ported DRprotein=MKT's DR implementation of the protein folding problem. still...

ported DRprotein=MKT's DR implementation of the protein folding problem. still needs comments, but it runs.

DRprotein_demo.py

+#Input, Output and Logfiles
+problemName = '1PTQ'
+inputFile   = '../inputdata/1PTQ.pdb' #in InputFiles directory
+outputFile  = '1PTQrecon.pdb'
+
+#Parameters used by all variants of the algorithm
+gapEps = 1e-5
+maxIterations = 5000
+P1Eps = 1e-12
+P2Rank = 3
+
+#Data simulation parameters
+maxBondLength = 6
+
+startingSeed = 2
+replications = 1
+
+from proxtoolbox.Problems import DRprotein
+
+for rep in range(replications):
+    problem = DRprotein(problemName,startingSeed+rep)
+
+    problem.readInputFile(inputFile)
+    problem.addOutputFile(outputFile)
+
+    problem.setGapEps(gapEps)
+    problem.setMaxIterations(maxIterations)
+    problem.setP1Eps(P1Eps)
+    problem.setP2Rank(P2Rank)
+
+    problem.simulateNMR(maxBondLength)
+    problem.addAminoInfo()
+
+    problem.solve()
+    problem.printStats()
+
+    problem.savePDB()
+    #problem.saveJPG()
+    problem.show()
+
+    del problem

proxtoolbox/Problems/__init__.py

@@ -9,5 +9,6 @@ The "Problems"-module contains all mathematical problems that can already be sol
 
 from .ptychography import *
 from .sudoku import *
+from .DRprotein import *
 
-__all__ = ["Ptychography","Ptychography_NTT_01_26210","Sudoku"]
+__all__ = ["Ptychography","Ptychography_NTT_01_26210","Sudoku","DRprotein"]