extractDrugKierHallSmarts: Descriptor that Counts the Number of Occurrences of the...

In Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Description

Descriptor that Counts the Number of Occurrences of the E-State Fragments

Usage

extractDrugKierHallSmarts(molecules, silent = TRUE)

Arguments

molecules	Parsed molucule object.
silent	Logical. Whether the calculating process should be shown or not, default is TRUE.

Details

A fragment count descriptor that uses e-state fragments. Traditionally the e-state descriptors identify the relevant fragments and then evaluate the actual e-state value. However it has been shown in Butina et al. that simply using the counts of the e-state fragments can lead to QSAR models that exhibit similar performance to those built using the actual e-state indices.

Atom typing and aromaticity perception should be performed prior to calling this descriptor. The atom type definitions are taken from Hall et al. The SMARTS definitions were obtained from RDKit.

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 79 columns:

ID	Name	Pattern
0	khs.sLi	[LiD1]-*
1	khs.ssBe	[BeD2](-*)-*
2	khs.ssssBe	[BeD4](-*)(-*)(-*)-*
3	khs.ssBH	[BD2H](-*)-*
4	khs.sssB	[BD3](-*)(-*)-*
5	khs.ssssB	[BD4](-*)(-*)(-*)-*
6	khs.sCH3	[CD1H3]-*
7	khs.dCH2	[CD1H2]=*
8	khs.ssCH2	[CD2H2](-*)-*
9	khs.tCH	[CD1H]#*
10	khs.dsCH	[CD2H](=*)-*
11	khs.aaCH	[C,c;D2H](:*):*
12	khs.sssCH	[CD3H](-*)(-*)-*
13	khs.ddC	[CD2H0](=*)=*
14	khs.tsC	[CD2H0](#*)-*
15	khs.dssC	[CD3H0](=*)(-*)-*
16	khs.aasC	[C,c;D3H0](:*)(:*)-*
17	khs.aaaC	[C,c;D3H0](:*)(:*):*
18	khs.ssssC	[CD4H0](-*)(-*)(-*)-*
19	khs.sNH3	[ND1H3]-*
20	khs.sNH2	[ND1H2]-*
21	khs.ssNH2	[ND2H2](-*)-*
22	khs.dNH	[ND1H]=*
23	khs.ssNH	[ND2H](-*)-*
24	khs.aaNH	[N,nD2H](:*):*
25	khs.tN	[ND1H0]#*
26	khs.sssNH	[ND3H](-*)(-*)-*
27	khs.dsN	[ND2H0](=*)-*
28	khs.aaN	[N,nD2H0](:*):*
29	khs.sssN	[ND3H0](-*)(-*)-*
30	khs.ddsN	[ND3H0](~[OD1H0])(~[OD1H0])-,:*
31	khs.aasN	[N,nD3H0](:*)(:*)-,:*
32	khs.ssssN	[ND4H0](-*)(-*)(-*)-*
33	khs.sOH	[OD1H]-*
34	khs.dO	[OD1H0]=*
35	khs.ssO	[OD2H0](-*)-*
36	khs.aaO	[O,oD2H0](:*):*
37	khs.sF	[FD1]-*
38	khs.sSiH3	[SiD1H3]-*
39	khs.ssSiH2	[SiD2H2](-*)-*
40	khs.sssSiH	[SiD3H1](-*)(-*)-*
41	khs.ssssSi	[SiD4H0](-*)(-*)(-*)-*
42	khs.sPH2	[PD1H2]-*
43	khs.ssPH	[PD2H1](-*)-*
44	khs.sssP	[PD3H0](-*)(-*)-*
45	khs.dsssP	[PD4H0](=*)(-*)(-*)-*
46	khs.sssssP	[PD5H0](-*)(-*)(-*)(-*)-*
47	khs.sSH	[SD1H1]-*
48	khs.dS	[SD1H0]=*
49	khs.ssS	[SD2H0](-*)-*
50	khs.aaS	[S,sD2H0](:*):*
51	khs.dssS	[SD3H0](=*)(-*)-*
52	khs.ddssS	[SD4H0](~[OD1H0])(~[OD1H0])(-*)-*
53	khs.sCl	[ClD1]-*
54	khs.sGeH3	[GeD1H3](-*)
55	khs.ssGeH2	[GeD2H2](-*)-*
56	khs.sssGeH	[GeD3H1](-*)(-*)-*
57	khs.ssssGe	[GeD4H0](-*)(-*)(-*)-*
58	khs.sAsH2	[AsD1H2]-*
59	khs.ssAsH	[AsD2H1](-*)-*
60	khs.sssAs	[AsD3H0](-*)(-*)-*
61	khs.sssdAs	[AsD4H0](=*)(-*)(-*)-*
62	khs.sssssAs	[AsD5H0](-*)(-*)(-*)(-*)-*
63	khs.sSeH	[SeD1H1]-*
64	khs.dSe	[SeD1H0]=*
65	khs.ssSe	[SeD2H0](-*)-*
66	khs.aaSe	[SeD2H0](:*):*
67	khs.dssSe	[SeD3H0](=*)(-*)-*
68	khs.ddssSe	[SeD4H0](=*)(=*)(-*)-*
69	khs.sBr	[BrD1]-*
70	khs.sSnH3	[SnD1H3]-*
71	khs.ssSnH2	[SnD2H2](-*)-*
72	khs.sssSnH	[SnD3H1](-*)(-*)-*
73	khs.ssssSn	[SnD4H0](-*)(-*)(-*)-*
74	khs.sI	[ID1]-*
75	khs.sPbH3	[PbD1H3]-*
76	khs.ssPbH2	[PbD2H2](-*)-*
77	khs.sssPbH	[PbD3H1](-*)(-*)-*
78	khs.ssssPb	[PbD4H0](-*)(-*)(-*)-*

Author(s)

Nan Xiao <https://nanx.me>

References

Butina, D. , Performance of Kier-Hall E-state Descriptors in Quantitative Structure Activity Relationship (QSAR) Studies of Multifunctional Molecules, Molecules, 2004, 9:1004-1009.

Hall, L.H. and Kier, L.B. , Electrotopological State Indices for Atom Types: A Novel Combination of Electronic, Topological, and Valence State Information, Journal of Chemical Information and Computer Science, 1995, 35:1039-1045.

Examples

smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')

mol = readMolFromSmi(smi, type = 'mol')
dat = extractDrugKierHallSmarts(mol)
head(dat)

Rcpi documentation built on Nov. 8, 2020, 8:23 p.m.