fix iterative algorithm which found positions between atoms. now it recursively
add special #reference? method to atoms classes
pre fix
#used?
graphs of dependent species presented as directed graphs where each bond or position between two atoms of one specie presented as two edges in both directions, but if atom has relations to some another atom (which isn't used in current specie) then relation take plase only in one direction (from used atom to unused atom); atom properties now doesn't contain position relations
uncomment dependent base specie constructor
rename are_atoms_different? to atoms_different?
fix new line
Merge pull request #5 from newmen/nes

Да здравствует Nes