Class: Diadem::IsotopeDistribution

Inherits:
Object
  • Object
show all
Defined in:
lib/diadem/isotope_distribution.rb

Constant Summary collapse

DEFAULT_ISOTOPE_TABLE = 
Mspire::Isotope::BY_ELEMENT

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(intensities = [], nucleon_start = 0) ⇒ IsotopeDistribution

Returns a new instance of IsotopeDistribution.



14
15
16
 
# File 'lib/diadem/isotope_distribution.rb', line 14

def initialize(intensities=[], nucleon_start=0)
  @intensities, @nucleon_start = intensities, nucleon_start
end

Instance Attribute Details

#intensities ⇒ Object

should always add up to 1



11
12
13
 
# File 'lib/diadem/isotope_distribution.rb', line 11

def intensities
  @intensities
end

#nucleon_start ⇒ Object

should be inclusive of last value



13
14
15
 
# File 'lib/diadem/isotope_distribution.rb', line 13

def nucleon_start
  @nucleon_start
end

Class Method Details

.average(distributions, weights = nil) ⇒ Object

returns a new distribution, uses equal weights if none given



29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
 
# File 'lib/diadem/isotope_distribution.rb', line 29

def average(distributions, weights=nil)
  weights ||= Array.new(distributions.size, 1)
  min_nucleon_num = distributions.map(&:nucleon_start).min
  max_nucleon_num = distributions.map(&:nucleon_end).max

  new_intensity_arrays = distributions.zip(weights).map do |dist, weight|
    new_pcts = dist.intensities.dup
    right_pad = max_nucleon_num - dist.nucleon_end
    left_pad = dist.nucleon_start - min_nucleon_num
    [[right_pad, new_pcts.size], [left_pad, 0]].each do |pad, loc|
      new_pcts[loc,0] = Array.new(pad, 0.0)
    end
    new_pcts.map! {|v| v * weight }
    new_pcts
  end

  summed_intensities = new_intensity_arrays.transpose.map do |col|
    col.reduce(:+)
  end

  new_dist = self.new(summed_intensities, min_nucleon_num)
  new_dist.normalize!
end

.from_formula(formula) ⇒ Object 



24
25
26
 
# File 'lib/diadem/isotope_distribution.rb', line 24

def from_formula(formula)
  Mspire::MolecularFormula[formula].isotope_distribution
end

Instance Method Details

#normalize!(normalize_to = 1.0) ⇒ Object

normalizes intensity values and returns self



55
56
57
58
59
 
# File 'lib/diadem/isotope_distribution.rb', line 55

def normalize!(normalize_to=1.0)
  sum = intensities.reduce(:+)
  intensities.map! {|v| (v.to_f/sum)*normalize_to }
  self
end

#nucleon_end ⇒ Object 



18
19
20
 
# File 'lib/diadem/isotope_distribution.rb', line 18

def nucleon_end
  nucleon_start + intensities.size - 1
end