In file analysis.C:(vector<Real> & pfolds,
int numPfoldsRequested,
int maxNumNeighbors, int runIndex,
float foldedMacrostateRMSDRadius,
float unfoldedMacrostateRMSDRadius,
int numberOfNodes,
Protein** allNodes,
int foldedStateIndex,
int unfoldedStateIndex,
const ccInfoType* ccInfo)
computes pfold, writes the result to a file
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computes pfold, writes the result to a file
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