code: public static IAtom getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon) {
          IAtom closestAtom = null;
          IAtom currentAtom;
          double smallestMouseDistance = -1;
          double mouseDistance;
          double atomX;
          double atomY;
          for (int i = 0; i < atomCon.getAtomCount(); i++) {
              currentAtom = atomCon.getAtom(i);
              atomX = currentAtom.getPoint2d().x;
              atomY = currentAtom.getPoint2d().y;
              mouseDistance = Math.sqrt(Math.pow(atomX - xPosition, 2) + Math.pow(atomY - yPosition, 2));
              if (mouseDistance < smallestMouseDistance || smallestMouseDistance == -1) {
                  smallestMouseDistance = mouseDistance;
                  closestAtom = currentAtom;
              }
          }
          return closestAtom;
      }
docs: Returns the atom of the given molecule that is closest to the given
  coordinates.
  See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
  
  @param  xPosition  The x coordinate
  @param  yPosition  The y coordinate
  @param  atomCon    The molecule that is searched for the closest atom
  @return            The atom that is closest to the given coordinates