bool OEExpandSuperAtoms(OEMolBase &mol)
The OEExpandSuperAtoms
function expands (or instantiates) the
recognized super-atoms in a connection table. Superatoms are commonly
found in MDL mol files and some SMILES variants as a way of specifying
a common functional group by a single superatom. This function replaces
each pseudo atom with the set of atoms and bonds it represents.
Currently this function expands the 20 naturally occuring amino acids and ``Abu'' (2-amino butyric acid). Additional superatoms, such as common protecting groups, may be supported in the future. Unrecognized superatoms are unmodified by this function.
This function determines connectivity for multi-valent superatoms from
2D co-ordinates when available, and failing that from atom indices, i.e.
the order in which atoms are created. These heuristics allow correct
interpretation of most common uses of superatoms, such as the SMILES
variant ``[Ala][Asn][Thr]
''.