Welcome: an Introduction to this Site
NMRPipe: a Comprehensive Software System for Biomolecular NMR
Special Applications: NMR Drug Screening, Automation, and so on
Dipolar Couplings, Chemical Shifts, and Protein Structure
Miscellaneous

Frank's CV, Recent Slides, and Thesis

 

 

 

  Frank Delaglio, Ph.D.

  Software Science Consultant
  13840 Grey Colt Drive
  North Potomac MD 20878 USA


  Tel: 301 806-0867
  Fax: 301 309-8717
  E-mail: delaglio@nmrscience.com



Programs of the NMRPipe System
modelXY: Command-line Utility for Non-Linear Least-Squares Optimization

Flag Argument Default Description
 -iseed seed 54321 Random Number Seed.
 -iter maxIt 500 Maximum Iterations.
 -maxf maxEv 500 Maximum Function Evaluations.
 -dig nDig 5 Number of Digits in Target.
 -tol relTol 1e-6 Relative Function Tolerance.
 -cf confid 0.90 Confidence Interval for Error.
 -verb Verbose Mode ON (Default).
 -noverb Verbose Mode Off.
 -silent Suppress Warning/Error Messages.
 -signal Allow interrupt via Control-C.
X/Y and Model Specification (Use -x/-y or -data)
 -x xList List of X Coords for Model.
 -y yList List of Y Coords for Model.
 -data specName Spectral Data for Y Coords of Model.
 -p pList List of Initial Values for Variables.
 -macro macName Macro Which Defines Model Function.
Optional User Flags:
 -a aList None List of Auxiliary Values.
 -pHi hiList Inf Upper Parameter Bound List.
 -pLo loList -Inf Lower Parameter Bound List.
 -noise nList 0.0 List of Noise Estimates for Y Coords.
 -yScale sFactor 1.0 Scale Factor for Y Coords.
 -gc guessCnt 1 Number of Monte Carlo Trials.
 -id fitID 0 An ID Number for this Analysis.
 -res No Macro returns residual, not function.
User-Defined Macro Variables:
 -var vList Variable Name/Numerical Value Pairs.
 -str sList String Name/Text Value Pairs.
M-Language Spectral Variables (requires -data):
 quadSize                    X-Axis Complex Adjust Factor (1=Real, 2=Complex).
 xSize                       X-Axis Size.
 ySize                       Y-Axis Size.
 zSize                       Z-Axis Size.
 aSize                       A-Axis Size.
 dimCount                    Dimension Count.
 fdata[FDATSIZE]             Spectral Data Header.
M-Language Macro Variables:
 id                 (Input)  ID Number for this Analysis.
 lsRes              (Input)  Current Least-Squares Residual.
 confid             (Input)  Confidence Interval, 0.0 to 1.0.
 reportFlag         (Input)  1=Optimization is Finished.
 xList[xyCount]     (Input)  X-Coords for Model.
 dList[xyCount]     (Input)  Y-Coords from Original Data.
 qList[xyCount]     (Input)  Y-Coords from Monte Carlo Data.
 nList[xyCount]     (Input)  Corresponding Noise Values.
 eList[pCount]      (Input)  Monte Carlo Error Estimates.  (Only When reportFlag = 1)
 pList[pCount]      (Input)  Current Model Parameters.  (Optimal When reportFlag = 1)
 aList[aCount]      (Input)  Auxiliary values, if any.
 yList[xyCount]     (Output) Y-Coords for Model, computed by User Macro.

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last updated: Jan 22, 2009 / big frank

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