seqinr (version 1.0-1)

pmw: Protein Molecular Weight

Description

With default parameter values, returns the apparent molecular weight of one mole (6.0221415 e+23) of the input protein expressed in gram at see level on Earth with terrestrial isotopic composition.

Usage

pmw(seqaa, Ar = c(C = 12.0107, H = 1.00794, O = 15.9994,
N = 14.0067, P = 30.973762, S = 32.065), gravity = 9.81,
unit = "gram", checkseqaa = TRUE)

Arguments

seqaa

a protein sequence as a vector of single chars. Allowed values are "*ACDEFGHIKLMNPQRSTVWY", non allowed values are ignored.

Ar

a named vector for the mean relative atomic masses of CHONPS atoms. Defaults values are from to the natural terrestrial sources according to the 43rd IUPAC General Assembly in Beijing, China in August 2005 (See http://www.iupac.org/reports/pe

gravity

gravitational field constant in standard units. Defaults to 9.81 m/s2, that is to the average value at see level on Earth. Negative values are not allowed.

unit

a string that could be "gram" to get the result in grams (1 g = 0.001 kg) or "N" to get the result in Newton units (1 N = 1 kg.m/s2).

checkseqaa

if TRUE pmw() warns if a non-allowed character in seqaa is found.

Value

• The protein molecular weight as a single numeric value.

Details

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

References

citation("seqinr")

See Also

s2c, c2s, aaa, a

Examples

allowed <- s2c("*ACDEFGHIKLMNPQRSTVWY") # All allowed chars in a protein
pmw(allowed)
all.equal(pmw(allowed), 2395.71366) # Should be true on most platforms
#
# Compute the apparent molecular weight on Moon surface:
#
pmw(allowed, g = 1.6)
#
# Compute the apparent molecular weight in absence of gravity:
#
pmw(allowed, g = 0) # should be zero
#
# Reports results in Newton units:
#
pmw(allowed, unit = "N")
#
# Compute the mass in kg of one mol of this protein:
#
pmw(allowed)/10^3
#
# Compute the mass for all amino-acids:
#
sapply(allowed[-1], pmw) -> aamw
names(aamw) <- aaa(names(aamw))
aamw