Class PDBConvention

All Implemented Interfaces:

public class PDBConvention extends CMLCoreModule
Implements the PDB convention used by PDB2CML.

This is a lousy implementation, though. Problems that will arise:

  • when this new convention is adopted in the root element no currentFrame was set. This is done when <list sequence=""> is found
  • multiple sequences are not yet supported
  • the frame is now added when the doc is ended, which will result in problems but work for one sequence files made by PDB2CML v.??

What is does:

  • work for now
  • give an idea on the API of the plugable CML import filter (a real one will be made)
  • read CML files generated with Steve Zara's PDB 2 CML converter (of which version 1999 produces invalid CML 1.0)
Egon Willighagen <>
Source code:
Belongs to CDK module: