Class: Mspire::Ident::Pepxml::SampleEnzyme

Inherits:

Object

• Object
• Mspire::Ident::Pepxml::SampleEnzyme

show all

Includes:

Merge

Defined in:

lib/mspire/ident/pepxml/sample_enzyme.rb

Instance Attribute Summary (collapse)

• - (Object) cut

  amino acids after which to cleave.

• - (Object) name

  an identifier.

• - (Object) no_cut

  cleave at 'cut' amino acids UNLESS it is followed by 'no_cut'.

• - (Object) sense

  'C' or 'N'.

Class Method Summary (collapse)

• + (Object) from_pepxml_node(node)

Instance Method Summary (collapse)

• - (Object) from_pepxml_node(node)

  returns self.

• - (SampleEnzyme) initialize(arg = {}) constructor

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

• - (Object) num_missed_cleavages(aaseq)

  takes an amino acid sequence (e.g. PEPTIDE).

• - (Object) num_tol_term(prev_aa, middle, next_aa)

  No arguments should contain non-standard amino acids.

• - (Object) set_trypsin
• - (Object) to_xml(builder = nil)

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

Methods included from Merge

#merge!

trypsin

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# File 'lib/mspire/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

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

def cut
  @cut
end

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

def name
  @name
end

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

def no_cut
  @no_cut
end

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

def sense
  @sense
end

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

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

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# File 'lib/mspire/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

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# File 'lib/mspire/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

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# File 'lib/mspire/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

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

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

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# File 'lib/mspire/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