code: public static ReasonerAtomicQuery atomic(ReasonerAtomicQuery q, ConceptMap sub){
          return q.withSubstitution(sub).inferTypes();
      }
docs: create an atomic query by combining an existing atomic query and a substitution
  @param q base query for substitution to be attached
  @param sub (partial) substitution
  @return atomic query with the substitution contained in the query