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module MS
module Mass
# takes a molecular formula in this format: C2BrH12O
def self.formula_to_exact_mass(formula)
# TODO: add other input methods
pairs = formula.scan(/([A-Z][a-z]?)(\d*)/).map do |match|
if match.last == ''
match[-1] = 1
end
[match[0], match[1].to_i]
end
pairs.map do |pair|
MONO[pair.first.downcase] * pair.last
end.reduce(:+)
end
ELECTRON = 0.0005486 # www.mikeblaber.org/oldwine/chm1045/notes/Atoms/.../Atoms03.htm
H_PLUS = 1.00727646677
# + http://www.unimod.org/masses.html
MONO_STR = {
'c' => 12.0, # +
'br' => 78.9183361, # +
'd' => 2.014101779, # +
'f' => 18.99840322, # +
'n' => 14.003074, # +
'o' => 15.99491463, # +
'na' => 22.9897677, # +
'p' => 30.973762, # +
's' => 31.9720707, # +
'li' => 7.016003, # +
'cl' => 34.96885272, # +
'k' => 38.9637074, # +
'si' => 27.9769265325, # http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=Si&ascii=html&isotype=some
'i' => 126.904473, # +
'h+' => 1.00727646677,
'h' => 1.007825035, # +
'h2o' => 18.0105647,
'oh' => 17.002739665,
'e' => 0.0005486,
'se' => 79.9165196
}
AVG_STR = {
'h+' => 1.007276, # using Mascot_H_plus mass (is this right for AVG??)
'h' => 1.00794,
'h2o' => 18.01528,
'oh' => 17.00734,
}
# sets MONO_STR, MONO, AVG_STR, and AVG
%w(MONO AVG).each do |type|
const_set "#{type}_SYM", Hash[ const_get("#{type}_STR").map {|k,v| [k.to_sym, v] } ]
const_set type, const_get("#{type}_STR").merge( const_get("#{type}_SYM") )
end
end
end
Version data entries
10 entries across 10 versions & 1 rubygems