/
fragments-utils.R
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/
fragments-utils.R
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##' Returns a `data.frame` of amino acid properties: `AA`,
##' `ResidueMass`, `Abbrev3`, `ImmoniumIonMass`, `Name`,
##' `Hydrophobicity`, `Hydrophilicity`, `SideChainMass`, `pK1`, `pK2`
##' and `pI`.
##'
##' @title Amino acids
##'
##' @return `data.frame`
##'
##' @author Laurent Gatto
##'
##' @export
##'
##' @examples
##'
##' getAminoAcids()
getAminoAcids <- function()
data.frame(AA = c("peg","A","R","N","D","C","E",
"Q","G","H","I","L", "K","M","F",
"P","S","T","W","Y","V"),
ResidueMass = c(44.00000,
71.03711, 156.10111, 114.04293, 115.02694,
103.00919, 129.04259, 128.05858, 57.02146,
137.05891, 113.08406, 113.08406, 128.09496,
131.04049, 147.06841, 97.05276, 87.03203,
101.04768, 186.07931, 163.06333, 99.06841),
Abbrev3 = c(NA,
"Ala", "Arg", "Asn", "Asp", "Cys",
"Glu", "Gln", "Gly", "His", "Ile",
"Leu", "Lys", "Met", "Phe", "Pro",
"Ser", "Thr", "Trp", "Tyr", "Val"),
ImmoniumIonMass = c(NA,
44.05003, 129.11400, 87.05584, 88.03986, 76.02210,
102.05550, 101.07150, 30.03438, 110.07180, 86.09698,
86.09698, 101.10790, 104.05340, 120.08130, 70.06568,
60.04494, 74.06059, 159.09220, 136.07620, 72.08133),
Name = c("Polyethylene glycol",
"Alanine", "Arginine", "Asparagine", "Aspartic acid",
"Cysteine", "Glutamic acid", "Glutamine", "Glycine",
"Histidine", "Isoleucine", "Leucine", "Lysine",
"Methionine", "Phenylalanine", "Proline", "Serine",
"Threonine", "Tryptophan", "Tyrosine", "Valine"),
## The hydrophobicity values are from JACS, 1962, 84: 4240-4246. (C. Tanford)
Hydrophobicity = c(NA, 0.62, -2.53, -0.78, -0.9, 0.29,
-0.74, -0.85, 0.48, -0.4, 1.38, 1.06, -1.5, 0.64, 1.19,
0.12, -0.18, -0.05, 0.81, 0.26, 1.08),
## The hydrophilicity values are from PNAS, 1981, 78:3824-3828 (T.P.Hopp & K.R.Woods)
Hydrophilicity = c(NA, -0.5, 3, 0.2, 3, -1, 3, 0.2, 0,
-0.5, -1.8, -1.8, 3, -1.3, -2.5, 0, 0.3, -0.4, -3.4,
-2.3, -1.5),
SideChainMass = c(NA, 15, 101, 58, 59, 47, 73, 72,
1, 82, 57, 57, 73, 75, 91, 42, 31, 45, 130, 107, 43),
## CRC Handbook of Chemistry and Physics, 66th ed., CRC Press, Boca Raton, Florida (1985).
## R.M.C. Dawson, D.C. Elliott, W.H. Elliott, K.M. Jones, Data for Biochemical Research 3rd ed., Clarendon Press Oxford
pK1 = c(NA, 2.35, 2.18, 2.18, 1.88, 1.71, 2.19,
2.17, 2.34, 1.78, 2.32, 2.36, 2.2, 2.28, 2.58,
1.99, 2.21, 2.15, 2.38, 2.2, 2.29),
pK2 = c(NA, 9.87, 9.09, 9.09, 9.6, 10.78, 9.67, 9.13,
9.6, 8.97, 9.76, 9.6, 8.9, 9.21, 9.24, 10.6, 9.15,
9.12, 9.39, 9.11, 9.74),
pI = c(NA, 6.11, 10.76, 10.76, 2.98, 5.02, 3.08,
5.65, 6.06, 7.64, 6.04, 6.04, 9.47, 5.74, 5.91,
6.3, 5.68, 5.6, 5.88, 5.63, 6.02))
##' Returns a `double` of used atomic mass.
##'
##' @title Atomic mass.
##'
##' @return A named `double`.
##'
##' @author Sebastian Gibb
##'
##' @export
##'
##' @examples
##' getAtomicMass()
getAtomicMass <- function() {
## taken from:
## http://www.chem.ualberta.ca/~massspec/atomic_mass_abund.pdf
c(H = 1.007825,
C = 12,
N = 14.003074,
O = 15.994915,
p = 1.007276)
}