1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
|
//
// Copyright (C) 2021 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
namespace defaults {
std::vector<std::pair<std::string, std::string>> defaultNormalizations = {
// Opposite of #2.1 in InChI technical manual? Covered by RDKit
// Sanitization.
{"Nitro to N+(O-)=O",
"[N,P,As,Sb;X3:1](=[O,S,Se,Te:2])=[O,S,Se,Te:3]>>[*+1:1]([*-1:2])=[*:3]"},
{"Sulfone to S(=O)(=O)",
"[S+2:1]([O-:2])([O-:3])>>[S+0:1](=[O-0:2])(=[O-0:3])"},
{"Pyridine oxide to n+O-", "[nH0+0:1]=[OH0+0:2]>>[n+:1][O-:2]"},
{"Azide to N=N+=N-", "[*:1][N:2]=[N:3]#[N:4]>>[*:1][N:2]=[N+:3]=[N-:4]"},
{"Diazo/azo to =N+=N-", "[*:1]=[N:2]#[N:3]>>[*:1]=[N+:2]=[N-:3]"},
{"Sulfoxide to -S+(O-)-",
"[!O:1][S+0;X3:2](=[O:3])[!O:4]>>[*:1][S+1:2]([O-:3])[*:4]"},
// Equivalent to #1.5 in InChI technical manual
{"Phosphate to P(O-)=O",
"[O,S,Se,Te;-1:1][P+;D4:2][O,S,Se,Te;-1:3]>>[*+0:1]=[P+0;D5:2][*-1:3]"},
// Equivalent to #1.8 in InChI technical manual
{"C/S+N to C/S=N+",
"[C,S&!$([S+]-[O-]);X3+1:1]([NX3:2])[NX3!H0:3]>>[*+0:1]([N:2])=[N+:3]"},
// Equivalent to #1.8 in InChI technical manual
{"P+N to P=N+", "[P;X4+1:1]([NX3:2])[NX3!H0:3]>>[*+0:1]([N:2])=[N+:3]"},
{"Normalize hydrazine-diazonium",
"[CX4:1][NX3H:2]-[NX3H:3][CX4:4][NX2+:5]#[NX1:6]>>[CX4:1][NH0:2]=[NH+:3]["
"C:4][N+0:5]=[NH:6]"},
// Equivalent to #1.3 in InChI technical manual
{"Recombine 1,3-separated charges",
"[N,P,As,Sb,O,S,Se,Te;-1:1]-[A+0:2]=[N,P,As,Sb,O,S,Se,Te;+1:3]>>[*-0:1]=[*"
":2]-[*+0:3]"},
{"Recombine 1,3-separated charges",
"[n,o,p,s;-1:1]:[a:2]=[N,O,P,S;+1:3]>>[*-0:1]:[*:2]-[*+0:3]"},
{"Recombine 1,3-separated charges",
"[N,O,P,S;-1:1]-[a:2]:[n,o,p,s;+1:3]>>[*-0:1]=[*:2]:[*+0:3]"},
{"Recombine 1,5-separated charges",
"[N,P,As,Sb,O,S,Se,Te;-1:1]-[A+0:2]=[A:3]-[A:4]=[N,P,As,Sb,O,S,Se,Te;+1:5]"
">>[*-0:1]=[*:2]-[*:3]=[*:4]-[*+0:5]"},
{"Recombine 1,5-separated charges",
"[n,o,p,s;-1:1]:[a:2]:[a:3]:[c:4]=[N,O,P,S;+1:5]>>[*-0:1]:[*:2]:[*:3]:[c:"
"4]-[*+0:5]"},
{"Recombine 1,5-separated charges",
"[N,O,P,S;-1:1]-[c:2]:[a:3]:[a:4]:[n,o,p,s;+1:5]>>[*-0:1]=[c:2]:[*:3]:[*:"
"4]:[*+0:5]"},
// Conjugated cation rules taken from Francis Atkinson's standardiser. Those
// that can reduce aromaticity aren't included
{"Normalize 1,3 conjugated cation",
"[N,O;+0!H0:1]-[A:2]=[N!$(*[O-]),O;+1H0:3]>>[*+1:1]=[*:2]-[*+0:3]"},
{"Normalize 1,3 conjugated cation",
"[n;+0!H0:1]:[c:2]=[N!$(*[O-]),O;+1H0:3]>>[*+1:1]:[*:2]-[*+0:3]"},
{"Normalize 1,5 conjugated cation",
"[N,O;+0!H0:1]-[A:2]=[A:3]-[A:4]=[N!$(*[O-]),O;+1H0:5]>>[*+1:1]=[*:2]-[*:"
"3]=[*:4]-[*+0:5]"},
{"Normalize 1,5 conjugated cation",
"[n;+0!H0:1]:[a:2]:[a:3]:[c:4]=[N!$(*[O-]),O;+1H0:5]>>[n+1:1]:[*:2]:[*:3]:"
"[*:4]-[*+0:5]"},
// Equivalent to #1.6 in InChI technical manual. RDKit Sanitization handles
// this for perchlorate.
{"Charge normalization", "[F,Cl,Br,I,At;-1:1]=[O:2]>>[*-0:1][O-:2]"},
{"Charge recombination", "[N,P,As,Sb;-1:1]=[C+;v3:2]>>[*+0:1]#[C+0:2]"},
};
} // namespace defaults
|
