code: public static boolean isCisTrans(IAtom firstOuterAtom, IAtom firstInnerAtom, IAtom secondInnerAtom,
              IAtom secondOuterAtom, IAtomContainer ac) throws CDKException {
          if (!isValidDoubleBondConfiguration(ac, ac.getBond(firstInnerAtom, secondInnerAtom))) {
              throw new CDKException("There is no valid double bond configuration between your inner atoms!");
          }
          boolean firstDirection = isLeft(firstOuterAtom, firstInnerAtom, secondInnerAtom);
          boolean secondDirection = isLeft(secondOuterAtom, secondInnerAtom, firstInnerAtom);
          return firstDirection == secondDirection;
      }
docs: Says if two atoms are in cis or trans position around a double bond.
  The atoms have to be given to the method like this:  firstOuterAtom - firstInnerAtom = secondInnterAtom - secondOuterAtom
  
  @param  firstOuterAtom    See above.
  @param  firstInnerAtom    See above.
  @param  secondInnerAtom   See above.
  @param  secondOuterAtom   See above.
  @param  ac                The atom container the atoms are in.
  @return                   true=trans, false=cis.
  @exception  CDKException  The atoms are not in a double bond configuration (no double bond in the middle, same atoms on one side)