CDK Descriptor Calculator GUI (v 1.4.2)

(screenshot, screenshot)

Features

  1. Automatically detects descriptor classes defined in the CDK QSAR descriptor dictionary
  2. Groups of descriptors and individual descriptors can be selected for evaluation
  3. Input can be SDF or SMI formats
  4. Output can be a variety of delimited text formats, annotated SDF or ARFF
  5. Can evaluate fingerprints (hashed, MACCS, EState)
  6. See here for a summary overview of the available descriptors and their names. Note that since the list is generated from the nightly build, there may be some listed that are ot available in the current GUI

Download

  1. CDKDescUI.jar (1.4.2) - with all dependencies included
  2. CDKDescUIsmall.jar (1.4.2) - contains only the GUI program. Thus you will need to have the CDK libraries and their associated dependencies in your CLASSPATH
  3. Sources

Updates in the new version

Building the sources

The project was written using JDK 1.5. You'll also probably need to change the paths in cdkdescui.properties. After that the available ant targets are
  1. clean - self-explanatory
  2. jar - create a jar file containing the application. Requires the CDK libraries and depdendencies to be in the CLASSPATH
  3. bigjar - creates a standalone jar file with all dependencies included

Stuff to do

  1. Get the preferences to work
  2. Add icons to the descriptors indicating whether they are 3D or 2D
  3. Add timeout settings
  4. Implement the plugin mechanism
  5. Get CML output working
  6. Add descriptor reduction
  7. Report descriptor calculation errors
  8. Descriptor descriptions (help file)
  9. In the case of SMI formatted molecules add ability to evaluate only topological descriptors if 2D coords are available or all descriptors if 3D coords can be generated.