From: Miguel <mt...@mt...> - 2003-08-17 17:04:18
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I just checked in code which is partially successful in displaying files which are read into the CDK library. You can run this by executing ./jmol -Dcdkmodel This will tell Jmol to use the cdk.io.ReaderFactory instead of using the jmol.io package. I say "partially successful" because the following atom properties are not being defined by cdk: vanderwaals radius covalent bonding radius atomicNumber (at least for .xyz files) atom Color Therefore, they are showing up in Jmol as pink atoms which are highly connected. More details: - the Jmol rendering and script execution is now packaged under org.openscience.jmol.viewer - The former jmol.DisplayControl is now called jmol.viewer.JmolViewer - The adapter interface for connecting an external molecular representation is jmol.viewer.JmolModelAdapter - the Jmol implementation of this is jmol.adapters.DeprecatedJmolModelAdapter - the Cdk implementation of this is jmol.adapters.CdkJmolModelAdapter From the Jmol side, all changes to get Jmol to properly work with cdk should be restricted to jmol/adapters/CdkJmolModelAdapter.java Miguel |