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Open Source Science

https://github.com/cdk/depict

SMILES Depiction Generator

https://github.com/cdk/depict

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

SMILES Depiction Generator

Basic Info
  • Host: GitHub
  • Owner: cdk
  • License: lgpl-2.1
  • Language: Java
  • Default Branch: master
  • Homepage:
  • Size: 426 KB
Statistics
  • Stars: 55
  • Watchers: 9
  • Forks: 16
  • Open Issues: 9
  • Releases: 13
Created over 10 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

CDK Depict

A web application for generating chemical structure depictions from SMILES.

https://www.simolecule.com/cdkdepict

Docker

An image is available on DockerHub, https://hub.docker.com/r/simolecule/cdkdepict/. To launch a CDK Depict web serivce running on 8081:

$ docker run -p 8081:8080 simolecule/cdkdepict:latest

Prepacked release

You can download prebuilt release from GitHub, this is a runnable WAR and will launch a standalone server using Spring Boot:

Build

$ mvn clean install

This generates a web archive (WAR) and a runnable java archive (JAR) in the target directory. The WAR file can be deployed to an application server (e.g. TomCat, Jetty, GlassFish, JBOSS) whilst the JAR launches it's own embedded server.

$ target/cdkdepict-1.10.war

Standalone Bootable App

When launching the embedded application the HTTP port is optional (default: 8080). Run the following command and access the site 'http://localhost:8081' by web browser.

$ java -Dserver.port=8081 -jar ./cdkdepict-webapp/target/cdkdepict-webapp-10.war

Caching

When running your own CDK Depict it's useful to enable caching of the generated content. To enable caching you need to add the following setting to either the WebApp or TomCat's global context.xml:

<Valve className="org.apache.catalina.authenticator.BasicAuthenticator" disableProxyCaching="false" />

Docker container

A docker container (using alpine linux) can be built and run as follows:

$ cd docker && ./build.sh $ docker run -p 8180:8080 cdkdepict

Libraries

License

LGPL v2.1 or later

Owner

  • Name: The Chemistry Development Kit
  • Login: cdk
  • Kind: organization

Chem- and bioinformatics library

GitHub Events

Total
  • Create event: 3
  • Issues event: 7
  • Release event: 1
  • Watch event: 1
  • Delete event: 1
  • Issue comment event: 11
  • Push event: 5
  • Pull request event: 3
  • Fork event: 4
Last Year
  • Create event: 3
  • Issues event: 7
  • Release event: 1
  • Watch event: 1
  • Delete event: 1
  • Issue comment event: 11
  • Push event: 5
  • Pull request event: 3
  • Fork event: 4

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • swamidass (1)
  • DavidWalz (1)
  • nbehrnd (1)
  • JonasSchaub (1)
  • IngvarLa (1)
  • nbosc (1)
  • schymane (1)
  • vthimmakondu (1)
Pull Request Authors
  • mjw99 (3)
  • dependabot[bot] (1)
  • johnmay (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1) java (1)

Dependencies

cdkdepict-lib/pom.xml maven
  • org.springframework:spring-webmvc provided
  • com.simolecule.centres:centres-cdk 1.1
  • org.openscience.cdk:cdk-depict ${cdk.version}
  • org.openscience.cdk:cdk-silent ${cdk.version}
  • org.openscience.cdk:cdk-smarts ${cdk.version}
  • org.slf4j:slf4j-api 1.7.36
  • junit:junit test
cdkdepict-webapp/pom.xml maven
  • org.openscience.cdk:cdkdepict-lib 1.9.2
  • org.springframework:spring-webmvc
pom.xml maven
  • junit:junit 4.13.2
  • org.openscience.cdk:cdk-atomtype 2.8-SNAPSHOT
  • org.openscience.cdk:cdk-ctab 2.8-SNAPSHOT
  • org.openscience.cdk:cdk-interfaces 2.8-SNAPSHOT
  • org.openscience.cdk:cdk-io 2.8-SNAPSHOT
  • org.openscience.cdk:cdk-ioformats 2.8-SNAPSHOT
  • org.openscience.cdk:cdk-isomorphism 2.8-SNAPSHOT
  • org.openscience.cdk:cdk-silent 2.8-SNAPSHOT
  • org.openscience.cdk:cdk-smiles 2.8-SNAPSHOT
  • org.openscience.cdk:cdk-standard 2.8-SNAPSHOT
  • org.springframework:spring-webmvc 5.3.21
.github/workflows/maven.yml actions
  • actions/checkout v3 composite
  • actions/setup-java v3 composite
docker/Dockerfile docker
  • maven 3.5-jdk-8-alpine build
  • openjdk 8u212-jre-alpine build