Jmol viewer full#
The full source code can be retrieved from: CDKIntegration2.java (for AtomContainer) and CDKIntegration3.java (for Crystal). Or, a Crystal in which the unit cell is rendered too. Instead of an AtomContainer, you can also pass a ChemFile for which the ChemSequence is interpreted a sequence of Jmol models. In addition, local structure files can be viewed. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). (This requires the CdkJmolAdapter from SVN, or the first release after 10.00). Jena3D Viewer (Jena3D) - Jena3D is a web-based interactive viewer for three-dimensional biopolymer structures, based on Jmol. The source code for this method is quite similar to that above. This CdkJmolAdapter can be used to interface between CDK and Jmol when integrating the two. These JmolAdapters convert internal representations - CDK or Jmol, respectively - into an API (the JmolAdapter) used by the JmolViewer. The JmolViewer can be instantiated such that it uses the CdkJmolAdapter, instead of the SmarterJmolAdapter. The full source code can be retrieved from Jmol SVN: CDKIntegration.java. JmolViewer viewer = jmolPanel.getViewer() There are many formats that match these criteria, and the two formats mentioned earlier are two examples. It assumes that CDK has a writer for this common format, and that Jmol has a reader for this format. This method defines the interface between CDK and Jmol as a plain text file format, e.g. This page will introduce ways in which Jmol can be integrated into CDK programs, so that the first can be used as a 3D viewer for the CDK data structures.
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