Class: Mascot::DAT::Enzyme

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(enz_section) ⇒ Enzyme

Returns a new instance of Enzyme.



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# File 'lib/mascot/dat/enzyme.rb', line 22

def initialize(enz_section)
  @title = ""
  @independent = false
  @semi_specific = false
  @cleavages = []
  @restrictions = []
  @terminals  = []

  enz_section.split(/\n/).each do |line|
    k,v = line.chomp.split(":")
    case k
    when "Title"
      @title = v
    when "Independent"
      @independent = v.to_i > 0 ? true : false
    when "SemiSpecific"
      @semi_specific = v.to_i > 0 ? true : false
    when /^Cleavage/
      k =~ /\[(\d)\]/
      if $1
        @cleavages[$1.to_i] = v
      else
        @cleavages << v
      end
    when /^Restrict\[?(\d?)\]?/
      if $1
        @restrictions[$1.to_i] = v
      else
        @restrictions << v
      end
    when /^(\w)term\[?(\d?)\]?/
      idx = $2.empty? ? 0 : $2.to_i
      @terminals[idx] = $1
    end
  end
end

Instance Attribute Details

#cleavages ⇒ Object

example enzyme section

--gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="enzyme"

Title:V8-DE/Trypsin
Independent:0
SemiSpecific:0
Cleavage[0]:KR
Restrict[0]:P
Cterm[0]
Cleavage[1]:BDEZ
Restrict[1]:P
Cterm[1]
*



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# File 'lib/mascot/dat/enzyme.rb', line 19

def cleavages
  @cleavages
end

#independent ⇒ Object

example enzyme section

--gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="enzyme"

Title:V8-DE/Trypsin
Independent:0
SemiSpecific:0
Cleavage[0]:KR
Restrict[0]:P
Cterm[0]
Cleavage[1]:BDEZ
Restrict[1]:P
Cterm[1]
*



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# File 'lib/mascot/dat/enzyme.rb', line 19

def independent
  @independent
end

#restrictions ⇒ Object

example enzyme section

--gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="enzyme"

Title:V8-DE/Trypsin
Independent:0
SemiSpecific:0
Cleavage[0]:KR
Restrict[0]:P
Cterm[0]
Cleavage[1]:BDEZ
Restrict[1]:P
Cterm[1]
*



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# File 'lib/mascot/dat/enzyme.rb', line 19

def restrictions
  @restrictions
end

#semi_specific ⇒ Object

example enzyme section

--gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="enzyme"

Title:V8-DE/Trypsin
Independent:0
SemiSpecific:0
Cleavage[0]:KR
Restrict[0]:P
Cterm[0]
Cleavage[1]:BDEZ
Restrict[1]:P
Cterm[1]
*



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# File 'lib/mascot/dat/enzyme.rb', line 19

def semi_specific
  @semi_specific
end

#terminals ⇒ Object

example enzyme section

--gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="enzyme"

Title:V8-DE/Trypsin
Independent:0
SemiSpecific:0
Cleavage[0]:KR
Restrict[0]:P
Cterm[0]
Cleavage[1]:BDEZ
Restrict[1]:P
Cterm[1]
*



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# File 'lib/mascot/dat/enzyme.rb', line 19

def terminals
  @terminals
end

#title ⇒ Object

example enzyme section

--gc0p4Jq0M2Yt08jU534c0p
Content-Type: application/x-Mascot; name="enzyme"

Title:V8-DE/Trypsin
Independent:0
SemiSpecific:0
Cleavage[0]:KR
Restrict[0]:P
Cterm[0]
Cleavage[1]:BDEZ
Restrict[1]:P
Cterm[1]
*



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# File 'lib/mascot/dat/enzyme.rb', line 19

def title
  @title
end