coordinates of genes should be normalized differently than proteins

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java

@@ -445,8 +445,8 @@ public class ModelContructor {
       if (gene.getModificationResidues().size() > 0) {
         CellDesignerAliasConverter converter = new CellDesignerAliasConverter(species, true);
         for (ModificationResidue mr : gene.getModificationResidues()) {
-          double angle = converter.getAngleForPoint(species, mr.getPosition());
-          mr.setPosition(converter.getResidueCoordinates(species, angle));
+          double angle = converter.getCellDesignerPositionByCoordinates(mr);
+          mr.setPosition(converter.getCoordinatesByPosition(species, angle));
         }
       }