3
N,1,3,0,1,2
O,1,2,0,1,1
S,1,2,0,1,4


NOTE The first number in this file is the number of atoms. That tells Combimol how many lines to input.  Everything below the last atom (i.e. these lines) is ignored.
Columns: 
* First – letter code for atom
* Second and third – minimum and maximum number of bonds for that atom 
* Fourth – ‘0’ if this is a default element in the SMILES specification, ‘1’ otherwise
* Fifth – can it support double bonds? 1= yes, 0=no
* Sixth – how many atoms can there be between this atom and a carbon atoms for a stable molecule? 0 = this must be bonded to carbon. [NB the non-zero number currently does not matter here – one day I will implement a more sophisticated chain-counting algorithm to use the >0 values in this column.]

For internal coding, some groups of atoms are given atom designations starting with Q (there are no real elements whose letter abbreviations start with Q). 
Qd – S=O
Qe – S=S
Qf – S(=O)=O
Qg – S(=S)=O
Qh - P=O
Qi - P=S
Qk – N=N

The first atom of these SMILES is the one replacing the C atom in the target molecule, the rest are attached to it. Note that this means the Cn molecules can generate variants with more than n non-H atoms. 

Carbon is not on the list. The ‘default’ atom is carbon, and Combimol uses this list as a list of atoms to exchange for carbon. 

Note that Hydrogen is not explicitly coded as an atom in this version. As there are no non-SMILES-standard atoms in the set, you do not need to define H  it is a default for unfilled valancies.

