Function computing an atomic composition from amono acid sequence.

Description

Function computing an atomic composition from (naturally occuring) amino acid sequence.

Usage

getAtomsFromSeq(seq)

Arguments

Details

The atomic composition is just a summaric atomic composition of all amino acids composing the sequence minus (n-1) times the water molecule, where n is a length of given amino acid sequence.

Value

Named list with the following fields with number of correcponding atoms (integer non-negative values):

• C,

• H,

• N,

• O,

• S

Author(s)

Piotr Dittwald <piotr.dittwald@mimuw.edu.pl>

Examples

  seq1 <-  "AACD"
  aC1 <- getAtomsFromSeq(seq = seq1)
  seq2 <-  AAString("ACCD")
  aC2 <- getAtomsFromSeq(seq = seq2)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(BRAIN)
Loading required package: PolynomF
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/BRAIN/getAtomsFromSeq.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getAtomsFromSeq
> ### Title: Function computing an atomic composition from amono acid
> ###   sequence.
> ### Aliases: getAtomsFromSeq
> 
> ### ** Examples
> 
>   seq1 <-  "AACD"
>   aC1 <- getAtomsFromSeq(seq = seq1)
>   seq2 <-  AAString("ACCD")
>   aC2 <- getAtomsFromSeq(seq = seq2)
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>