https://github.com/cmwoodley/plip_to_2d
Science Score: 13.0%
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○CITATION.cff file
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✓DOI references
Found 1 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (11.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: cmwoodley
- License: gpl-3.0
- Language: Jupyter Notebook
- Default Branch: main
- Size: 3.4 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
PLIP To 2D
A package to run PLIP analysis on a ligand bound pdb and generate a 2D representation of binding interactions.
Installation
- Clone or download this repo
git clone https://github.com/cmwoodley/plip_to_2D.git - Create environment and install dependencies
conda create -n PLIP_2D -c conda-forge openbabel plip pandas numpy pymol-open-source conda activate PLIP_2D pip install pycairo
Running analysis
- By command line
plip2D.py provides interactive commandline functionality. Running analysis is as simple as: ``` python .\plip2D.py -f .\examplepdb\5ml3.pdb ``` **utils.py must be in the same folder as plip2D.py**
Output of python .\plip_2D.py -h:
```
usage: plip2D.py [-h] -f FILE [--pymol PYMOL] [--canvasheight CANVASHEIGHT] [--canvaswidth CANVASWIDTH]
[-o OUT_FILE] [-y ANALYSEALL]
Generate 2D and 3D representations from X-ray or simulated protein-ligand binding poses
options: -h, --help show this help message and exit -f FILE, --file FILE pdb for analysis --pymol PYMOL Save pymol session --canvasheight CANVASHEIGHT Output Canvas Height --canvaswidth CANVASWIDTH Output Canvas Width -o OUTFILE, --outfile OUTFILE Output name - must be a .png or .svg file -y ANALYSEALL, --analyseall ANALYSEALL Analyse all small molecules ``` 2. As an importable function See example jupyter notebook.
Referencing
If using this code in your work, please cite this repo, PLIP and RDKIT:
Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294
RDKit: Open-source cheminformatics; http://www.rdkit.org
Limitations and Issues
Label placement in 2D interaction diagram isn't perfect - the ability to output an SVG file editable in vector graphics software somewhat gets around this.
Owner
- Login: cmwoodley
- Kind: user
- Repositories: 1
- Profile: https://github.com/cmwoodley