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Class: ChainStateSet


    Defines a set of states that apply to a chain. The ChainStates in a ChainStateSet are mutually exclusive. Their exact nature is defined by the StateSiteType.

    ChainStates serve to distinguish Resonances that arise from the same atom in different states of the chain, to describe the State of molecules used for a structure generation, and to define the state (including fast exchange) of a chain under the conditions of a given experiment.

    A ChainState only describes the situation for one particular set of alternatives, and implies nothing about others. For example, a molecule with seven prolines in slow cis/trans equilibrium would have seven ChainStateSets. A given resonance could then be described (by linking it to ChainStates) as Pro-47 cis, Pro-112 trans, without implying anything about the state of the remaining five prolines.  

    stateSetType and ChainState.name are freely changeable, reflecting the fact that the origin of sets of observed resonances is often unknown until a late stage of analysis. Once the precise situation is known, the following procedures should be used where applicable:

    stateSetType: cis/trans
    ChainState names: cis, trans
    Links: to the two atoms that are cis or trans (in the case of peptide bonds to the two alpha carbons of the residues involved).

    stateSetType: protonation
    ChainState names: protonated, deprotonated
    Links: To the proton that is removed on deprotonation.

    stateSetType: isotopomer
    ChainState names : isotope codes of the relevant isotopes (e.g. 12C, 13C)
    Links: To the atom(s) that change isotope.
    NB this mechanism only handles atoms of the same type that change in parallel. If the isotope substitution pattern is more complex, is may be necessary to define several ChainStateSets, possibly redefining the ChainStates when the situation has been analysed.

    stateSetType: folding
    ChainState names: folded, unfolded
    Links : to the residues involved in the transition.

    stateSetType : conformation
    ChainState names: can be chosen freely
    Links: to the residues changing conformation.
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: chain
Known Subclasses: None
Children:
link chainStates to class ChainState
Constructor: newObj = ChainStateSet( nmrProject,chain=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
details Text 0..1 Free text, for notes, explanatory comments, etc.  
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  
stateSetType ChainStateSetType 0..1 Type of State Set. Describes which factor distinguishes the various chainstates, be it protonation state, cis/trants isomerism, conformation, ... If the distinguishing factor is unknown, stateSetType should not be set.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
atoms ccp.api.molecule.MolSystem.Atom 0..* Atoms 'involved' in a ChainStateSet. The intention is that the link should describe atoms that change chemically or conformationally, rather than atoms that merely have changed NMR parameters. See documentation of ChainStateSet for recommendations for handling protonation, cis/trans, and isotopomers.  
chain ccp.api.molecule.MolSystem.Chain 1..1 Chain to which ChainStateSet belongs  
chainStates ChainState 0..* (Child link). child link to class ChainState  
nmrProject NmrProject 1..1 (Parent link). parent link  
parent NmrProject 1..1 link to parent object - synonym for nmrProject  
residues ccp.api.molecule.MolSystem.Residue 0..* Residues involved in chainStates.  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
details
getDetails Text -
setDetails - Text
serial
getSerial Int -
setSerial - Int
stateSetType
getStateSetType ChainStateSetType -
setStateSetType - ChainStateSetType

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
atoms
getAtoms ccp.api.molecule.MolSystem.Atom Set -
setAtoms - ccp.api.molecule.MolSystem.Atom Set
sortedAtoms ccp.api.molecule.MolSystem.Atom List -
addAtom - ccp.api.molecule.MolSystem.Atom
removeAtom - ccp.api.molecule.MolSystem.Atom
findFirstAtom ccp.api.molecule.MolSystem.Atom keyword=value pairs
findAllAtoms ccp.api.molecule.MolSystem.Atom Set keyword=value pairs
chain
getChain ccp.api.molecule.MolSystem.Chain -
setChain - ccp.api.molecule.MolSystem.Chain
chainStates
getChainStates ChainState Set -
sortedChainStates ChainState List -
findFirstChainState ChainState keyword=value pairs
findAllChainStates ChainState Set keyword=value pairs
nmrProject
getNmrProject NmrProject -
parent
getParent NmrProject -
residues
getResidues ccp.api.molecule.MolSystem.Residue Set -
setResidues - ccp.api.molecule.MolSystem.Residue Set
sortedResidues ccp.api.molecule.MolSystem.Residue List -
addResidue - ccp.api.molecule.MolSystem.Residue
removeResidue - ccp.api.molecule.MolSystem.Residue
findFirstResidue ccp.api.molecule.MolSystem.Residue keyword=value pairs
findAllResidues ccp.api.molecule.MolSystem.Residue Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey ChainStateSet 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
newChainState ChainState ...

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:46_00018

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  Mon Mar 2 17:24:53 2015    from data model package  ccp.api.nmr.Nmr.ChainStateSet   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk