code: private void saveMatrix() {
  
  		for (String chainId : currentChainIDs) {
  			BiologicalAssemblyTransformation transformation = new BiologicalAssemblyTransformation();
  			transformation.setRotationMatrix(currentMatrix.getArray());
  			transformation.setTranslation(shift);
  			transformation.setId(String.valueOf(modelNumber));
  			transformation.setChainId(chainId);
  			transformations.add(transformation);
  		}
  
  		if (!transformationMap.containsKey(currentBioMolecule)) {
  			BioAssemblyInfo bioAssembly = new BioAssemblyInfo();
  			bioAssembly.setId(currentBioMolecule);
  			bioAssembly.setTransforms(transformations);
  			transformationMap.put(currentBioMolecule,bioAssembly);
  		}
  	}
docs: Saves transformation matrix for the list of current chains