In file analysis.C:

void computeAndPrintPfold

(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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