cmpstd

This project demonstrates a simple compound standardization service that can be run on the cloud.

The service is written in C++ and uses gRPC for the RPC implementation and RDKit for the simple standardization functionality. In practice a production system would most likely have a more elaborate standardization procedure. However, for the use case here we just use the simplest StandardizeSmiles call in RDKit.

The service can be build in Docker ensuring that it can be deployed on a cloud system for production use.

Finally, an illustrative Python client has been written to illustrate how this can be incorporated into back end data processing workflows.

Simple Example Service

The build is demonstrated in a multistage Dockerfile so that you don't need to build all the code to run the server. A simple example is provided in the simple directory. To build and run this in docker build with

docker build --tag cmpstd-server --target simple . # build the deployment application

Running the application can then be done using port forwarding.

docker run -it -p 9999:9999 --tag cmpstd-service

Then we can use a program like insomnia or grpcurl to run a simple query against the service.

Modular Example Service

This modular build replicates the functionality of the simple build but splits the functionality into different modules, which is better suited to a more complex tool. A build of this in the Dockerfile is in the modular build.

docker build --tag cmpstd-server --target modular . # build the deployment application
docker run -it -p 9999:9999 --tag cmpstd-service

Example Python client