Data Model version 2.1.2
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Class: Run


    Haddock Run
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link haddockProject to class HaddockProject
Main key: serial
Mandatory Attributes: None
Known Subclasses: None
Children:
link haddockEnergyTerms to class HaddockEnergyTerm
link scoringWeights to class ScoringWeight
Constructor: newObj = Run( haddockProject, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
analysisClustRmsd PositiveFloat 1..1  
analysisClustSize NonNegativeInt 1..1  
analysisDistHBond PositiveFloat 1..1  
analysisDistNonbond PositiveFloat 1..1  
calcDesolvation Boolean 1..1  
centerOfMassConstant NonNegativeFloat 1..1  
centerOfMassRestraints Boolean 1..1 (cmrest)  
cnsExecutable PathString 1..1 Defines the path to the CNS exacutable  
cpuNumber NonNegativeInt 1..1 Defines the number of cpu's used in a cluster for submission of Haddock jobs.  
dielectricType DielectricType 1..1 (dielec)  
doAirScaling Boolean 1..1 Use automated distance restraints weighting. cns name: air_scaling  
doIncludeDihEnergy Boolean 1..1 (dihedflag)  
doRigidBodyElectrostatics Boolean 1..1 (elecflag_0)  
doRigidBodyWaterTrans Boolean 1..1 Allows translation of water molecules during rigid-body docking. cns name: transwater  
doRigidTranslations Boolean 1..1  
doSAElectrostatics Boolean 1..1 (elecflag_1)  
doWaterAnalysis Boolean 1..1 Do some water analysis. cns name: water_analysis  
doWaterDock Boolean 1..1 Do water docking (waterdock)  
epsilon Float 1..1 (epsilon)  
haddockDir PathString 1..1 Defines the path to the Haddock software directory.  
initialRigidBodyMinim Boolean 1..1  
nTrails NonNegativeInt 1..1  
ncsRestraintConstant Float 1..1 Force constant for ncs restraints (kncs)  
nonBondedType NonBondedType 1..1 Run non-bonded interaction type  
numAmbRestautoAir NonNegativeInt 1..1 Define the number of AIR restraints for automated weighting. cns name: numAmbRestautoAir  
numAnalysisStructures NonNegativeInt 1..1 Number of structures to nalyse (anastruc_1)  
numInitWaterShells NonNegativeInt 1..1 Number of different initial solvation shells to generate. cns name: waterensemble  
numIt0Structures NonNegativeInt 1..1 Number of iteration 0 (rigid dynamics) structures. (structures_0)  
numIt1Structures NonNegativeInt 1..1 Number of iteration 1 (flexible dynamics) structures.  
numUnambRestautoAir NonNegativeInt 1..1 Number of distance restraints for automated weighting. cns name: tot_unamb  
numWrefStructures NonNegativeInt 1..1 Number of water refinemetn structures (waterrefine)  
queueCommand Line 1..1 Defines the queue type for Haddock job submission. 'csh' is default for running on a single machine in C-shell.  
radomizeStartOriention Boolean 1..1  
randomAmbigRestraints Boolean 1..1 Use random ambiguos interaction restraints (ranair)  
randomExclParts Int 1..1 Number of partitons for random exclusion (ncvpart)  
randomExcludeAir Boolean 1..1 Randomly exclude ambiguous interaction restraints (noecv)  
randomSeed Int 1..1  
removeNonPolarH Boolean 1..1 Remove non-polar hydrogens (delenph)  
rigidbodyIMinteractScaling Float 1..1 (inter_rigid)  
rotate180It0 Boolean 1..1  
rotate180It1 Boolean 1..1  
serial Int 1..1 Serial number of object. Serves as object main key. Serial numbers of deleted objects are not re-used. Serial numbers can only be set by the implementation. Values are in practice always positive, since negative values are interpreted as a signal to set the next free serial  
skipStructures NonNegativeInt 1..1  
solvent Solvent 1..1  
surfaceContactConstant NonNegativeFloat 1..1 (ksurf)  
surfaceContactRestraints Boolean 1..1  
symmetryRestraintConstant Float 1..1 Force constant for symmetry restraints ((ksym)  
useDbSolvateMethod Boolean 1..1 Use database driven solvation method? cns name: solvate_method  
useDnaRestraints Boolean 1..1 (dnarest_on)  
useHBondRestraints Boolean 1..1  
waterInitRestCutoff NonNegativeFloat 1..1 Initial cutoff for restraints solvating method. cns name water_restraint_initial  
waterRestCutoff NonNegativeFloat 1..1 Cutoff for restraints solvating method. cns name: waterRestCutoff  
waterRestScale NonNegativeFloat 1..1 Force constant for restraints solvating method. cns name: water_restraint_scale  
waterSurfaceCutoff NonNegativeFloat 1..1 Water-protein surface-cutoff. cns name water_surfcutoff  
waterToAddRandom FloatRatio 1..1 Random fraction to be added to the fraction of water to keep. cns name: water_randfrac  
waterToKeep FloatRatio 1..1 Fraction of water to keep. cns name: water_tokeep  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
annealProtocol molsim.api.AnnealProtocol.AnnealProtocol 0..1  
haddockEnergyTerms HaddockEnergyTerm 0..* (Child link). child link to class HaddockEnergyTerm  
haddockProject HaddockProject 1..1 (Parent link). parent link  
nmrConstraintStore ccp.api.nmr.NmrConstraint.NmrConstraintStore 0..1 CCP NmrConstraintStore where data come from  
parent HaddockProject 1..1 link to parent object - synonym for haddockProject  
scoringWeights ScoringWeight 0..* (Child link). child link to class ScoringWeight  
symmetryRestraints molsim.api.Symmetry.Symmetry 0..* MolSystem symmetry operations used as restraints. The type depends on the symmetryCode of the Symmetry linked to.  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
analysisClustRmsd
getAnalysisClustRmsd PositiveFloat -
setAnalysisClustRmsd - PositiveFloat
analysisClustSize
getAnalysisClustSize NonNegativeInt -
setAnalysisClustSize - NonNegativeInt
analysisDistHBond
getAnalysisDistHBond PositiveFloat -
setAnalysisDistHBond - PositiveFloat
analysisDistNonbond
getAnalysisDistNonbond PositiveFloat -
setAnalysisDistNonbond - PositiveFloat
calcDesolvation
getCalcDesolvation Boolean -
setCalcDesolvation - Boolean
centerOfMassConstant
getCenterOfMassConstant NonNegativeFloat -
setCenterOfMassConstant - NonNegativeFloat
centerOfMassRestraints
getCenterOfMassRestraints Boolean -
setCenterOfMassRestraints - Boolean
cnsExecutable
getCnsExecutable PathString -
setCnsExecutable - PathString
cpuNumber
getCpuNumber NonNegativeInt -
setCpuNumber - NonNegativeInt
dielectricType
getDielectricType DielectricType -
setDielectricType - DielectricType
doAirScaling
getDoAirScaling Boolean -
setDoAirScaling - Boolean
doIncludeDihEnergy
getDoIncludeDihEnergy Boolean -
setDoIncludeDihEnergy - Boolean
doRigidBodyElectrostatics
getDoRigidBodyElectrostatics Boolean -
setDoRigidBodyElectrostatics - Boolean
doRigidBodyWaterTrans
getDoRigidBodyWaterTrans Boolean -
setDoRigidBodyWaterTrans - Boolean
doRigidTranslations
getDoRigidTranslations Boolean -
setDoRigidTranslations - Boolean
doSAElectrostatics
getDoSAElectrostatics Boolean -
setDoSAElectrostatics - Boolean
doWaterAnalysis
getDoWaterAnalysis Boolean -
setDoWaterAnalysis - Boolean
doWaterDock
getDoWaterDock Boolean -
setDoWaterDock - Boolean
epsilon
getEpsilon Float -
setEpsilon - Float
haddockDir
getHaddockDir PathString -
setHaddockDir - PathString
initialRigidBodyMinim
getInitialRigidBodyMinim Boolean -
setInitialRigidBodyMinim - Boolean
nTrails
getNTrails NonNegativeInt -
setNTrails - NonNegativeInt
ncsRestraintConstant
getNcsRestraintConstant Float -
setNcsRestraintConstant - Float
nonBondedType
getNonBondedType NonBondedType -
setNonBondedType - NonBondedType
numAmbRestautoAir
getNumAmbRestautoAir NonNegativeInt -
setNumAmbRestautoAir - NonNegativeInt
numAnalysisStructures
getNumAnalysisStructures NonNegativeInt -
setNumAnalysisStructures - NonNegativeInt
numInitWaterShells
getNumInitWaterShells NonNegativeInt -
setNumInitWaterShells - NonNegativeInt
numIt0Structures
getNumIt0Structures NonNegativeInt -
setNumIt0Structures - NonNegativeInt
numIt1Structures
getNumIt1Structures NonNegativeInt -
setNumIt1Structures - NonNegativeInt
numUnambRestautoAir
getNumUnambRestautoAir NonNegativeInt -
setNumUnambRestautoAir - NonNegativeInt
numWrefStructures
getNumWrefStructures NonNegativeInt -
setNumWrefStructures - NonNegativeInt
queueCommand
getQueueCommand Line -
setQueueCommand - Line
radomizeStartOriention
getRadomizeStartOriention Boolean -
setRadomizeStartOriention - Boolean
randomAmbigRestraints
getRandomAmbigRestraints Boolean -
setRandomAmbigRestraints - Boolean
randomExclParts
getRandomExclParts Int -
setRandomExclParts - Int
randomExcludeAir
getRandomExcludeAir Boolean -
setRandomExcludeAir - Boolean
randomSeed
getRandomSeed Int -
setRandomSeed - Int
removeNonPolarH
getRemoveNonPolarH Boolean -
setRemoveNonPolarH - Boolean
rigidbodyIMinteractScaling
getRigidbodyIMinteractScaling Float -
setRigidbodyIMinteractScaling - Float
rotate180It0
getRotate180It0 Boolean -
setRotate180It0 - Boolean
rotate180It1
getRotate180It1 Boolean -
setRotate180It1 - Boolean
serial
getSerial Int -
setSerial - Int
skipStructures
getSkipStructures NonNegativeInt -
setSkipStructures - NonNegativeInt
solvent
getSolvent Solvent -
setSolvent - Solvent
surfaceContactConstant
getSurfaceContactConstant NonNegativeFloat -
setSurfaceContactConstant - NonNegativeFloat
surfaceContactRestraints
getSurfaceContactRestraints Boolean -
setSurfaceContactRestraints - Boolean
symmetryRestraintConstant
getSymmetryRestraintConstant Float -
setSymmetryRestraintConstant - Float
useDbSolvateMethod
getUseDbSolvateMethod Boolean -
setUseDbSolvateMethod - Boolean
useDnaRestraints
getUseDnaRestraints Boolean -
setUseDnaRestraints - Boolean
useHBondRestraints
getUseHBondRestraints Boolean -
setUseHBondRestraints - Boolean
waterInitRestCutoff
getWaterInitRestCutoff NonNegativeFloat -
setWaterInitRestCutoff - NonNegativeFloat
waterRestCutoff
getWaterRestCutoff NonNegativeFloat -
setWaterRestCutoff - NonNegativeFloat
waterRestScale
getWaterRestScale NonNegativeFloat -
setWaterRestScale - NonNegativeFloat
waterSurfaceCutoff
getWaterSurfaceCutoff NonNegativeFloat -
setWaterSurfaceCutoff - NonNegativeFloat
waterToAddRandom
getWaterToAddRandom FloatRatio -
setWaterToAddRandom - FloatRatio
waterToKeep
getWaterToKeep FloatRatio -
setWaterToKeep - FloatRatio

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
annealProtocol
getAnnealProtocol molsim.api.AnnealProtocol.AnnealProtocol -
setAnnealProtocol - molsim.api.AnnealProtocol.AnnealProtocol
haddockEnergyTerms
getHaddockEnergyTerms HaddockEnergyTerm Set -
sortedHaddockEnergyTerms HaddockEnergyTerm List -
findFirstHaddockEnergyTerm HaddockEnergyTerm keyword=value pairs
findAllHaddockEnergyTerms HaddockEnergyTerm Set keyword=value pairs
haddockProject
getHaddockProject HaddockProject -
nmrConstraintStore
getNmrConstraintStore ccp.api.nmr.NmrConstraint.NmrConstraintStore -
setNmrConstraintStore - ccp.api.nmr.NmrConstraint.NmrConstraintStore
parent
getParent HaddockProject -
scoringWeights
getScoringWeights ScoringWeight Set -
sortedScoringWeights ScoringWeight List -
findFirstScoringWeight ScoringWeight keyword=value pairs
findAllScoringWeights ScoringWeight Set keyword=value pairs
symmetryRestraints
getSymmetryRestraints molsim.api.Symmetry.Symmetry Set -
setSymmetryRestraints - molsim.api.Symmetry.Symmetry Set
sortedSymmetryRestraints molsim.api.Symmetry.Symmetry List -
addSymmetryRestraint - molsim.api.Symmetry.Symmetry
removeSymmetryRestraint - molsim.api.Symmetry.Symmetry
findFirstSymmetryRestraint molsim.api.Symmetry.Symmetry keyword=value pairs
findAllSymmetryRestraints molsim.api.Symmetry.Symmetry Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey Run memops.api.Implementation.MemopsObject, Any List static
getFullKey Any List Boolean
getLocalKey Any -
get Any String
set - String, Any

Factory Methods (in package)

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Method Return Parameters
newHaddockEnergyTerm HaddockEnergyTerm code, termId, ...
newScoringWeight ScoringWeight stage, term, ...

Other Methods (in package)

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Method Return Parameters Comment
resetNmrConstraintStore - ccp.api.nmr.NmrConstraint.NmrConstraintStore non-std. reset nmrConstraintStore. Note this link is frozen and cannot be modified normally. NB Will delete the link from any HaddockEnergyTerm to its constraintList.

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-10-11-22:58:43_00007

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraints:

None
Known inward one-way links: None
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Thu Oct 2 16:09:51 2014    from data model package  utrecht.api.Haddock.Run   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk