Class: Mascot::DAT::Masses

Inherits:
Object
  • Object
show all
Defined in:
lib/mascot/dat/masses.rb

Overview

A Hash of the mass table section. See the masstable instance method for details.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(masses_section) ⇒ Masses

Returns a new instance of Masses.



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# File 'lib/mascot/dat/masses.rb', line 54

def initialize masses_section
  @masstable = {}
  @deltas = []
  @fixed_modifications = []

  masses_section.split("\n").each do |l|
    k,v = l.split("=")
    next unless k && v
    case k
    when /delta(\d+)/
      idx = $1.to_i - 1
      @deltas[idx] = v.split(",")
      @deltas[idx][0] = @deltas[idx][0].to_f
      @masstable[k.to_sym] = @deltas[idx][0]
    when /FixedMod(.*)(\d+)/
      idx = $2.to_i - 1
      if $1.empty?
        # new fixed mod record
        @fixed_modifications[idx] = v.split(",")
        @fixed_modifications[idx][0] = @fixed_modifications[idx][0].to_f
        @masstable[k.to_sym] = @fixed_modifications[idx][0]
      else
        # append the modified residue to the array
        @fixed_modifications[idx] << v
      end
    else
      @masstable[k.to_sym] = v.to_f
    end
    @masstable.keys.each do |m|
      self.class.send(:define_method,m, lambda { @masstable[m] })
    end
  end
end

Instance Attribute Details

#deltas ⇒ Object (readonly) Also known as: mods, d

A subset of the mass table defining the variable modications. For example, given the following delta in a DAT file:

delta1=15.994915,Oxidation (M)

Then the following gets defined:

@deltas = [[15.994915,"Oxidation (M)"], ... ]



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# File 'lib/mascot/dat/masses.rb', line 36

def deltas
  @deltas
end

#fixed_modifications ⇒ Object (readonly) Also known as: fixed_mods, f

A subset of the mass table defining the fixed modifications. For example:

FixedMod1=57.021464,Carbamidomethyl (C)
FixedModResidues1=C

Then the following gets defined:

@fixed_modifications = [[57.021464, "Carbamidomethyl (C)", "C"], ...]



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# File 'lib/mascot/dat/masses.rb', line 50

def fixed_modifications
  @fixed_modifications
end

#masstable ⇒ Object (readonly) Also known as: m

The main table of masses. Given the following examples from a DAT file:

W=186.079313
X=111.000000
Y=163.063329
Z=128.550590
Hydrogen=1.007825
Carbon=12.000000

You can access the value for Hydrogen as:

mydat.masses.masstable[:Hydorgen] # => 1.007825

or

mydat.masses.m[:Hydrogen] # => 1.007825

or

mydat.masses.hydorgen # =>  1.007825



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# File 'lib/mascot/dat/masses.rb', line 21

def masstable
  @masstable
end