An RNA manipulation library.
Python
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README.md

forgi Library for RNA Secondary Structure Analysis

Full documentation: http://www.tbi.univie.ac.at/~thiel/forgi/

Build the documentation

sphinx-build -b html doc ~/public_html/forgi

Installation

python setup.py install

Examples
  • Color elements by name in a gradient and visualize a coarse-grain RNA

    python examples/visualize_cg.py examples/1y26.cg --color-gradual h0,s2,m1,s0,m0,m2,s3,h1 -x --virtual-atoms --sidechain-atoms

  • Create HTML code for a fornaContainer with colors according to the order of coarse grain elements provided on the commandline

    python examples/ordered_elements_to_forna_colors.py examples/1y26.cg h0,s2,m1,s0,m0,m2,s3,h1

  • Display an rna structure, save it to file, trim it and view it using eog

    pdb_id="ideal_1_3_4_6.pdb"; venv/bin/python examples/visualize_pdb.py forgi/threedee/data/${pdb_id} --output /tmp/${pdb_id}.png; mogrify -trim /tmp/${pdb_id}.png; eog /tmp/${pdb_id}.png