riboconstruct — Generate and evaluate riboswitches¶

This module provides methods and techniques to generate riboswitch instances for a given model and evaluate these instances with respect to their folding behaviour.

riboconstruct is mainly based on two subpackages:

• riboconstruct.riboswitch provides methods to traverse and evaluate the space of riboswitch instances defined by the underlying model. A riboswitch instance fixes the different parts of the riboswitch model into a concrete setting by defining the size, structure or position of its elements.

  The actual evaluation of a riboswitch instance is done using riboconstruct.rna_f.

• Once a riboswitch instance is fixed while iterating the riboswitch space, only the two structures and some of the bases are known. Therefore, a RNA sequence that is likely to fold into the structures has to be identified. The necessary methods are provided in riboconstruct.inverse_folding.

To generate and evaluate riboswitches the following subpackage can be used:

• riboconstruct.eval_mp provides methods to generate and evaluate a riboswitch model within given constraints. The methods are based on Python’s multiprocessing and can be used to do the calculations on a multiprocessing system in parallel.

Besides, riboconstruct offers helper classes and functions e.g. to represent RNA structures or sequences:

• riboconstruct.rna
• riboconstruct.helper