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lib/Bio/Network/ProteinNet.pm  view on Meta::CPAN

}

sub unconnected_nodes {
	my $self = shift;
	return $self->SUPER::isolated_vertices;
}

=head2 articulation_points

 Name      : articulation_points
 Purpose   : Find nodes in a graph that if removed will fragment
             the graph into sub-graphs.
 Usage     : my @nodes = $gr->articulation_points
                            or
             my $count = $gr->articulation_points
 Arguments : None
 Returns   : An array or a count of the array of nodes that will fragment 
             the graph if deleted. 
 Notes     : This method is currently broken due to bugs in Graph v. .69
             and later

=cut

sub articulation_points {
 	my $self = shift;
 	my @nodes = $self->SUPER::articulation_points; 
 	wantarray ? @nodes : scalar @nodes;

t/data/bovin_small_intact.xml  view on Meta::CPAN

             </names>
             <xref>
               <primaryRef db="psi-mi" id="MI:0407"/>
               <secondaryRef db="pubmed" id="14755292"/>
             </xref>
           </interactionType>
           <xref>
             <primaryRef db="intact" id="EBI-698541" secondary="arf1-ddef1-1"/>
           </xref>
           <attributeList>
             <attribute name="comment">liposome sedimentation: only 27% of myr-Arf1 GDP and 34% of ASAP1 PZA fragment were recovered in the pelleted membrane fraction if alone. The addition of AlFx did not change the sedimentation properties of each ...
             <attribute name="stimulation">AlFx (Aluminum fluoride) stabilize the complex formation between Arf1-GDP and PZA fragment of ASAP1 by mimicking activated form of Arf1, Arf1-GDP-AlFx.</attribute>
             <attribute name="comment">Both proteins are purified to homogeneity. Myristoylated Arf1 was produced by co-expressing in E. coli the yeast N-myristoyl-transferase.</attribute>
             <attribute name="kd">1.0</attribute>
           </attributeList>
         </interaction>
         <interaction>
           <names>
             <shortLabel>copa-cope-3</shortLabel>
             <fullName>Cop IP: interaction between bovin COP alpha (bait) and bovin COP epsilon (prey)</fullName>
           </names>
           <experimentList>

t/data/sv40_small.xml  view on Meta::CPAN

             </names>
             <xref>
               <primaryRef db="psi-mi" id="MI:0218"/>
               <secondaryRef db="pubmed" id="14755292"/>
             </xref>
           </interactionType>
           <xref>
             <primaryRef db="intact" id="EBI-617778" secondary="epor-socs2-3"/>
           </xref>
           <attributeList>
             <attribute name="caution">SOCS2 described as fragment but no detail given</attribute>
             <attribute name="agonist">Erythropoietin</attribute>
             <attribute name="resulting-ptm">Phosphorylation of SOCS2 - dependent on treatment of cells with erythropoietin</attribute>
             <attribute name="kd">1.0</attribute>
           </attributeList>
         </interaction>
       </interactionList>
     </entry>
   </entrySet>