[OoiParameters]
key:type value:radius value:g value:h value:c value:comment
@unit_g=kJ/(mol A^2)
@unit_h=kJ/(mol A^2)
@unit_c=J/(mol A^2 K)
;
; Parameters for the calculation of protein hydration energies
; taken from:
;
; T. Ooi, M. Oobatake, G. Nemethy, H. A. Scheraga:
;   Accessible surface areas as a measure off the thermodynamic parameters
;   of hydration of peptides
; Proc. Natl. Acad. Sci. USA, Vol. 84 (1987), pp. 3086-3090
;
0   0.00   0.000    0.000   0.000   "Hydrogen (ignored)"
1   2.00   0.035   -0.107   1.547   "Aliphatic -CH3/=CH2/=CH-"
2   1.75  -0.034   -0.157   1.240   "Aromatic =CH-"
3   1.40  -0.719   -0.995   0.034   "Hydroxyl -OH"
4   1.55  -0.552   -0.805  -0.051   "Amide and amine -NH2, -NH-"
5   1.55   1.785    1.728   2.563   "Carboxyl and carbonyl =C="
6   1.40  -0.160    0.135  -0.954   "Carboxyl and carbonyl =O"
7   2.00  -0.086    0.000   0.000   "Sulfur -S- and thiol -SH"
8   1.40  -3.950    0.000   0.000   "Carboxylate O"
9   2.00  -3.693    0.000   0.000   "Ammonium N"
10  1.75  -3.793    0.000   0.000   "C/N in aromatic heterocycles bearing positive charge"

[OoiTypes]
ver:ver key:name value:type
;
;  this table assigns one of the above types to each residue:atom
;



[TypeRules:H]
; hydrogens are not considered -> mark them with type 0
 0 = true()

[TypeRules:C]
; carbonyl and carboxyl C
 5 = numberOfBonds(3) AND connectedTo((.O)) 
; aliphatic CH, CH2, CH3
 1 = sp3Hybridized()
; aromatic CH
 2 = sp2Hybridized() 

[TypeRules:N]
; imidazolium ion 
10 = inRing(5) AND connectedTo((-*)(~C(-*)(~N(-*)))(~C(-*)(~C(-*)(~*))))
; amide and amine N 
 4 = numberOfBonds(=3)
; charged ammonium N
 9 = numberOfBonds(=4)


[TypeRules:O]
; hydroxyl group OH
 3 = connectedTo((-H)(-*))
; carboxylic acids
 6 = connectedTo((-H)(-C(=O)(-*))) OR connectedTo((=C(-O(-H))(-*)))
; carboxylate O
 8 = connectedTo((~C(~O)(-*))) OR connectedTo((-C(=O)(-*))) OR connectedTo((=C(-O)(-*)))
; carbonyl and carboxyl group O
 6 = connectedTo((~C)) OR connectedTo((=C))

[TypeRules:S]
; thiol S and SH
 7 = true()

[TypeRules:*]
; default rule: unknown type -> error message
 -1 = true()

[]
