NMRPipe: Software for multidimensional NMR

Applications and examples

NMR and protein structure

Resume, lecture slides, and thesis

Frank Delaglio, Ph.D.

19804 Maycrest Way
Germantown MD 20876 USA

301 806-0867
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