Groovy CDK-JChemPaint
Groovy
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.gitignore
README.md
cdk-1.5.4.jar
cdk-jchempaint-31.jar
dumpParameters.groovy
greyBGMol.groovy
renderAromaticity.groovy
renderAtomNumbers.groovy
renderImplicitHydrogens.groovy
renderIsotopes.groovy
renderMol.groovy
renderRS.groovy
renderReaction.groovy
renderSelection.groovy
svgMol.groovy
swing.groovy

README.md

Groovy JChemPaint

Disclaimer: the code examples in this repository require the CDK-JChemPaint patch, and not the JChemPaint 3.0 applet code. The required jars are provided in this repository.

This is the repository matching the scripts listed in the following blog posts:

Running Groovy from the command line

The below commands require you have a checkout of this repository. You can clone it from the command line with something in the line of:

$ git clone git://github.com/egonw/groovy-jcp.git
$ cd groovy-jcp

I am not sure how this works on OS/X or Windows (please let me know!), but you can run the scripts provided here on GNU/Linux systems with the following commands.

For the following scripts, you can use a stock CDK release:

$ export CLASSPATH=cdk-1.5.4.jar
$ groovy script.groovy

Where script.groovy is one of:

  • renderMol.groovy
  • dumpParameters.groovy
  • renderRS.groovy
  • swing.groovy
  • greyBG.groovy
  • renderAromaticity.groovy
  • renderAtomNumbers.groovy
  • renderImplicitHydrogens.groovy
  • renderIsotopes.groovy

For the editor interaction, selection highlighting, reaction rendering, and SVG output you need to rest of the CDK-JChemPaint patch:

$ export CLASSPATH=cdk-1.5.4.jar:cdk-jchempaint-31.jar
$ groovy script.groovy

where script.groovy is one of the remaining scripts provided in this repository:

  • svgMol.groovy
  • renderReaction.groovy
  • renderSelection.groovy