This script provides a simple means of applying the functional group alerts from the ChEMBL database and property alerts from the RDKit to a set of compounds. As of ChEMBL 23, the database table structural_alerts contains 8 sets of alerts. ChEMBL doesn't have much documentation on the different alert sets.
| Rule Set | Number of Alerts |
|---|---|
| BMS | 180 |
| Dundee | 105 |
| Glaxo | 55 |
| Inpharmatica | 91 |
| LINT | 57 |
| MLSMR | 116 |
| PAINS | 479 |
| SureChEMBL | 166 |
The SMARTS for some alerts are incompatible with RDKit, so I edited them. A complete list of the changes I made is in the file Notes.txt.
- Python 3.7+
- rdkit
Run pip install rd-filters
Directly from GitHub:
pip install git+https://github.com/PatWalters/rd_filters.git
Install locally:
git clone https://github.com/PatWalters/rd_filters
cd rd_filters
pip install .For command-line help, run:
`rd-filter --help`Usage is simple. To filter a file test.smi containing line-by-line SMILES:
rd-filters filter test.smi > filtered.smiIf I want to understand the violations that occurred:
rd-filters report test.smi > report.txt2 config files are used. Both can be passed at the command-line.
alerts.csv- the set of structural alerts You shouldn't have to mess with this unless you want to add your own structural alerts.rules.json- the set of other violations.
As always please let me know if you have questions, comments, etc.
Copyright Pat Walters, August 2018