Addition to Original Barnaba Code:

This is modified version of Barnaba package to calculate RNA pseudotorsion angles eta, theta, eta', and theta'.

Please refer original github here: https://github.com/srnas/barnaba

Following files are modified to include calculation of RNA pseudotorsion angles:

nucleic.py, functions.py, definitions.py, and commandline.py

Definitions of RNA pseudotorsion angles:

Please refer to this nice blog by Dr. Xiang-Jun Lu (x3DNA-DSSR software page) for definitions of pseudotorsions:

https://x3dna.org/highlights/pseudo-torsions-to-simplify-the-representation-of-dna-rna-backbone-conformation

Requirements

Barnaba requires:

• Python 2.7.x or > 3.3
• Numpy
• Scipy
• Mdtraj 1.9
• future

Barnaba requires mdtraj (http://mdtraj.org/) for manipulating structures and trajectories. To perform cluster analysis, scikit-learn is required too.

Required packages can be installed using pip, e.g.:

pip install mdtraj

Installation (if you want RNA pseudotorsions !!!)

git clone https://github.com/mandar5335/barnaba_pseudotor

then move to the barnaba directory and run the command

pip install -e .

Usage:

RNA pseudotorsions can be calculated using the command line or in jupyter-notebook.

command line:

barnaba TORSION --pseudo --pdb foo.pdb

Jupyter Notebook:

import barnaba as bb
from barnaba import definitions
angle, res =  bb.eta_theta_angles("foo.pdb")
definitions.pseudo_angles

This will calculate four pseudotorsions: ['eta', 'theta', 'eta_prime', 'theta_prime']

References

[1] Bottaro, Sandro, Francesco Di Palma, and Giovanni Bussi.
"The role of nucleobase interactions in RNA structure and dynamics."
Nucleic acids research 42.21 (2014): 13306-13314.

[2] Pinamonti, Giovanni, et al.
"Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments."
Nucleic acids research 43.15 (2015): 7260-7269.

If you use Barnaba in your work, please cite the following paper::

@article{bottaro2019barnaba,
	title={Barnaba: software for analysis of nucleic acid structures and trajectories},
	author={Bottaro, Sandro and Bussi, Giovanni and Pinamonti, Giovanni and Rei{\ss}er, Sabine and Boomsma, Wouter and Lindorff-Larsen, Kresten},
	journal={RNA},
	volume={25},
	number={2},
	pages={219--231},
	year={2019},
	publisher={Cold Spring Harbor Lab}
}