tmoerman / sourire

A minimal web API rendering SMILES molecules

Sourire

"D'un enfant le sourire - Agrandit l'univers" -- Charles de Leusse

In the grand tradition of Clojure libraries we begin with an irrelevant quote.

Sourire is a minimal web API on top of the Smiles molecule rendering function of the GGA Software Indigo cheminformatics toolkit.

Usage

[base-url]/molecule/[url-encoded-smiles-string]?indigo-param-name=param-value

Smiles notation uses characters that are considered unsafe for use in URLs. Therefore the API only accepts smiles strings in URL encoded format.

Pull and run Docker image

Sourire is automatically built as a Docker image and available from the Docker registry.

Pull the image from the registry:

docker pull thomasjmoerman/sourire

Launch the container as a daemon bound to host port 9999 (or another port of your choice):

docker run -d -p 9999:8080 thomasjmoerman/sourire:latest

Build and run manually

Use leiningen to create a runnable jar (assuming you are in the project folder):

$ lein create-standalone

Launch the application:

java -jar target/sourire-0.1.0-SNAPSHOT-standalone.jar

You can provide a Java argument to specify the web server port:

java -jar target/sourire-0.1.0-SNAPSHOT-standalone.jar :port 8080

REPL

You can run a Clojure REPL supporting the famous Stuart Sierra Workflow, Reloaded pattern.

$ lein user-repl
WARNING: user-level profile defined in project files.
nREPL server started on port 8777 on host 127.0.0.1
REPL-y 0.3.0
Clojure 1.7.0-alpha5
    Docs: (doc function-name-here)
          (find-doc "part-of-name-here")
  Source: (source function-name-here)
 Javadoc: (javadoc java-object-or-class-here)
    Exit: Control+D or (exit) or (quit)
 Results: Stored in vars *1, *2, *3, an exception in *e

user=> (launch)

Examples

Vitamin B1

Smiles code: OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2

Sourire URL: http://localhost:8000/molecule/OCCc1c%28C%29%5Bn%2B%5D%28%3Dcs1%29Cc2cnc%28C%29nc%28N%292?render-comment=Vitamin%20B1

Glucose

Smiles code: OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)1

Sourire URL: http://localhost:8000/molecule/OC%5BC%40%40H%5D%28O1%29%5BC%40%40H%5D%28O%29%5BC%40H%5D%28O%29%5BC%40%40H%5D%28O%29%5BC%40%40H%5D%28O%291?render-comment=glucose

Caffeine

Smiles code: CN1C=NC2=C1C(=O)N(C)C(=O)N2C

Sourire URL: http://localhost:8000/molecule/CN1C%3DNC2%3DC1C%28%3DO%29N%28C%29C%28%3DO%29N2C?render-comment=caffeine

Oenanthotoxin

Smiles code: CCC[C@@H](O)CC\\C=C\\C=C\\C#CC#C\\C=C\\CO

Sourire URL: http://localhost:8000/molecule/CCC%5BC%40%40H%5D%28O%29CC%5CC%3DC%5CC%3DC%5CC%23CC%23C%5CC%3DC%5CCO?render-comment=oenanthotoxin

License

The Do Whatever The Hell You Like License.

I am not liable for accidentally launched intercontinental ballistic missionaries.

sourire's Issues

SMILES loader errors

http://localhost:5555/molecule/OCCN1CCN%28CC%2FC%3DC%5C2c3ccccc3Sc4ccc%28Cl%29cc%5C24%29CC1

returns a bad request response:

SMILES loader: cycle 2: closing bond direction does not match pending bond direction

Look into whether GGA Indigo accepts a parameter to suppress this kind of errors and renders a "best effort" molecule.

Image size parameter

It would be nice to have a parameter to set the height or width of the image or both.
In case of both it would resize the image according to the lowest value.

Sanitize url parameter values

It is possible to crash the renderer by supplying parameters without values e.g.:
http://localhost:8000/molecule/CN1CCC%5BC%40H%5D1c2cccnc2?render-image-width=300&render-image-height

Sanitize them (i.e. no nil values) before passing through as Indigo options.