cheminee

Crates.iocheminee
lib.rscheminee
version0.1.19
sourcesrc
created_at2022-12-16 19:55:23.885032
updated_at2024-04-02 20:12:59.99789
descriptionMolecule indexing and search
homepagehttps://rdkit-rs.github.io
repositoryhttps://github.com/rdkit-rs/cheminee
max_upload_size
id739117
size235,231
Javier Pineda (JJ-Pineda)

documentation

https://github.com/rdkit-rs/cheminee

README

Cheminée

The chemistry search stack. Index chemical structures and include arbitrary extra properties. Fast to search and your callers don't need RDKit.

  • RDKit provides the smarts
  • Rust provides the type safety and relative ease of use

See rdkit-sys for more on how the bindings work.

Tested on Rust Stabe 1.76 (rustup default 1.76)

Intended Functionality

Cheminée is intended to work via CLI (e.g. for diagnostics) and API endpoints. "Substructure search" is the first intended functionality, but Cheminée will eventually support "superstructure search", "similarity search", and exact matches. Aside from structure searching, the API also supports standardization of SMILES in bulk as well as indexing via Tantivy. Users can also search for compounds by RDKit chemical descriptors (e.g. "exactmw", "NumAtoms", etc).

The API

To boot up the API server, you can run the following:

cargo run --color=always --release --package cheminee --bin cheminee -- rest-api-server

The simplest way to test out the API is by going to localhost:4001 in your browser and testing out the functionality of the different endpoints.

This repo is also set to automatically update a ruby gem whenever a new release is published. That gem is "cheminee-ruby". This gem is particularly helpful for interacting with the API in a ruby-friendly, programmatic environment.

See cheminee-ruby for more information into how the gem works.

The CLI

Assuming compounds are already present in an index path, you can search by:

Basic Search

For example:

 cargo run -- search -i "/tmp/cheminee/scaffolds-index0" -q "exactmw: [10 TO 10000] AND NumAtoms: [8 TO 100]" -l 10

Here, "i" refers to the index path, "q" refers to the composite query of chemical descriptor values, and "l" refers to the number of desired results.

Substructure Search

For example:

cargo run -- substructure-search -i /tmp/cheminee/scaffolds-index0 -s CCC -r 10 -t 10 -e "exactmw: [20 TO 200]"

Similar to basic search, "i" refers to the index path, "s" refers to the query SMILES, "r" refers to the number of desired results, "t" refers to the number of tautomers to be used for the query SMILES (if applicable), and "e" refers to the "extra query" which is a composite query for chemical descriptors as in the basic search implementation.

Docker builds

The cross project has a nice cross compiler docker image but it uses the old Ubuntu 16.04. We should try upgrading to Ubuntu 20.04 and see how it works for our case.

Logging in to ghcr.io:

# generate a personal access token in your github settings
echo ghp_123 | docker login ghcr.io -u your_gh_username --password-stdin

You'll want to build and run the multi-stage docker container:

docker build . -f Dockerfile.multi-stage --tag cheminee
docker run --rm --name cheminee cheminee

Cutting A New Release

cargo release patch --tag-prefix='' --execute
Commit count: 249

cargo fmt