apfp: Frequent Atom Pairs

In ChemmineR: Cheminformatics Toolkit for R

Description

Ranked set of 4096 most frequent atom pairs observed in the compound collection from DrugBank with a MW < 1000. Their atom pairs were generated with the sdf2ap function. The provided data frame is sorted row-wise by atom pair frequency and only the 4096 most frequent atom pairs are included. This data set can be used as predefined atom pair selection when computing atom pair fingerprints with the desc2fp function.

Usage

data(apfp)

Format

Object of class data.frame. First column contains atom pair (AP) IDs and the second column their frequency in DrugBank compounds.

Details

Object stores 4096 most frequent atom pairs generated from DrugBank compounds.

Source

DrugBank: http://www.drugbank.ca/

References

Chen X and Reynolds CH (2002). "Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients", J Chem Inf Comput Sci.

Examples

data(apfp)
apfp[1:4,]

Example output

           AP Freq
1 54897199232 4747
2 54896150656 4619
3 54897199233 4611
4 54898247808 4393

ChemmineR documentation built on Feb. 28, 2021, 2:02 a.m.