{
    "info": {
        "author": "Sandro Bottaro",
        "author_email": "sandro.bottaro@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.6",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": ".. image:: https://travis-ci.org/srnas/barnaba.svg\n    :target: https://travis-ci.org/srnas/barnaba\n.. image:: https://badge.fury.io/py/barnaba.svg\n    :target: https://badge.fury.io/py/barnaba\n.. image:: https://repology.org/badge/version-for-repo/macports/python:barnaba.svg\n    :target: https://repology.org/metapackage/python:barnaba\n.. image:: https://codecov.io/gh/srnas/barnaba/branch/master/graph/badge.svg\n    :target: https://codecov.io/gh/srnas/barnaba\n\n\nIntroduction\n============\n\nBarnaba is a tool for analyzing RNA three-dimensional structures and simulations. Barnaba uses MDtraj to read/write topology and trajectory files, as such it supports several formats including pdb, xtc, trr, dcd, binpos, netcdf, mdcrd, prmtop, and more.  \nBarnaba has been developed by Sandro Bottaro with the crucial help of Giovanni Bussi, Giovanni Pinamonti, Sabine Rei{\\ss}er and Wouter Boomsma.   \n\nThis is what you can do with Barnaba:  \n\n1. Calculate eRMSD [1]\n2. Calculate RMSD after optimal alignment  \n3. Search for single/double stranded RNA motifs in the PDB database or in simulations [1]  \n4. Annotate PDB structures and trajectories with the Leontis-Westhof classification\n5. Produce dynamic secondary structure figures in SVG format\n6. Cluster nucleic acids structures using the eRMSD as a metric distance\n7. Calculate elastic network models for nucleic acids and nucleic acids/protein complexes [2]\n8. Calculate backbone and pucker torsion angles in a PDB structure or trajectory\n9. Back-calculate 3J scalar couplings from PDB structure or trajectory\n10. Score three-dimensional structures using eSCORE [1]\n\nFor bugs, questions or comments contact Sandro at sandro dot bottaro (guesswhat) gmail dot com\n\nIf you use Barnaba in your work,  please cite the following paper::\n\n\t@article{bottaro2019barnaba,\n  \t\ttitle={Barnaba: software for analysis of nucleic acid structures and trajectories},\n  \t\tauthor={Bottaro, Sandro and Bussi, Giovanni and Pinamonti, Giovanni and Rei{\\ss}er, Sabine and Boomsma, Wouter and Lindorff-Larsen, Kresten},\n  \t\tjournal={RNA},\n  \t\tvolume={25},\n  \t\tnumber={2},\n  \t\tpages={219--231},\n\t\tyear={2019},\n  \t\tpublisher={Cold Spring Harbor Lab}\n\t}\n\nThe manuscript is also available on biorXiv here: \nhttps://www.biorxiv.org/content/10.1101/345678v3\n\n\n\n\nRequirements\n-------------\nBarnaba requires:\n   - Python 2.7.x or > 3.3\n   - Numpy\n   - Scipy\n   - Mdtraj 1.9\n   - future\n     \nBarnaba requires mdtraj (http://mdtraj.org/) for manipulating structures and trajectories. \nTo perform cluster analysis, scikit-learn is required too.\n\nRequired packages can be installed using `pip`, e.g.:\n\n    pip install mdtraj\n\nInstallation\n-------------\n\nYou can obtain the latest tagged version of barnaba using pip:\n\n    pip install barnaba\n\nOn MacOS, you can install the same tagged version using the python distributed with MacPorts:\n\n    sudo port install py36-barnaba\n\nJust replace 36 with the python version that you prefer to use.\n  \nAlternatively, you can find the most recent version of barnaba on Github:\n\n    git clone git://github.com/srnas/barnaba.git\n\nthen move to the barnaba directory and run the command\n\n    pip install -e .\n\nNotice that barnaba is installed using `setuptools_scm` that is not compatible with git archives. Thus,\nyou would not be able to install barnaba from a git tarball.\n\nSome users might experience issues installing MDtraj using pip. If this is the case, we recommend installing MDtraj using conda:\n\n    conda install --channel omnia mdtraj\n    \nUsage\n------------\nBarnaba can be either used as a Python library or as a commandline tool.\nA number of Notebook examples can be found in the examples_ directory.\nThe notebooks for conducting the analyses and producing the figures in the manuscript can be found in the folder manuscript_figures_ .\n\nAlternatively, the command-line interface can be found in the bin directory. Here's a minimal how-to\n\n0.  minimal help:\n    barnaba --help  \n  \n1. Calculate the ERMSD between structures  \n\n   barnaba ERMSD --ref ../test/data/sample1.pdb --pdb ../test/data/sample2.pdb\n  \n   trajectories can be provided as well, by specifying a topology file  \n\n   barnaba ERMSD --ref ../test/data/sample1.pdb --top ../test/data/sample1.pdb --trj ../test/data/samples.xtc  \n\n   other accepted options are shown in a function-specific help  \n\n   barnaba ERMSD --help\n  \n2. Calculate the RMSD between structures  \n  \n   barnaba RMSD --ref ../test/data/sample1.pdb --pdb ../test/data/sample2.pdb --dump\n   \n3. Find single stranded motif  \n  \n   barnaba SS_MOTIF --query ../test/data/GNRA.pdb --pdb ../test/data/1S72.pdb   \n   \n4. Find double stranded motif. l1 and l2 are the lengths of the two strands\n  \n   barnaba DS_MOTIF --query ../test/data/SARCIN.pdb --pdb ../test/data/1S72.pdb --l1 8 --l2 7  \n \n5. Annotate structures/trajectories according to the Leontis/Westhof classification.\n   \n   barnaba ANNOTATE --pdb ../test/data/SARCIN.pdb  \n\n6. Produce dynamic secondary-structure figures. It requires as input the files .pairing\tand .stacking produced with the\tANNOTATE command.\n\n   barnaba SEC_STRUCTURE --ann outfile.ANNOTATE.stacking.out outfile.ANNOTATE.pairing.out\n\n7. Calculate backbone/sugar/pseudorotation angles\n    \n   barnaba TORSION --pdb ../test/data/GNRA.pdb --backbone --sugar --pucker \n \n\n8. Calculate J-couplings \n\n   barnaba JCOUPLING --pdb ../test/data/sample1.pdb \n\n9. Calculate elastic network models for RNA and predict SHAPE reactivity. NB: only works with PDB.\n   \n   barnaba ENM --pdb ../test/data/GNRA.pdb --shape\n\n10. Calculate relative positions between bases R_ij  ang G vectors for pairs within ellipsoidal cutoff  \n\n   barnaba DUMP --pdb ../test/data/GNRA.pdb --dumpG --dumpR  \n\n11. Extract fragments from structures with a given sequence. NB: only works with PDB.  \n\n    barnaba SNIPPET --pdb ../test/data/1S72.pdb  --seq NNGNRANN\n \n12. Calculate ESCORE  \n    \n   barnaba ESCORE --ff ../test/data/1S72.pdb --pdb ../test/data/sample1.pdb\n\n\nReferences\n------------\n\n[1] Bottaro, Sandro, Francesco Di Palma, and Giovanni Bussi.  \n    \"The role of nucleobase interactions in RNA structure and dynamics.\"  \n    Nucleic acids research 42.21 (2014): 13306-13314.  \n\n[2] Pinamonti, Giovanni, et al.  \n   \"Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.\"  \n   Nucleic acids research 43.15 (2015): 7260-7269.\n\n.. _examples: https://github.com/srnas/barnaba/tree/master/examples\n.. _manuscript_figures: https://github.com/srnas/barnaba/tree/master/manuscript_figures",
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