Class: IndistinguishablePeptide

Inherits:
Peptide
  • Object
show all
Defined in:
lib/protk/peptide.rb

Overview

<indistinguishable_peptide peptide_sequence=“MEYENTLTAAMK” charge=“2” calc_neutral_pep_mass=“1416.63”>

<modification_info modified_peptide="M[147]EYENTLTAAMK"/>
</indistinguishable_peptide>

Instance Attribute Summary

Attributes inherited from Peptide

#charge, #indistinguishable_peptides, #modifications, #modified_sequence, #probability, #protein_name, #sequence, #theoretical_neutral_mass

Class Method Summary collapse

Methods inherited from Peptide

#as_protxml, #coords_in_protein, from_mzid, from_sequence, #gff_record_for_peptide_fragment, #gff_records_for_coords_in_protein, #initialize, #modifications_from_sequence, #mods_to_gff3_records, #to_gff3_records

Constructor Details

This class inherits a constructor from Peptide

Class Method Details

.from_protxml(xmlnode) ⇒ Object 



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# File 'lib/protk/peptide.rb', line 291

def from_protxml(xmlnode)
	pep=new()
	pep.sequence=xmlnode['peptide_sequence']
	pep.charge=xmlnode['charge'].to_i

	mod_info_node = xmlnode.find('protxml:modification_info','protxml:http://regis-web.systemsbiology.net/protXML')

	if ( mod_info_node.length > 0 )
		throw "Encountered multiple modification_info nodes for an indistinguishable peptide" if mod_info_node.length > 1
		pep.modified_sequence = mod_info_node[0]['modified_peptide']
		mod_nodes = mod_info_node[0].find('protxml:mod_aminoacid_mass','protxml:http://regis-web.systemsbiology.net/protXML')
		if ( mod_nodes.length > 0 )
			pep.modifications = mod_nodes.collect { |e| PeptideMod.from_protxml(e) }
		else
			pep.modifications = pep.modifications_from_sequence(pep.modified_sequence)
		end
	end
	pep
end