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Table 1 Examples of Encodings

From: jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints

Encoding Eq.a c paramb Pattern produced by f
DFS 4 0 C.2-N.3-C.3:1, C.3-C.2-N.3:1, C.3-N.3-C.3:1, C.3-N.3:1, C.2-C.3-N.3:1, C.3-C.3-N.3:1, ...
ASP 5 1 N.3-C.3 = O.1:1, C.1-C.3-N.3:1, C.2-N.3:1, C.2-N.3-C.3:1, C.3-C.2-N.3:1, C.3-N.3:1, ...
AP2D 6 2 N.3-1-C.2:1, N.3-1-C.3:1, N.3-2-C.2:1, N.3-2-C.1:1, N.3-2-C.3:1, O.1-2-N.3:1
AT2D 7 3 C.2-2-N.3-1-C.3-1:1, N.3-2-C.2-2-C.2-1:1, N.3-2-C.2-2-C.3-2:1, ...
CATS2D 8 6 0:5, 2:2, 3:4, ...
PHAP2POINT2D 9 8 A-2-A:1, L-2-A:1, N-2-A:1
PHAP3POINT2D 10 9 A-2-A-2-L-2:1, A-2-A-2-L-2:1, ...
SHED 11 14 AA:2.8, AL:3.596, AN:2.872, ...
ECFP - 12 [*]N([*])C(= O)C:1, [*] = C([*])N(C[*])C([*])[*]:1, [*]N([*])[*]:1, ...
RAD2D 12 15 0[N]1[C C C]:1, 0[N]1[C C C]2[C C C C O]:1
LSTAR 13 13 [N.3-C.2, N.3-C.3, N.3-C.3]:1, [N.3-C.2-C.3, N.3-C.3-C.1, N.3-C.3-C.2, N.3-C.3-C.3, N.3-C.3 = O.1]:1
AP3D 14 4 N.3-1-C.2:1, N.3-1-C.3:1, N.3-2-C.1:1, N.3-2-C.2:1, N.3-2-C.3:1, O.1-2-N.3:1
AT3D 15 5 C.3-1-O.1-2-N.3-1:1, O.1-2-C.1-2-N.3-2:1, C.2-2-C.2-2-N.3-1:1, ...
CATS3D 16 7 0:5, 2:2, 3:4, ...
PHAP2POINT3D 17 10 A-2-A:1, L-2-A:1, N-2-A:1
PHAP3POINT3D 18 11 A-2-A-2-L-2:1, A-2-L-2-A-2:1, L-2-A-2-A-2:1
RAD3D 19 16 0[N.3]1[C.2 C.3 C.3]2[C.1 C.2 C.3 C.3 O.1]:1, 0[N.3]1[C.2 C.3 C.3]:1
  1. Examples and numeric values (counts, or, in the case of SHED, entropies) for the string representations for the different encodings of Oxaceprol (Figure 1) with d = 2, default element atom typing and delimiter symbol "-". The patterns are extracted around the nitrogen atom. For some of the encodings, only a subset of the features is shown.
  2. aEquation number b Parameter for command-line interface