viennarna

library2.7.2pypypi✓ verified 85d ago

A library for the prediction and comparison of RNA secondary structures. Version 2.7.2 supports Python >=3.8. Released monthly to quarterly. Provides RNA folding, sequence design, and structure comparison algorithms.

devops

pip install viennarna

INSTALL

IMPORT

SIG · VIENNARNA

viennarna

devopspythonv2.7.2

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

RNA

✓ import RNA

All functions are accessed from the RNA module. No submodule imports.

Fold an RNA sequence and print the minimum free energy and structure.

import RNA seq = 'GGCGCUUCCUGGCUUU' (fc, mfe) = RNA.fold(seq) print(f"MFE: {mfe} kcal/mol") print(f"Structure: {fc}")

Debug

Known issues

breakingPython 2 support removed in ViennaRNA 2.5.0. Use Python >=3.8.

fix

Upgrade Python to 3.8+.

affects: >=2.5.0

breakingThe RNA.fold() function now returns (fc, mfe) tuple instead of (fc, mfe, dp). The dynamic programming matrix is no longer returned.

fix

Update code to unpack only two values from RNA.fold().

affects: >=2.4.0

deprecatedRNA.fold_compound() is deprecated. Use RNA.fold() or RNA.pf_fold() directly.

fix

Replace RNA.fold_compound() with appropriate direct folding call.

affects: >=2.5.0

gotchaRNA module functions expect sequences as strings, not list or bytes. Passing bytes will raise TypeError.

fix

Ensure input sequences are str objects, e.g., seq = str(seq).

affects: all

Errors

Common errors & fixes

ImportError: No module named RNA

ViennaRNA Python bindings are not installed or not in PYTHONPATH.

fix

Install viennarna with 'pip install viennarna' or ensure the package is available.

RuntimeError: ViennaRNA package not properly installed. The C library is missing.

Installation via pip failed to locate or compile the C library.

fix

Install precompiled wheel (e.g., from PyPI) or install via conda: 'conda install -c bioconda viennarna'.

TypeError: expected string or bytes-like object

Passing a non-string or non-ASCII sequence to RNA functions.

fix

Ensure the sequence is a plain string with only standard RNA bases (A,U,G,C).

Upgrade

Version history

2.7.2latest on PyPI · released Dec 30, 2025

Audit

Dependencies

swigoptionalRequired for building from source; not needed if using precompiled wheels.

numpyoptionalUsed for array operations; often required at runtime.

Agent activity

6 hits · last 30 days

node

Resources

No resource links recorded.