private void convertPlantPathwayDiagrams(File dir, boolean saveatxml, String version) {
		Collection<?> diagrams;
		try {
			diagrams = adaptor
					.fetchInstancesByClass(ReactomeJavaConstants.PathwayDiagram);
			SchemaClass cls = adaptor.fetchSchema().getClassByName(
					ReactomeJavaConstants.PathwayDiagram);
			SchemaAttribute att = cls
					.getAttribute(ReactomeJavaConstants.representedPathway);
			adaptor.loadInstanceAttributeValues(diagrams, att);

			for (Object name : diagrams) {
				GKInstance diagram = (GKInstance) name;
				GKInstance pathway = (GKInstance) diagram
						.getAttributeValue(ReactomeJavaConstants.representedPathway);
				GKInstance species = (GKInstance) pathway
						.getAttributeValue(ReactomeJavaConstants.species);
				if (species == null) {
					continue;
				} else {

					try {
						String fileName = AbstractConverterFromReactome
								.getFileName(pathway);
						if (saveatxml) {
							File atxmlfile = new File(dir, fileName + ".atxml");
							atxmlfile.createNewFile();
							r2g3Converter.queryATXML(pathway, atxmlfile);
						}
						File gpmlfile = new File(dir, fileName + ".gpml");
						gpmlfile.createNewFile();
						convertReactomeToGPML(pathway, gpmlfile, version);
					} catch (Exception e) {
						e.printStackTrace();
					}
				}
			}
		} catch (Exception e) {
			e.printStackTrace();
		}

	}