Frank Delaglio NMR Science Home

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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

NMRWish Built-In TCL Functions
geco: Genetic Algorithm for Combinatorial Optimization.

Arguments and Defaults for 0 Nodes:

Flag	Argument	Default	Description
`-iseed`	`randomSeed`	`54321`
`-verb`			Verbose mode ON (Default).
`-noverb`			Verbose mode Off.

GECO: Genetic Algorithm Combinatorial Optimization:

`-pop`	`populationSize`	`50`
`-gen`	`generationCount`	`10`
`-pMUT`	`mutationProb`	`0.0100`
`-pPTM`	`pathTransProb`	`0.0000`
`-pPMX`	`PMXcrossProb`	`0.1500`
`-pOX`	`OXcrossProb`	`0.1500`
`-pGX`	`GXcrossProb`	`0.1500`
`-fc`	`fscaleCount`	`0`
`-fi`	`fscaleInitial`	`1.20`
`-ff`	`fscaleFinal`	`2.00`
`-min`	`minTargetVal`	`0.00`
`-max`	`maxTargetVal`	`1.000000e+17`
`-noGBM`	`maxFailBeforeGBM`	`4`
`-GBM`	`greedyMutCount`	`4`
`-noI`	`maxNoImprove`	`0`
`-rb`	`restoreBestAfter`	`4`
`-bc`	`bestCountToSave`	`1`

SACO: Simulated Annealing Combinatorial Optimization.

`-noSA`	`maxFailBeforeSA`	`8`
`-tiSA`	`sacoInitialT`	`0.10`
`-tfSA`	`sacoFinalT`	`0.00`
`-tcSA`	`sacoTCount`	`32`
`-ocSA`	`sacoOpCount`	`0`
`-scSA`	`sacoSucCount`	`32`
`-mfSA`	`sacoMaxFail`	`24`

Parallel Optimization:

`-parCount`	`parallelCount`	`1`
`-parID`	`parallelID`	`0`

TCL Parameters:

`-nc`	`nCount`	`0`
`-idList`	`idList`	`None`
`-locList`	`locList`	`None`
`-placeArray`	`pName`	`placeArray`	P(id,loc)
`-joinArray`	`jName`	`joinArray`	D(idI,idJ)
`-nodeArray`	`nName`	`nodeList`	Current Result.
`-defPlace`	`pVal`	`0.0`	Default Penalty
`-defJoin`	`jVal`	`0.0`	Default Dist
`-scoreOffset`	`sVal`	`0.0`	Score Offset

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last updated: Apr 20, 2011 / big frank

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