Flexible heuristic algorithm for automatic molecule fragmentation: application to the UNIFAC group contribution model

Müller, Simon

doi:10.1186/s13321-019-0382-3

Table 1 Fragmentation scheme developed in this work for the published UNIFAC groups and the respective pattern described used for sorting

From: Flexible heuristic algorithm for automatic molecule fragmentation: application to the UNIFAC group contribution model

Group information			Descriptors
Number	Name	SMILES	1	2	3	4	5	6	7	8
1	CH3	[CH3;X4]	False	False	1	True	0	False	0	0
2	CH2	[CH2;X4]	False	False	1	False	0	False	0	0
3	CH	[CH1;X4]	False	False	1	False	0	False	0	0
4	C	[CH0;X4], [CH0;X3]	False	False	1	False	0	False	0	0
5	CH2=CH	[CH2]=[CH]	False	False	2	True	0	False	0	1
6	CH=CH	[CH]=[CH]	False	False	2	False	0	False	0	1
7	CH2=C	[CH2]=[C], [CH2]=[c]	False	False	2	False	0	False	0	1
8	CH=C	[CH]=[CH0], [CH]=[cH0]	False	False	2	False	0	False	0	1
9	ACH	[cH]	False	False	1	False	0	True	0	0
10	AC	[cH0]	False	False	1	False	0	True	0	0
11	ACCH3	[c][CH3;X4]	False	False	2	False	0	True	0	0
12	ACCH2	[c][CH2;X4]	False	False	2	False	0	True	0	0
13	ACCH	[c][CH;X4]	False	False	2	False	0	True	0	0
14	OH	[OH]	False	False	1	True	1	False	0	0
15	CH3OH	[CH3][OH]	True	False	2	False	1	False	0	0
16	H2O	[OH2]	True	False	1	False	1	False	0	0
17	ACOH	[c][OH]	False	False	2	False	1	True	0	0
18	CH3CO	[CH3][CH0]=O	False	False	3	True	1	False	0	1
19	CH2CO	[CH2][CH0]=O	False	False	3	False	1	False	0	1
20	CH=O	[CH]=O	False	False	2	True	1	False	0	1
21	CH3COO	[CH3]C(=O)[OH0]	False	False	4	True	2	False	0	1
22	CH2COO	[CH2]C(=O)[OH0]	False	False	4	False	2	False	0	1
23	HCOO	[CH](=O)[OH0]	False	False	3	True	2	False	0	1
24	CH3O	[CH3][OH0]	False	False	2	True	1	False	0	0
25	CH2O	[CH2][OH0]	False	False	2	False	1	False	0	0
26	CHO	[CH][OH0]	False	False	2	False	1	False	0	0
27	THF	[CH2;R][OH0]	False	False	2	False	1	True	0	0
28	CH3NH2	[CH3][NH2]	True	False	2	False	1	False	0	0
29	CH2NH2	[CH2][NH2]	False	False	2	True	1	False	0	0
30	CHNH2	[CH][NH2]	False	False	2	False	1	False	0	0
31	CH3NH	[CH3][NH]	False	False	2	True	1	False	0	0
32	CH2NH	[CH2][NH]	False	False	2	False	1	False	0	0
33	CHNH	[CH][NH]	False	False	2	False	1	False	0	0
34	CH3N	[CH3][N], [CH3][n]	False	False	2	False	1	False	0	0
35	CH2N	[CH2][N]	False	False	2	False	1	False	0	0
36	ACNH2	[c][NH2]	False	False	2	False	1	True	0	0
37	C5H5N	n1[cH][cH][cH][cH][cH]1	True	False	6	False	1	True	0	0
38	C5H4N	n1[c][cH][cH][cH][cH]1, n1[cH][c][cH][cH][cH]1, n1[cH][cH][c][cH][cH]1	False	False	6	True	1	True	0	0
39	C5H3N	n1[c][c][cH][cH][cH]1, n1[c][cH][c][cH][cH]1, n1[c][cH][cH][c][cH]1, n1[c][cH][cH][cH][c]1, n1[cH][c][c][cH][cH]1, n1[cH][c][cH][c][cH]1	False	False	6	False	1	True	0	0
40	CH3CN	[CH3]C#N	True	False	3	False	1	False	1	0
41	CH2CN	[CH2]C#N	False	False	3	True	1	False	1	0
42	COOH	C(=O)[OH]	False	False	3	True	2	False	0	1
43	HCOOH	[CH](=O)[OH]	True	False	3	False	2	False	0	1
44	CH2Cl	[CH2]Cl	False	True	2	True	1	False	0	0
45	CHCl	[CH]Cl	False	True	2	False	1	False	0	0
46	CCl	[CH0]Cl	False	True	2	False	1	False	0	0
47	CH2Cl2	[CH2](Cl)Cl	True	False	3	False	2	False	0	0
48	CHCl2	[CH](Cl)Cl	False	True	3	True	2	False	0	0
49	CCl2	C(Cl)Cl	False	True	3	False	2	False	0	0
50	CHCl3	[CH](Cl)(Cl)Cl	True	False	4	False	3	False	0	0
51	CCl3	C(Cl)(Cl)(Cl)	False	True	4	True	3	False	0	0
52	CCl4	C(Cl)(Cl)(Cl)(Cl)	True	False	5	False	4	False	0	0
53	ACCl	[c]Cl	False	True	2	False	1	True	0	0
54	CH3NO2	[CH3][N+](=O)[O−]	False	False	4	True	3	False	0	1
55	CH2NO2	[CH2][N+](=O)[O−]	False	False	4	False	3	False	0	1
56	CHNO2	[CH][N+](=O)[O−]	False	False	4	False	3	False	0	1
57	ACNO2	[c][N+](=O)[O−]	False	False	4	False	3	True	0	1
58	CS2	C(=S)=S	True	False	3	False	2	False	0	2
59	CH3SH	[CH3][SH]	True	False	2	False	1	False	0	0
60	CH2SH	[CH2][SH]	False	False	2	True	1	False	0	0
61	Furfural	O=[CH]c1[cH][cH][cH]o1	True	False	7	False	2	True	0	1
62	DOH	[OH][CH2][CH2][OH]	True	False	4	False	2	False	0	0
63	I	[IH0]	False	True	1	True	1	False	0	0
64	Br	[BrH0]	False	True	1	True	1	False	0	0
65	CH#C	[CH]#C	False	False	2	True	0	False	1	0
66	C#C	C#C	False	False	2	False	0	False	1	0
67	DMSO	[CH3]S(=O)[CH3]	True	False	4	False	2	False	0	1
68	ACRY	[CH2]=[CH1][C]#N	True	False	4	False	1	False	1	1
69	Cl(C=C)	[$(Cl[C]=[C])]	False	True	3	True	1	False	0	0
70	C=C	[CH0]=[CH0]	False	False	2	False	0	False	0	1
71	ACF	[c]F	False	True	2	False	1	True	0	0
72	DMF	[CH](=O)N([CH3])[CH3]	True	False	5	False	2	False	0	1
73	HCON(CH2)2	[CH](=O)N([CH2])[CH2], [CH](=O)N([CH2])[CH3]	False	False	5	False	2	False	0	1
74	CF3	C(F)(F)F	False	True	4	True	3	False	0	0
75	CF2	C(F)F	False	True	3	False	2	False	0	0
76	CF	[C]F	False	True	2	False	1	False	0	0
77	COO	[CH0](=O)[OH0], [cH0](=O)[oH0]	False	False	3	False	2	False	0	1
78	SiH3	[SiH3]	False	False	1	True	1	False	0	0
79	SiH2	[SiH2]	False	False	1	False	1	False	0	0
80	SiH	[SiH]	False	False	1	False	1	False	0	0
81	Si	[Si]	False	False	1	False	1	False	0	0
82	SiH2O	[SiH2][OH0]	False	False	2	False	2	False	0	0
83	SiHO	[SiH][OH0]	False	False	2	False	2	False	0	0
84	SiO	[Si][OH0]	False	False	2	False	2	False	0	0
85	NMP	[CH3]N1[CH2][CH2][CH2]C(=O)1	True	False	7	False	2	False	0	1
86	CCl3F	C(Cl)(Cl)(Cl)F	True	False	5	False	4	False	0	0
87	CCl2F	C(Cl)(Cl)F	False	True	4	True	3	False	0	0
88	HCCl2F	[CH](Cl)(Cl)F	True	False	4	False	3	False	0	0
89	HCClF	[CH](Cl)F	False	True	3	True	2	False	0	0
90	CClF2	C(Cl)(F)F	False	True	4	True	3	False	0	0
91	HCClF2	[CH](Cl)(F)F	True	False	4	False	3	False	0	0
92	CClF3	C(Cl)(F)(F)F	True	False	5	False	4	False	0	0
93	CCl2F2	C(Cl)(Cl)(F)F	True	False	5	False	4	False	0	0
94	CONH2	C(=O)[NH2]	False	False	3	True	2	False	0	1
95	CONHCH3	C(=O)[NH][CH3]	False	False	4	True	2	False	0	1
96	CONHCH2	C(=O)[NH][CH2]	False	False	4	False	2	False	0	1
97	CON(CH3)2	C(=O)N([CH3])[CH3]	False	False	5	True	2	False	0	1
98	CONCH3CH2	C(=O)N([CH3])[CH2]	False	False	5	False	2	False	0	1
99	CON(CH2)2	C(=O)N([CH2])[CH2]	False	False	5	False	2	False	0	1
100	C2H5O2	[OH0;!$(OC=O);!R][CH2;!R][CH2;!R][OH]	False	False	4	True	2	False	0	0
101	C2H4O2	[OH0;!$(OC=O);!R][CH;!R][CH2;!R][OH], [OH0;!$(OC=O);!R][CH2;!R][CH;!R][OH]	False	False	4	False	2	False	0	0
102	CH3S	[CH3]S	False	False	2	True	1	False	0	0
103	CH2S	[CH2]S	False	False	2	False	1	False	0	0
104	CHS	[CH]S	False	False	2	False	1	False	0	0
105	MORPH	[CH2]1[CH2][NH][CH2][CH2]O1	True	False	6	False	2	False	0	0
106	C4H4S	[cH]1[cH][s;X2][cH][cH]1	True	False	5	False	1	True	0	0
107	C4H3S	[c]1[cH][s;X2][cH][cH]1, [cH]1[c][s;X2][cH][cH]1	False	False	5	True	1	True	0	0
108	C4H2S	[c]1[c][s;X2][cH][cH]1, [c]1[cH][s;X2][cH][c]1, [cH]1[c][s;X2][c][cH]1, [cH]1[c][s;X2][cH][c]1	False	False	5	False	1	True	0	0
109	NCO	N=C=O	False	False	3	True	2	False	0	2
118	(CH2)2SU	[CH2]S(=O)(=O)[CH2]	False	False	5	False	3	False	0	2
119	CH2CHSU	[CH2]S(=O)(=O)[CH]	False	False	5	False	3	False	0	2

In the name of the group, AC stands for aromatic carbon atom. The names of the groups are based on the original UNIFAC names as described on their webpage [44]. If several patterns were employed to find one group, these are shown separated by a comma. The underlined patterns were added to improve the matching of the algorithm in comparison to the results of the reference database. The values of the descriptors for each group, as described in “Simple fragmentation” section, are also shown in this table. For sorting, the boolean descriptor values can be replace by integer values (True: 1, False: 0). Descriptors: 1: Whether the pattern has zero bonds 2: Whether the pattern is simple 3: Number of atoms defining the group. 4: Whether the number of available bonds is one: first the patterns with one bond, then patterns with more bonds. 5: Number of atoms in the pattern that are neither hydrogen nor carbon. 6: Whether the pattern includes atoms in a ring. 7: Number of triple bonds. 8: Number of double bonds

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