https://github.com/brsynth/biorgroup
Systematic expansion of R-group for ChEBI molecules from the RHEA database
Science Score: 39.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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○Scientific vocabulary similarity
Low similarity (5.4%) to scientific vocabulary
Keywords
Repository
Systematic expansion of R-group for ChEBI molecules from the RHEA database
Basic Info
Statistics
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 1
Topics
Metadata Files
README.md
BioRGroup dataset
https://doi.org/10.57745/V3URYA
Installation
sh
conda env create --file recipes/worklow.yaml --name biorgroup
pip install --no-deps -e .
Build dataset
1 - Download PubChem
sh
python -m biorgroup.pubchem.download \
--output-pubchem-dir <output dir> \
--output-pubchem-db <output sql database>
2 - Download Rhea
sh
python -m biorgroup.rhea.download \
--output-rhea-dir <output dir> \
--parameter-release-int <int>
3 - R-group search
sh
snakemake \
-p \
-j 48 \
-c 48 \
--workflow-profile template/biorgroup \
-s ./src/biorgroup/rgroup/Snakefile \
--use-conda \
--latency-wait 5 \
--rerun-incomplete \
--config input_depot_str=./src/biorgroup/rgroup input_chebi_csv=rhea-chebi-smiles.csv input_pubchem_db=pubchem.db output_dir_str=chebi parameter_search_timeout_int=10
Dataset overview
The Snakemake workflow produces a csv.gz file containing:
| column name | type |
| --- | --- |
| smilesrhea | str|
| chebi | List[str] |
| numheavyatoms | int |
| exactmolwt | float |
| coresuperstructuresmiles | List[str] |
| coresuperstructurepubchemcid | List[List[str]] |
| rgroupextendedsmiles | List[str] |
| rgroupextendedpubchem_cid | List[List[str]] |
Owner
- Name: BioRetroSynth
- Login: brsynth
- Kind: organization
- Website: http://www.jfaulon.com
- Repositories: 33
- Profile: https://github.com/brsynth
Our group is interested in synthetic biology and systems metabolic engineering in whole-cell and cell-free systems.
GitHub Events
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- Delete event: 1
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- Pull request event: 1
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Last Year
- Delete event: 1
- Push event: 1
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- Create event: 3
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 0
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- guillaume-gricourt (1)