SmartFilter-API

API code for SmartFilter with Flasgger Docs.

Requirements

• Docker
• Docker Compose

Documentation

The /apidocs/ page provides detailed information on every API call available.

• Production: https://chiltepin.health.unm.edu/smartsfilter/apidocs/
• Local: http://localhost:8000/apidocs/

UI Repository: SmartFilter-UI

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Screenshot

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Setup (Development)

1. git clone https://github.com/bivek2003/SmartFilter-API.git
2. cd SmartFilter-API
3. Copy .env.dev..example to .env (in the ./ folder)
4. Edit the .env credentials as needed
5. Run:

   docker-compose -f compose-development.yml up --build
   
   

Setup (Production on Chiltepin)

1. Copy .env.prod.example to .env
2. Fill in/edit the .env credentials as needed
3. Update apache2 config:
   • Create a new file for apache2 config: /etc/apache2/sites-available/smartsfilterapi.conf
   • Add the following line to /etc/apache2/apache2.conf:

     Include /etc/apache2/sites-available/smartsfilterapi.conf
     

   • Update the apache2 virtual config file: /etc/apache2/sites-enabled/000-default.conf
   • Run config check: sudo apachectl configtest
   • (If config check passed) reload apache: sudo systemctl reload apache2
4. (If server was previously up): docker-compose -f compose-production.yml down
5. Run docker-compose -f compose-production.yml up --build -d

API Endpoints

1. /get_matchcounts Description: Counts matches of a single SMARTS pattern against a list of SMILES strings.

Query Parameters:

• smarts: The SMARTS string to match.

• SMILES: Comma or space-separated list of SMILES.

2. /get_matchFilter Description: Filters molecules that match a single SMARTS pattern.

Query Parameters:

• smarts: The SMARTS pattern to apply.
• SMILES: List of molecules to filter.

3. /get_multi_matchcounts Description: Counts matches of multiple SMARTS patterns against a list of SMILES strings.

Query Parameters:

• smarts: Comma/space-separated SMARTS patterns.

• SMILES: List of molecules to match.

4. /get_multi_matchfilter Description: Filters molecules that match all of the provided SMARTS patterns.

Query Parameters:

• smarts: Comma/space-separated SMARTS patterns.
• SMILES: List of molecules to filter.

5. /get_filterpains Description: Filters molecules against PAINS (Pan Assay Interference Compounds) substructure patterns. Returns the filtered molecules and which PAINS patterns were matched.

Query Parameters:

• SMILES: List of SMILES strings to evaluate.

Libraries Used

This API was developed with the help of the rdkit-tools library for SMARTS pattern handling and molecular analysis.

Thank you to the rdkit-tools developers for providing this powerful library.

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Author / Support

Author / Support: Jeremy Yang, Jack Ringer
Developer: Bivek Sharma Panthi

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Acknowledgment

This API was developed based on concepts and architecture inspired by the Badapple2-API repository:
https://github.com/unmtransinfo/Badapple2-API