@classmethod
get_prop_adjacency_matrix(cls, atoms, bonds): 

Returns the adjacency matrix for the molecule

• bonds: Iterable[int]

• :returns: _

@classmethod
get_prop_connectivity(cls, atoms, bonds): 

Returns the adjacency matrix for the molecule

• bonds: Iterable[int]

• :returns: _

@classmethod
get_prop_fragments(cls, atoms, bonds): 

Returns the fragments for the molecule

• bonds: Iterable[int]

• :returns: _

@classmethod
get_prop_zmat_ordering(cls, atoms, bonds): 

Gets a guessed Z-matrix ordering for the molecule with connectivity defined by bonds based on the following:

1. Fragments are separated out
2. The atom with the highest degree of connectivity in each fragment is chosen as the fragment “label”
3. Fragments are ordered by connectivity of the label from high to low
4. Fragment labels reference each other with: a) the second label on the x-axis b) the 3rd in the xy-plane c) all others relative to the first three
5. All other atoms are sorted first by fragment label, then by connection to the fragment label, and then by connectivity
6. Atoms reference each other based on the following: a) if the atom has one bond: i) the atom it is bound to ii) the lowest-connectivity atom that one is bound to iii) the second-lowest-connectivity atom OR the next fragment label b) if the atom has two bonds: i) the highest-connectivity atom it is bound to ii) the lowest-connectivity atom it is bound to iii) the lowest-connectivity atom (i) is bound to c) if the atom has three bonds: i) the highest-connectivity atom it is bound to ii) the lowest-connectivity atom it is bound to iii) the second-highest connectivity atom it is bound to if any of these atoms do not exist, the fragment labels will be used in their place
   • bonds: Any

   • :returns: _

@classmethod
get_prop_guessed_bonds(cls, mol, tol=1.05, guess_type=True, covalent_radius_scaling=1.1): 

Guesses the bonds for the molecule by finding the ones that are less than some percentage of a single bond for that pair of elements

• :returns: _