpy.array(float(4, 4, 4))

delH_init¶

float

del_init¶

float

Note

This class follows the singleton pattern so that only one instance is created. An instance is already initialized as primerize.Nearest_Neighbor.

class primerize.thermo.Singleton(*args, **kwargs)¶

Bases: object

Base class for singleton pattern

primerize.thermo.calc_Tm(sequence, DNA_conc=1e-05, monovalent_conc=1.0, divalent_conc=0.0)¶

Calculate melting temperature for a given sequence

Parameters:

• sequence – str: Annealing DNA sequence section.

• DNA_conc – float: (Optional) Concentration of DNA.

• monovalent_conc – float: (Optional) Monovalent cation concentration.

• divalent_conc – float: (Optional) Divalent cation concentration.

Returns:

float – Melting temperature in Celcius