26.1 The MDL Valence Model

The MDL valence model was developed for MDL for allowing hydrogen counts to be implicit in MDL SD and MOL file formats. It assumes that the bond orders to an atom are specified (ExplicitValence), and that the atomic number and formal charge are correctly set. The MDL valence model, then prescribes the number of implicit hydrogens on a particular atom. Table 26.1 shows the MDL Valence model as implemented in OEChem.

In OEChem, the MDL valence model is used for calls to the OEAssignMDLHydrogens function.

All the remaining elements not listed in Table 26.1 are assumed to have no implicit hydrogens.

Table 26.1: MDL Valence Model

At#	Symbol	-3	-2	-1	0	+1	+2	+3	+4	+5
1	H			0	1	0
3	Li			0	1	0
4	Be			0	2	1	0
5	B	2	3,5	4	3	2	1	0
6	C		2	3,5	4	3	2	1
7	N		1	2	3,5	4	3
8	O		0	1	2	3,5	4	3	2	1
9	F			0	1	2
11	Na			0	1	0
12	Mg			0	2	1	0
13	Al	2,4,6	3,5	4	3	2	1	0
14	Si		2,4,6	3,5	4	3	2	1	0
15	P			2,4,6	3,5	4	3	2	1	0
16	S		0	1,3,5,7	2,4,6	3,5	4	3
17	Cl			0	1,3,5,7	2,4,6	3,5	4
19	K			0	1	0
20	Ca			0	2	1	0
31	Ga			4	3	0	1	0
32	Ge		2,4,6	3,5	4	3	0	1
33	As			2,4,6	3,5	4	3	0	1	0
34	Se		0	1,3,5,7	2,4,6	3,5	4	3
35	Br			0	1,3,5,7	2,4,6	3,5	4
37	Rb			00	1	0
38	Sr			0	2	1	0
49	In	2,4,6	3,5	2,4	3	0	1	0
50	Sn		2,4,6	3,5	2,4	3	0	1
51	Sb	0	1,3,5,7	2,4,6	3,5	2,4	3	0	1	0
52	Te		0	1,3,5,7	2,4,6	3,5	2,4	3
53	I			0	1,3,5,7	2,4,6	3,5	2,4
55	Cs			0	1	0
56	Ba			0	2	1	0
81	Tl			2,4	1,3	0	0	0
82	Pb		2,4,6	3,5	2,4	3	0	1
83	Bi	0	1,3,5,7	2,4,6	3,5	2,4	3	0	1	0
84	Po		0	1,3,5,7	2,4,6	3,5	2,4	3
85	At			0	1,3,5,7	2,4,6	3,5	2,4
87	Fr			0	1	0
88	Ra			0	2	1	0

				OEChem - Python Theory Manual Version 1.3.1

				OEChem - Python Theory Manual Version 1.3.1