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TODO
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TODOs:
improve Import routine, do in ImportAtomsAndResiduesFromPDBFile, assign each Atom its residue name
-debug and compare results
-ProteinStructureCopy activate again
-clean up / return ImportPDBFile
-center issue Atom vs ResidueID
-if zeros coo legendre will produce nan's
q-based progress bar for ComputeModel and q-based and iteration-based ones for LM algorithm
Add notes:
-ProteinStructure is passed as Copies down to fit routines and Model (struct Protein ProteinStructure), no struct Protein * ProteinStructure, except for AllocateProteinStructure, CopyProteinStructure and ImportAtomsAndResiduesFromPDBFile -> use &ProteinStructure(Copy) there
-by contrast UserDefinedStructure is passed as Pointer down to fit routines and Model, do the same with UserDefinedStructureShared
-automatic CaPP call to add H and H2O?
-new arguments and assign arguments as in XNDiff and fit2dcorr:
+card <file>
+pdb <file>
+par <file>
+dat <file>
-res <file fold_steps>, default none
-out <subdir name for results>, pdb card par dat own_string -> chose the name of the file + append -results, default card
-Q min1 max1 min2 max2 min3 max3 ... (all ranges or only one range for all) -> check that it matches, default 0 1 or all
-fit <alg-index num_iter ...>, default LM 50 ..., check input
-log <logfile mode>, default logfile.log +1
-cov <1/0>, default 0
-con <confidence level>, default ?
-rm the stupid z option
after that check existence of all relevant files
generally better order input args in Opt algorithm functions
GridsearchLM(2)
---------------
mv output to logfile:
Parameter 0 = 0 BackN100
Parameter 1 = 1 ScaleN100
Parameter 2 = 0 BackN0
Parameter 3 = 1 ScaleN0
Parameter 4 = 0 BackX
Parameter 5 = 2e+07 ScaleX
Parameter 6 = 1 ScaleConc
Parameter 7 = 0.1 HYDR
Parameter 8 = 0.1 MOD
********************************************************************************
Cycle number = 1
Parameter nr. 5 = 2.11427e+07
Chisquare = 6.15815
********************************************************************************
Cycle number = 1
Parameter nr. 7 = 0.0376685
Chisquare = 2.67052
********************************************************************************
Cycle number = 1
Parameter nr. 8 = 0.0516037
Chisquare = 2.40156
********************************************************************************
Cycle number = 2
Parameter nr. 5 = 2.23073e+07
Chisquare = 1.24528
Fix output of LM in logfile:
Run fitting routine no. 2 GridsearchLM():
Initiating the Levenberg-Marquardt-algorithm
----------------------------------------------------------------
Algorithm terminated at maximal iteration step it = 2, maybe increase number of iteration steps
Initiating the Levenberg-Marquardt-algorithm
----------------------------------------------------------------
Algorithm terminated at maximal iteration step it = 2, maybe increase number of iteration steps
Initiating the Levenberg-Marquardt-algorithm
----------------------------------------------------------------
Algorithm terminated at maximal iteration step it = 2, maybe increase number of iteration steps
Initiating the Levenberg-Marquardt-algorithm
----------------------------------------------------------------
Algorithm terminated at maximal iteration step it = 2, maybe increase number of iteration steps
Initiating the Levenberg-Marquardt-algorithm
BFGS(3)
---------------
GridsearchBFGS(4)
-----------------
Swarm(5)
-----------------
Genetic(5)
-----------------