CDK Depict is a Java 25 Spring MVC application for rendering molecules and reactions from SMILES, molfiles, and mapped reaction inputs. In addition to plain depiction it supports SMARTS highlighting, reaction-center annotation, SMIRKS-based transforms, and reaction mapping through RDT (Reaction Decoder Tool).

The project is organized as a multi-module Maven build:

• cdkdepict-lib: core depiction logic, HTTP endpoints, reaction mapping, and tests
• cdkdepict-webapp: Spring Boot WAR packaging plus the static depict, react, and map frontends
• docker: container build files and container-specific notes
• docs: developer notes for endpoint contracts, RDT integration, and the private-to-public mirror workflow

• Depict molecules and reactions in svg, pdf, png, jpg, and gif
• Highlight SMARTS matches and explicit atom/bond subsets
• Annotate atom numbers, atom maps, CIP labels, and reaction-center changes
• Apply SMIRKS transforms through /react/{style}/{fmt}
• Map reaction SMILES with RDT through /map/{style}/{fmt} and /map/smi
• Serve a simple static UI with no frontend build step

• Java 25
• Maven 3.9+
• A local com.bioinceptionlabs:rdt:4.0.0 artifact built with Java 25

The CI workflow installs RDT from a pinned ReactionDecoder commit before building this repo. If your local machine does not already have a compatible RDT artifact in ~/.m2, install it first:

RDT_REF=0d6632251108e7a8f625d15c60607a136093c4d8
git clone https://github.com/asad/ReactionDecoder.git /tmp/ReactionDecoder
git -C /tmp/ReactionDecoder checkout --detach "${RDT_REF}"
mvn -B -f /tmp/ReactionDecoder/pom.xml clean install -DskipTests=true

If you previously installed an incompatible RDT build, remove ~/.m2/repository/com/bioinceptionlabs/rdt/4.0.0 and reinstall it with Java 25.

Build the full project:

mvn -B clean test package

Run the bootable WAR locally:

java -Dserver.port=8081 -jar cdkdepict-webapp/target/cdkdepict-webapp-*.war

There is also a tiny helper script:

./run_depict.sh

By default the UI is available at http://localhost:8081/depict.html when using the direct java command, or at port 8001 when using run_depict.sh.

Main routes:

• GET /depict/{style}/{fmt}?smi=...
• GET /react/{style}/{fmt}?smi=...&smirks=...
• GET /map/{style}/{fmt}?smi=...
• GET /map/smi?smi=...

Examples:

/depict/cot/svg?smi=CCO
/depict/bot/svg?smi=[CH3:1][CH3:2]>>[CH2:1]=[CH2:2]&annotate=colmap
/react/cot/svg?smi=CCO&smirks=[C:1]-[O:2]>>[C:1]-[N:2]
/map/smi?smi=CC(=O)O.OCC>>CC(=O)OCC.O

The detailed depict endpoint contract, supported styles, query parameters, and response behavior live in docs/depict-endpoint-agent.md.

At a high level:

• DepictController owns the main HTTP API and nearly all depiction, reaction-transform, and reaction-mapping logic.
• MolOp contains chemistry-specific helpers such as radical and dative-bond handling.
• Context wires Spring MVC resources and view resolution.
• Application is the Spring Boot entrypoint for the bootable WAR.
• cdkdepict-webapp/src/main/webapp/WEB-INF/static/ holds the static HTML, CSS, and small jQuery-based frontends for depict, react, and map modes.

Two architecture details matter for contributors:

• The "library" module is not just chemistry helpers. It also contains the HTTP controller and most request-handling logic.
• The map flow delegates reaction mapping to RDT, then feeds the mapped reaction back through the same depiction pipeline used by the normal depict endpoint.

For deeper background on the RDT integration, see docs/RDT_CDK_INTEGRATION.md.

• CI is defined in .github/workflows/maven.yml and uses Java 25 plus a pinned ReactionDecoder checkout.
• The private repo can publish a sanitized public mirror with scripts/publish_public_mirror.sh. See docs/public-mirror.md.
• Container notes live in docker/README.md.

Useful local commands:

mvn -B test
mvn -B -DskipTests compile
mvn -B -Dtest=DepictControllerTest test

Current tests live in cdkdepict-lib:

• DepictControllerTest: endpoint behavior and rendering-oriented coverage
• ReactionCenterDetectionTest: reaction-center detection and fallback logic
• MolOpTest: lower-level chemistry helpers

There are currently no dedicated cdkdepict-webapp tests.

This project is licensed under LGPL v2.1 or later. See LICENSE.