Class: Ms::Ident::Pepxml::SampleEnzyme

Inherits:
Object
  • Object
show all
Includes:
Merge
Defined in:
lib/ms/ident/pepxml/sample_enzyme.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Merge

#merge!

Constructor Details

#initialize(arg = {}) ⇒ SampleEnzyme

Can pass in a name of an enzyme that is recognized (meaning there is a set_<name> method), or 

trypsin

For other enzymes, you must set :cut, :no_cut, :name, and :sense will



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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 23

def initialize(arg={})
  if arg.is_a?(String)
    @name = arg
    send("set_#{@name}".to_sym)
  else
    merge!(arg)
  end
end

Instance Attribute Details

#cut ⇒ Object

amino acids after which to cleave



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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 13

def cut
  @cut
end

#name ⇒ Object

an identifier



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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 11

def name
  @name
end

#no_cut ⇒ Object

cleave at ‘cut’ amino acids UNLESS it is followed by ‘no_cut’



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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 15

def no_cut
  @no_cut
end

#sense ⇒ Object

‘C’ or ‘N’



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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 17

def sense
  @sense
end

Class Method Details

.from_pepxml_node(node) ⇒ Object 



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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 58

def self.from_pepxml_node(node)
  self.new.from_pepxml_node(node)
end

Instance Method Details

#from_pepxml_node(node) ⇒ Object

returns self



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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 49

def from_pepxml_node(node)
  self.name = node['name']
  ch = node.child
  self.cut = ch['cut']
  self.no_cut= ch['no_cut']
  self.sense = ch['sense']
  self
end

#num_missed_cleavages(aaseq) ⇒ Object

takes an amino acid sequence (e.g. PEPTIDE). returns the number of missed cleavages

Raises:

  • (NotImplementedError) 


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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 64

def num_missed_cleavages(aaseq)
  seq_to_scan = '  ' + aaseq + '  ' 
  raise NotImplementedError, 'need to implement for N terminal sense'  if sense == 'N'
  @num_missed_cleavages_regex = 
    if @num_missed_cleavages_regex ; @num_missed_cleavages_regex
    else
      regex_string = "[#{@cut}]"
      if @no_cut and @no_cut != ''
        regex_string << "[^#{@no_cut}]"
      end
      /#{regex_string}/
    end
  arr = aaseq.scan(@num_missed_cleavages_regex)
  num = arr.size
  if aaseq[-1,1] =~ @num_missed_cleavages_regex
    num -= 1
  end
  num
end

#num_tol_term(prev_aa, middle, next_aa) ⇒ Object

No arguments should contain non-standard amino acids

Raises:

  • (NotImplementedError) 


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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 85

def num_tol_term(prev_aa, middle, next_aa)
  raise NotImplementedError, 'need to implement for N terminal sense'  if sense == 'N'
  no_cut = @no_cut || ''
  num_tol = 0
  last_of_middle = middle[-1,1]
  first_of_middle = middle[0,1]
  if ( @cut.include?(prev_aa) && !no_cut.include?(first_of_middle) ) || prev_aa == '-'
    num_tol += 1
  end
  if @cut.include?(last_of_middle) && !no_cut.include?(next_aa) || next_aa == '-'
    num_tol += 1
  end
  num_tol
end

#set_trypsin ⇒ Object 



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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 32

def set_trypsin
  @sense = 'C'
  @cut = 'KR'
  @no_cut = 'P'
end

#to_xml(builder = nil) ⇒ Object

if an xml builder object is given, it adds to the object and returns the builder object, otherwise it returns an xml fragment string



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# File 'lib/ms/ident/pepxml/sample_enzyme.rb', line 40

def to_xml(builder=nil)
  xmlb = builder || Nokogiri::XML::Builder.new
  xmlb.sample_enzyme(:name => name) do |xmlb|
    xmlb.specificity(:cut => cut, :no_cut => no_cut, :sense => sense)
  end
  builder || xmlb.doc.root.to_xml
end