Welcome to rna-tools’ documentation!¶
rna-tools: a toolbox to analyze structures and simulations of RNA
The code of the project can be found at GitHub https://github.com/mmagnus/rna-tools.
This documentation can be found at http://rna-tools.rtfd.io.
The PDF version of documentation can be found at here.
If something does not work for you, please make an issue, using https://github.com/mmagnus/rna-tools/issues.
User Documentation
- Install
- Quickstart
- fetch a structure from the PDB database
- fetch a biologicaly assembly
- get sequences of a bunch of PDB files
- get secondary structures of your PDB files
- delete a part of of your structure
- get numbering of your structure and rename chains
- edit your structure (rename chain)
- extract part of your structure
- find missing atoms in my structure
- mutate residues
- add missing atoms
- rna-pdb-tools
- rna-tools
- RNA Sequence
- RNA Secondary Structure
- Search
- RNA Alignment
- Root Mean Square Deviation (RMSD)
- Interaction Network Fidelity (INF)
- RNA filter (DCA)
- Contacts classification & secondary structure detection
- RNA 3D model quality assessment
- RNA 3D structure prediction
- RNA Refinement (QRNAS)
- RNA Molecular Dynammics (MD)
- diffpdb
- RNA clustering with CLANS (clanstix)
- Misc
- rna-tools & PyMOL [PyMOL4RNA]
- rna-tools & Mac/Linux
- rna-tools & Jupyter Notebooks / Colab
- rna-tools & Emacs
- rna-tools & geekbook
- RNA Puzzle Submission
- Selection
- Tips
- Examples of workflows