Data Model version 2.1.2
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Class: Resonance


    A connection record for assignment. 'Stands for' a single Atom or group of atoms in fast exchange.

    The Resonance holds a central place in the Nmr package, as almost all assignment, of Chemical shifts, Atoms, Constraints, Peaks etc. is done through the intermediary of a Resonance. This allows the relationship between Shifts, Peaks, Constraints, (...) to be described precisely without first assigning the Nmr spectrum, provides a simple mechanism for handling prochiral groups, and in general permits greater flexibility.
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link nmrProject to class NmrProject
Main key: serial
Mandatory Attributes: isotopeCode
Known Subclasses: None
Children:
link resonanceProbs to class ResonanceProb
Constructor: newObj = Resonance( nmrProject,isotopeCode=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
assignNames Word 0..* Names of AtomSets to which Resonance should or could be assigned. Must be in the CCPN (=IUPAC) nomenclature. Allows you to fix assignments when you know only the residue type (e.g. Leu) not the residue number. Examples (all for Leu): ('HG'), ('CA'), non-stereospecific ('HB2','HB3') or ('HD1*','HD2*'), stereospecific ('HB2') or ('HD1*'), mixed ('HB2','HB3','HG').  
details Text 0..1 Free text, for notes, explanatory comments, etc.  
isotopeCode Word 1..1 Isotope code for the resonance. E.g. '1H', '13C', '2H', '235U'  
name Line 0..1 Name of Resonance. It is recommended to set it to the assignName (q.v.) if known, but the name can be set freely.  
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  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
analysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout 0..* AnalysisLayouts referring to Resonances  
analysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel 0..* AnalysisPanels referring to Resonances  
chainStates ChainState 0..* ChainState in which this Resonance can be found  
covalentlyBound Resonance 0..* Resonances on both ends stand for atoms that are covalently linked.  
datums Datum 0..* Measurements of non-predefined type relevant for Resonance  
dipolarRelaxations DipolarRelaxation 0..* Dipole-dipole relaxation measurements involving resonance.  
hExchProtections HExchProtection 0..* Hydrogen exchange rate protection factor measurements for resonance.  
hExchRates HExchRate 0..* Hydrogen exchange rate measurements for resonance.  
isotope ccp.api.molecule.ChemElement.Isotope 0..1 Derived. Isotope corresponding to Resonance  
isotropicS2s IsotropicS2 0..* Isotropic order parameter values that apply to reonance.  
jCouplings JCoupling 0..* J coupling measurements for resonance  
nmrProject NmrProject 1..1 (Parent link). parent link  
noes Noe 0..* Homonuclear NOEs in which Resonance is involved  
parent NmrProject 1..1 link to parent object - synonym for nmrProject  
peakDimContribNs PeakDimContribN 0..* PeakDimContribNs assigned to Resonance  
peakDimContribs PeakDimContrib 0..* PeakDimContribs assigned to Resonance  
pkas Pka 0..* pKa values associated with Resonance  
rdcs Rdc 0..* Reduced dipolar coupling measurements involving resonance.  
resonanceGroup ResonanceGroup 0..1 ResonanceGroup to which Resonance definitely belongs  
resonanceProbs ResonanceProb 0..* (Child link). ResonanceProbs connecting to ResonanceGroups to which this Resonace probably belongs.  
resonanceSet ResonanceSet 0..1 ResonanceSet to which Resonance belongs. Part of assignment of Resonance to Atoms.  
shiftAnisotropies ShiftAnisotropy 0..* Chemical shift anisotropies for resonance.  
shiftDifferences ShiftDifference 0..* Chemical SHift Differences for resonance.  
shifts Shift 0..* Chemical shifts for resonance  
spectralDensities SpectralDensity 0..* Spectral density measurements relevant to Resonance.  
t1Rhos T1Rho 0..* T1 rho measurements for resonance  
t1s T1 0..* T1 relaxation values for resonance.  
t2s T2 0..* T2 relaxation measurements for resonance.  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
assignNames
getAssignNames Word Tuple -
setAssignNames - Word List
addAssignName - Word
removeAssignName - Word
details
getDetails Text -
setDetails - Text
isotopeCode
getIsotopeCode Word -
setIsotopeCode - Word
name
getName Line -
setName - Line
serial
getSerial Int -
setSerial - Int

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
analysisLayouts
getAnalysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout Set -
setAnalysisLayouts - ccpnmr.api.AnalysisV3.AnalysisLayout Set
sortedAnalysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout List -
addAnalysisLayout - ccpnmr.api.AnalysisV3.AnalysisLayout
removeAnalysisLayout - ccpnmr.api.AnalysisV3.AnalysisLayout
findFirstAnalysisLayout ccpnmr.api.AnalysisV3.AnalysisLayout keyword=value pairs
findAllAnalysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout Set keyword=value pairs
analysisPanels
getAnalysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel Set -
setAnalysisPanels - ccpnmr.api.AnalysisV3.AnalysisPanel Set
sortedAnalysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel List -
addAnalysisPanel - ccpnmr.api.AnalysisV3.AnalysisPanel
removeAnalysisPanel - ccpnmr.api.AnalysisV3.AnalysisPanel
findFirstAnalysisPanel ccpnmr.api.AnalysisV3.AnalysisPanel keyword=value pairs
findAllAnalysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel Set keyword=value pairs
chainStates
getChainStates ChainState Set -
setChainStates - ChainState Set
sortedChainStates ChainState List -
addChainState - ChainState
removeChainState - ChainState
findFirstChainState ChainState keyword=value pairs
findAllChainStates ChainState Set keyword=value pairs
covalentlyBound
getCovalentlyBound Resonance Set -
setCovalentlyBound - Resonance Set
sortedCovalentlyBound Resonance List -
addCovalentlyBound - Resonance
removeCovalentlyBound - Resonance
findFirstCovalentlyBound Resonance keyword=value pairs
findAllCovalentlyBound Resonance Set keyword=value pairs
datums
getDatums Datum Set -
setDatums - Datum Set
sortedDatums Datum List -
addDatum - Datum
removeDatum - Datum
findFirstDatum Datum keyword=value pairs
findAllDatums Datum Set keyword=value pairs
dipolarRelaxations
getDipolarRelaxations DipolarRelaxation Set -
setDipolarRelaxations - DipolarRelaxation Set
sortedDipolarRelaxations DipolarRelaxation List -
findFirstDipolarRelaxation DipolarRelaxation keyword=value pairs
findAllDipolarRelaxations DipolarRelaxation Set keyword=value pairs
hExchProtections
getHExchProtections HExchProtection Set -
setHExchProtections - HExchProtection Set
sortedHExchProtections HExchProtection List -
findFirstHExchProtection HExchProtection keyword=value pairs
findAllHExchProtections HExchProtection Set keyword=value pairs
hExchRates
getHExchRates HExchRate Set -
setHExchRates - HExchRate Set
sortedHExchRates HExchRate List -
findFirstHExchRate HExchRate keyword=value pairs
findAllHExchRates HExchRate Set keyword=value pairs
isotope
getIsotope ccp.api.molecule.ChemElement.Isotope - non-std.
isotropicS2s
getIsotropicS2s IsotropicS2 Set -
setIsotropicS2s - IsotropicS2 Set
sortedIsotropicS2s IsotropicS2 List -
findFirstIsotropicS2 IsotropicS2 keyword=value pairs
findAllIsotropicS2s IsotropicS2 Set keyword=value pairs
jCouplings
getJCouplings JCoupling Set -
setJCouplings - JCoupling Set
sortedJCouplings JCoupling List -
findFirstJCoupling JCoupling keyword=value pairs
findAllJCouplings JCoupling Set keyword=value pairs
nmrProject
getNmrProject NmrProject -
noes
getNoes Noe Set -
setNoes - Noe Set
sortedNoes Noe List -
findFirstNoe Noe keyword=value pairs
findAllNoes Noe Set keyword=value pairs
parent
getParent NmrProject -
peakDimContribNs
getPeakDimContribNs PeakDimContribN Set -
setPeakDimContribNs - PeakDimContribN Set
sortedPeakDimContribNs PeakDimContribN List -
findFirstPeakDimContribN PeakDimContribN keyword=value pairs
findAllPeakDimContribNs PeakDimContribN Set keyword=value pairs
peakDimContribs
getPeakDimContribs PeakDimContrib Set -
setPeakDimContribs - PeakDimContrib Set
sortedPeakDimContribs PeakDimContrib List -
findFirstPeakDimContrib PeakDimContrib keyword=value pairs
findAllPeakDimContribs PeakDimContrib Set keyword=value pairs
pkas
getPkas Pka Set -
setPkas - Pka Set
sortedPkas Pka List -
findFirstPka Pka keyword=value pairs
findAllPkas Pka Set keyword=value pairs
rdcs
getRdcs Rdc Set -
setRdcs - Rdc Set
sortedRdcs Rdc List -
findFirstRdc Rdc keyword=value pairs
findAllRdcs Rdc Set keyword=value pairs
resonanceGroup
getResonanceGroup ResonanceGroup -
setResonanceGroup - ResonanceGroup
resonanceProbs
getResonanceProbs ResonanceProb Set -
sortedResonanceProbs ResonanceProb List -
findFirstResonanceProb ResonanceProb keyword=value pairs
findAllResonanceProbs ResonanceProb Set keyword=value pairs
resonanceSet
getResonanceSet ResonanceSet -
setResonanceSet - ResonanceSet
shiftAnisotropies
getShiftAnisotropies ShiftAnisotropy Set -
setShiftAnisotropies - ShiftAnisotropy Set
sortedShiftAnisotropies ShiftAnisotropy List -
findFirstShiftAnisotropy ShiftAnisotropy keyword=value pairs
findAllShiftAnisotropies ShiftAnisotropy Set keyword=value pairs
shiftDifferences
getShiftDifferences ShiftDifference Set -
setShiftDifferences - ShiftDifference Set
sortedShiftDifferences ShiftDifference List -
findFirstShiftDifference ShiftDifference keyword=value pairs
findAllShiftDifferences ShiftDifference Set keyword=value pairs
shifts
getShifts Shift Set -
setShifts - Shift Set
sortedShifts Shift List -
findFirstShift Shift keyword=value pairs
findAllShifts Shift Set keyword=value pairs
spectralDensities
getSpectralDensities SpectralDensity Set -
setSpectralDensities - SpectralDensity Set
sortedSpectralDensities SpectralDensity List -
findFirstSpectralDensity SpectralDensity keyword=value pairs
findAllSpectralDensities SpectralDensity Set keyword=value pairs
t1Rhos
getT1Rhos T1Rho Set -
setT1Rhos - T1Rho Set
sortedT1Rhos T1Rho List -
findFirstT1Rho T1Rho keyword=value pairs
findAllT1Rhos T1Rho Set keyword=value pairs
t1s
getT1s T1 Set -
setT1s - T1 Set
sortedT1s T1 List -
findFirstT1 T1 keyword=value pairs
findAllT1s T1 Set keyword=value pairs
t2s
getT2s T2 Set -
setT2s - T2 Set
sortedT2s T2 List -
findFirstT2 T2 keyword=value pairs
findAllT2s T2 Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey Resonance 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
newResonanceProb ResonanceProb possibility, ...

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:47_00033

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: ccp.api.nmr.NmrConstraint.FixedResonance.resonanceccpnmr.api.Analysis.AtomSetMapping.resonancesccpnmr.api.AnalysisV3.AtomSetMapping.resonances
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Thu Oct 2 16:09:39 2014    from data model package  ccp.api.nmr.Nmr.Resonance   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk