ViennaRNA/ViennaRNA v2.7.1

ViennaRNA Package 2.7.1

on GitHub

Programs

• Allow for FASTA header changes in ct2db
• Fix constraints parsing in RNAsubopt
• Add new command line options for structure probing data to RNAfold and RNAsubopt

Library

• API: Refactor structure probing data API to support multiple data at once, position-wise weighting, user-defined reactivity-to-energy strategies and more
• API: Refactor hard constraint wrappers
• API: Add ViennaRNA/math/ to provide several useful mathematical functions
• API: Add vrna_str_to_dbl_array()
• API: Add vrna_file_doubles_read()
• API: Fix backtracking issues in exterior loop
• API: Fix backtracking issues with odd dangles
• API: Fix segmentation fault in vrna_pt_pk_remove()
• API: Fix vrna_plist() and vrna_ptable() to deal with malformed input
• API: Fix soft constraints access in backtracking of QM2 (Boltzmann sampling)
• SWIG: Add wrappers for concentration dependency computations
• SWIG: Fix RNA.fold_compound.bpp() output for multistrand base pair probabilities
• SWIG: Do not return symmetric pair probability matrix by default
• SWIG: Fix Python object ownership in callbacks for unstructured domains, direct soft constraints and landscape moves

Package

• Update dlib to version 20.0
• Overall improvements to the documentation
• Fix energy parameter file markup
• Fix compilation with compilers that default to C23
• Update swig requirement to 4.2.0
• Fix compilation without libsvm
• Update breathe to version v5.0.0a5
• Add probing data priors (paired and unpaired) for 1M7 and DMS