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barnaba-0.1.9
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مشاهده بیشترتوضیحات
analyze nucleic acid 3D structures and MD trajectories
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | barnaba-0.1.9 |
| نام | barnaba |
| نسخه کتابخانه | 0.1.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Sandro Bottaro |
| ایمیل نویسنده | sandro.bottaro@gmail.com |
| آدرس صفحه اصلی | https://github.com/srnas/barnaba |
| آدرس اینترنتی | https://pypi.org/project/barnaba/ |
| مجوز | - |
.. image:: https://github.com/srnas/barnaba/workflows/CI/badge.svg
:target: https://github.com/srnas/barnaba/actions?query=workflow%3ACI
.. image:: https://badge.fury.io/py/barnaba.svg
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.. image:: https://repology.org/badge/version-for-repo/macports/python:barnaba.svg
:target: https://repology.org/metapackage/python:barnaba
.. image:: https://codecov.io/gh/srnas/barnaba/branch/master/graph/badge.svg
:target: https://codecov.io/gh/srnas/barnaba
Introduction
============
Barnaba 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.
Barnaba has been developed by Sandro Bottaro with the crucial help of Giovanni Bussi, Giovanni Pinamonti, Sabine Rei{\ss}er and Wouter Boomsma.
This is what you can do with Barnaba:
1. Calculate eRMSD [1]
2. Calculate RMSD after optimal alignment
3. Search for single/double stranded RNA motifs in the PDB database or in simulations [1]
4. Annotate PDB structures and trajectories with the Leontis-Westhof classification
5. Produce dynamic secondary structure figures in SVG format
6. Cluster nucleic acids structures using the eRMSD as a metric distance
7. Calculate elastic network models for nucleic acids and nucleic acids/protein complexes [2]
8. Calculate backbone and pucker torsion angles in a PDB structure or trajectory
9. Back-calculate 3J scalar couplings from PDB structure or trajectory
10. Score three-dimensional structures using eSCORE [1]
For bugs, questions or comments contact Sandro at sandro dot bottaro (guesswhat) gmail dot com
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}
}
The manuscript is also available on biorXiv here:
https://www.biorxiv.org/content/10.1101/345678v3
Requirements
-------------
Barnaba requires:
- Python >= 3.6
- 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
-------------
You can obtain the latest tagged version of barnaba using pip:
pip install barnaba
If you prefer to manage your dependencies with conda you can use:
conda -c conda-forge install barnaba
On MacOS, you can install the same tagged version using the python distributed with MacPorts:
sudo port install py36-barnaba
Just replace 36 with the python version that you prefer to use.
Alternatively, you can find the most recent version of barnaba on Github:
git clone git://github.com/srnas/barnaba.git
then move to the barnaba directory and run the command
pip install -e .
Usage
------------
Barnaba can be either used as a Python library or as a commandline tool.
A number of Notebook examples can be found in the examples_ directory.
The notebooks for conducting the analyses and producing the figures in the manuscript can be found in the folder manuscript_figures_ .
Alternatively, the command-line interface can be found in the bin directory. Here's a minimal how-to
0. minimal help:
barnaba --help
1. Calculate the ERMSD between structures
barnaba ERMSD --ref ../test/data/sample1.pdb --pdb ../test/data/sample2.pdb
trajectories can be provided as well, by specifying a topology file
barnaba ERMSD --ref ../test/data/sample1.pdb --top ../test/data/sample1.pdb --trj ../test/data/samples.xtc
other accepted options are shown in a function-specific help
barnaba ERMSD --help
2. Calculate the RMSD between structures
barnaba RMSD --ref ../test/data/sample1.pdb --pdb ../test/data/sample2.pdb --dump
3. Find single stranded motif
barnaba SS_MOTIF --query ../test/data/GNRA.pdb --pdb ../test/data/1S72.pdb
4. Find double stranded motif. l1 and l2 are the lengths of the two strands
barnaba DS_MOTIF --query ../test/data/SARCIN.pdb --pdb ../test/data/1S72.pdb --l1 8 --l2 7
5. Annotate structures/trajectories according to the Leontis/Westhof classification.
barnaba ANNOTATE --pdb ../test/data/SARCIN.pdb
6. Produce dynamic secondary-structure figures. It requires as input the files .pairing and .stacking produced with the ANNOTATE command.
barnaba SEC_STRUCTURE --ann outfile.ANNOTATE.stacking.out outfile.ANNOTATE.pairing.out
7. Calculate backbone/sugar/pseudorotation angles
barnaba TORSION --pdb ../test/data/GNRA.pdb --backbone --sugar --pucker
8. Calculate J-couplings
barnaba JCOUPLING --pdb ../test/data/sample1.pdb
9. Calculate elastic network models for RNA and predict SHAPE reactivity. NB: only works with PDB.
barnaba ENM --pdb ../test/data/GNRA.pdb --shape
10. Calculate relative positions between bases R_ij ang G vectors for pairs within ellipsoidal cutoff
barnaba DUMP --pdb ../test/data/GNRA.pdb --dumpG --dumpR
11. Extract fragments from structures with a given sequence. NB: only works with PDB.
barnaba SNIPPET --pdb ../test/data/1S72.pdb --seq NNGNRANN
12. Calculate ESCORE
barnaba ESCORE --ff ../test/data/1S72.pdb --pdb ../test/data/sample1.pdb
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.
.. _examples: https://github.com/srnas/barnaba/tree/master/examples
.. _manuscript_figures: https://github.com/srnas/barnaba/tree/master/manuscript_figures
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl barnaba-0.1.9:
pip install barnaba-0.1.9.whl
نصب پکیج tar.gz barnaba-0.1.9:
pip install barnaba-0.1.9.tar.gz