riboconstruct.inverse_folding package¶

Inverse folding is the task of identifying a sequence that is likely to fold into a given RNA target structure. riboconstruct.inverse_folding implements the inverse folding for the one and two target case.

The package is organized as follows:

• riboconstruct.inverse_folding.structure provides methods to handle RNA structures and their substructures.
• riboconstruct.inverse_folding.fillings provides methods to calculate the free energy fractions between two base pairs according to the nearest neighbour energy model and to assign bases such that a minimal free energy fraction is provided.
• riboconstruct.inverse_folding.subsolution defines methods to traverse the target structure along its substructures and to assign bases to its positions.
• riboconstruct.inverse_folding.two_target_subsolution extends the methods from the single target case to calculate RNA sequences likely to fold into two target structures.
  • riboconstruct.inverse_folding.dependency_graph is used to mark energy dependent base positions.
  • riboconstruct.inverse_folding.two_target_local_refinement is used to improve the identified RNA sequences by local search.

Calculations:

• riboconstruct.inverse_folding.inverse_fold() calculates the RNA sequence for the one target case.
• The methods in riboconstruct.inverse_folding.two_target_inverse_fold are used to calculate RNA sequences for the two target case.