class IndistinguishablePeptide

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

Public Class Methods

from_protxml(xmlnode) click to toggle source
# 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