thtools.crt.CelsiusRangeTest

class thtools.crt.CelsiusRangeTest(thtest, celsius_range)

Utility for running a ToeholdTest at a range of temperatures.

The name is sometimes abbreviated to CRT as a shorthand.

Note

There is no performance to be gained from using the run() method instead of generate(), unlike with ToeholdTest.

This is because each individual ToeholdTest in the temperature range already utilizes the specified number of CPU core, so further multiprocessing is impossible.

Parameters
thtestToeholdTest

The ToeholdTest to adjust the temperature of.

celsius_rangeSequence[float]

The array of temperature values in °C.

See also

CelsiusRangeResult

Examples

>>> import thtools as tt
>>> ths = "UUAGCCGCUGUCACACGCACAGGGAUUUACAAAAAGAGGAGAGUAAAAUGCUGUGCGUGCACCAUAAAACGAACAUAGAC"
>>> rbs = "AGAGGAGA"
>>> triggers = ["CUGUGCGUGUGACAGCGGCUGA", "CUAUACAAUCUACUGUCUUUCC", "UGUACAGCCUCCUAGCUUUCC"]
>>> temperatures = range(10, 61, 5)
>>> my_test = tt.autoconfig(ths, rbs, triggers)
>>> my_crt = tt.CelsiusRangeTest(my_test, temperatures)
>>> my_result = my_crt.run(max_size=3, n_samples=100)
>>> my_result.inferred_target
'CUGUGCGUGUGACAGCGGCUGA'
Attributes
thtestToeholdTest
celsius_rangeSequence[float]
resultCelsiusRangeResult
metaMapping[str, str | int | float]
generate(max_size, n_samples=100, n_nodes=2)

Run the test, returning a generator that the user must iterate through.

It stores a CelsiusRangeResult to the result attribute.

Parameters
max_sizeint

The maximum RNA complex size to simulate

n_samplesint, default = 100

The number of Boltzmann samples to take of each complex’s secondary structure.

n_nodesint, default = os.cpu_count()

The number of CPU cores to distribute work across using Pathos.

Yields
ToeholdResult

The result of the test at the nth temperature in the celsius_range.

Notes

Unlike generate(), this method has no significant performance penalty compared to run().

run(max_size, n_samples=100, n_nodes=2)

Run the test.

This is an alias to the generate() method and handles the iteration for you. Thus, there is no performance gain from using this over generate().

Parameters
max_sizeint

The maximum RNA complex size to simulate

n_samplesint, default=100

The number of Boltzmann samples to take of each complex’s secondary structure.

n_nodesint, default=os.cpu_count()

The number of CPU cores to distribute work across using Pathos.

Returns
ToeholdResult

A container for the data.

Notes

The result is also stored in the result attribute.