8000 Refactor path handling to use pathlib in generate_model_info.py by AntonPetrov · Pull Request #191 · r2dt-bio/R2DT · GitHub
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Refactor path handling to use pathlib in generate_model_info.py #191

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Refactor path handling to use pathlib in generate_model_info.py #191

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34b6757
Embed XRNA-GT video and link to playlist in docs
AntonPetrov Dec 4, 2024
a363a77
Add XRNA-React user manual
AntonPetrov Dec 17, 2024
f6c4c2a
Update examples in R2DT form in docs
AntonPetrov Dec 17, 2024
7d3d013
Change admonition type for xrna manual link
AntonPetrov Dec 17, 2024
4527ab9
Merge pull request #172 from r2dt-bio/develop
AntonPetrov Dec 22, 2024
3621be7
Release 2.1
AntonPetrov Feb 2, 2025
9216d9e
Update Readme.md
AntonPetrov Feb 10, 2025
25a40bd
Add R2DT NAR image for the timeline
AntonPetrov Feb 10, 2025
dd7cf01
Update year in docs
AntonPetrov Mar 15, 2025
4a0be6f
refactor: replace os and glob with pathlib for better path handling i…
AntonPetrov May 1, 2025
08b3a26
refactor: replace os.path with pathlib for better path handling
AntonPetrov May 1, 2025
6add630
refactor: update path handling in config.py to use pathlib for better…
AntonPetrov May 1, 2025
cecac5c
fix: simplify path handling in setup and crw_setup functions
AntonPetrov May 1, 2025
81a2866
refactor: replace os.path with pathlib for better path handling in co…
AntonPetrov May 1, 2025
0dddf74
refactor: replace os.path with pathlib for path handling in rfam.py
AntonPetrov May 1, 2025
895ff53
refactor: replace os.path with pathlib for better path handling
AntonPetrov May 1, 2025
3f9eccf
fix: update destination path assignment in RnaArtist class
AntonPetrov May 1, 2025
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17 changes: 10 additions & 7 deletions Readme.md
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**Version 2.1 (2025)**

**[See the R2DT documentation](https://r2dt.readthedocs.io/)** or read the [latest preprint](https://www.biorxiv.org/content/10.1101/2024.09.29.611006v1).
🚀 **[Read the R2DT documentation](https://r2dt.readthedocs.io/)** | 📄 [Latest paper](https://academic.oup.com/nar/article/53/4/gkaf032/8005627).

The [R2DT software](https://github.com/r2dt-bio/R2DT) automatically generates [RNA secondary structure](https://en.wikipedia.org/wiki/Nucleic_acid_secondary_structure) diagrams in consistent, reproducible and recongnisable layouts using a library of templates representing a wide range of RNAs.
[R2DT](https://r2dt.bio/) automatically generates [RNA secondary structure](https://en.wikipedia.org/wiki/Nucleic_acid_secondary_structure) diagrams in **consistent, reproducible and recongnisable layouts** using a library of templates representing a wide range of RNAs.

## Examples

Expand All @@ -14,17 +14,20 @@ The following example visualisations show LSU, SSU, and 5S rRNA, four tRNAs, two

## Getting started

R2DT can be used in a number of ways:
R2DT can be used in multiple ways:

* [Web application](https://rnacentral.org/r2dt) hosted by RNAcentral
* Web application at [r2dt.bio](https://r2dt.bio) or in [RNAcentral](https://rnacentral.org/r2dt)
* [API](https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=r2dt) powered by EMBL-EBI Web Services
* As a command line tool with [Docker](https://www.docker.com), [Singularity](https://sylabs.io/docs/#singularity), or in a bare metal installation

You can also [![open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/RNAcentral/R2DT)
[![open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/RNAcentral/R2DT)

## Citation
## 📄 Citation

If you use R2DT in your work, please consider citing the following paper:
If you use R2DT in your work, please cite one of the following papers:

> **R2DT: a comprehensive platform for visualizing RNA secondary structure**
> [Nucleic Acids Research](https://academic.oup.com/nar/article/53/4/gkaf032/8005627)

> **R2DT is a framework for predicting and visualising RNA secondary structure using templates**
> [Nature Communications](https://www.nature.com/articles/s41467-021-23555-5)
2 changes: 1 addition & 1 deletion docs/conf.py
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

project = "R2DT"
copyright = "2023"
copyright = "2025"
author = "R2DT Team"

# -- General configuration ---------------------------------------------------
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4 changes: 4 additions & 0 deletions docs/editors.md
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Expand Up @@ -64,6 +64,10 @@ Watch RNAcanvas editing R2DT output in action:

<a href="https://ldwlab.github.io/XRNA-React/?source_url=https://raw.githubusercontent.com/RNAcentral/R2DT/develop/docs/files/URS000044DFF6.json" target="_blank" class="btn btn-primary btn-lg">Edit an example structure in xRNA React</a>

:::{tip}
Explore [User Manual](xrna-react-user-guide.md) to watch video tutorials and see it in action.
:::

### Constraint modes

Within a given mode, all nucleotides in a group are automatically selected, upon left-clicking a mouse over a particular nucleotide within the desired region of the RNA scene. Nucleotide positions can further be transformed (edited) according to certain rules specific to a given mode. For example, the position of a single nucleotide can be adjusted in x and y directions; positions of nucleotides in a selected single-stranded region can be adjusted to an equally spaced straight line, or an arch of a given radius; positions of a single base pair can be adjusted in x or y directions, as well as their rotational orientation can also be specified. All selected objects are transformed as rigid bodies, respecing the existing base pairing topology.
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1 change: 1 addition & 0 deletions docs/files/5S_E_coli.json
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127 changes: 127 additions & 0 deletions docs/files/5S_E_coli.xrna
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