Commit adb762dc authored by Matthew Tam's avatar Matthew Tam
Browse files

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.
parent 64fafb5d
#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
This diff is collapsed.
......@@ -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"]
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