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<H3><A NAME="SECTION00050100000000000000">
Thermodynamic model for Crick's pairs computation</A>
</H3>
<P>
If it is possible, you directly can create a new class which extends the CricksNNMethod class. (melting.patternModels.cricksPair)
<BR>
<BR>
The CrickNNMethod class already implements the following public functions of the PatternComputationMethod interface.:
<SPAN CLASS="textit">ThermoResult computeThermodynamics(NucleotidSequences sequences,int pos1, int pos2, ThermoResult result)</SPAN>,
<SPAN CLASS="textit">isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)</SPAN>,
and <SPAN CLASS="textit">ThermoResult computesHybridizationInitiation(Environment environment)</SPAN>.
<BR>
<BR>
A CricksNNMethod can compute the enthalpy and entropy of a perfectly matching structure by adding
the thermodynamic parameters of each Crick's base pair. The implemented function
<SPAN CLASS="textit">isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)</SPAN> can determine if
a thermodynamic parameter for one of the Crick's pair is missing. Finally, the implemented function
<SPAN CLASS="textit">ThermoResult computesHybridizationInitiation(Environment environment)</SPAN> is the base implementation
of the hybridization initiation computation and the symetry correction for self complementary sequences.
<BR>
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<P>
If the hybridization initiation can be computed with the function
<SPAN CLASS="textit">public ThermoResult computesHybridizationInitiation(Environment environment)</SPAN> of one of the
following classes : DecomposedInitiation or GlobalInitiation, you directly can create a new class
which extends DecomposedInitiation or GlobalInitiation.
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<ADDRESS>
Computational Neurobiology
2009-08-24
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