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<H1><A NAME="SECTION00090000000000000000">
How to add new ion and denaturing agent species</A>
</H1>
<P>
<SPAN CLASS="textbf">1)</SPAN> Create a new method in the Environment class from the melting package. This method
must facilitate the usage of the new ion or denaturing agent species concentration in the
program.
<P>
<PRE>
public double getNewSpecies() {
if (concentrations.containsKey("newSpecies-Name")){
return concentrations.get("newSpecies-Name");
}
return 0;
}
</PRE>
<P>
<SPAN CLASS="textbf">2)</SPAN> If the new species concentration is a "required ion concentration", that's to say the new
species can be the only one species in the solution (no other ions are necessary), you have to
change the method <SPAN CLASS="textit">private boolean isRequiredConcentrations()</SPAN> in the Environment class.
<P>
<PRE>
private boolean isRequiredConcentrations(){
double Na = 0;
double Mg = 0;
double K = 0;
double Tris = 0;
// The new species must be initialised
double NewSpecies = 0;
if (concentrations.containsKey("Na")){
Na = concentrations.get("Na");
}
if (concentrations.containsKey("Mg")){
Mg = concentrations.get("Mg");
}
if (concentrations.containsKey("K")){
K = concentrations.get("K");
}
if (concentrations.containsKey("Tris")){
Tris = concentrations.get("Tris");
}
// To get the concentration of the new species
if (concentrations.containsKey("newSpecies")){
Tris = concentrations.get("newSpecies");
}
// the new species concentration must be strictly positive
if (Na > 0 || K > 0 || Mg > 0 || Tris > 0 || newSpecies > 0){
return true;
}
return false;
}
</PRE>
<P>
Now, the future steps depend on the identity of the new species you want to add.
<P>
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<LI><A NAME="tex2html235"
HREF="node16.html">New ion species</A>
<LI><A NAME="tex2html236"
HREF="node17.html">New denaturing agent species or other species</A>
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<ADDRESS>
Computational Neurobiology
2009-08-24
</ADDRESS>
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