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Class: MolResidue

The MolResidue constructor includes non-standard actions. The MolResidue destructor includes non-standard actions.
    Monomer/Residue belonging to a Molecule, e.g. in the sequence for Insulin A-chain as such, as opposed to a specific Insulin A-chain molecule with coordinates.

    Note that MolResidues can neither be created nor deleted while their parent Molecule is linked to one or more chains. When creating a Molecule all relevant MolResLinkEnds are created automatically.
    Note also that MolResidues can not be deleted, except as a consequence of deleting their molecule.

    It is guaranteed that the serials of molResidues form a continuous range, and that all linear polymer type links are between MolResidues with consecutive serials. The Molesidue.serials must start at one. This constraint is not checked (for technical reasons), but it can only be broken if someone has modified the data bypassing the API.
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link molecule to class Molecule
Main key: serial
Mandatory Attributes: descriptor, linking, seqCode, chemComp
Known Subclasses: None
Children:
link molResLinkEnds to class MolResLinkEnd
Constructor: newObj = MolResidue( molecule,descriptor=value, linking=value, seqCode=value, chemComp=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
ccpCode LongWord 1..1 Derived. ccpCode of ChemComp corresponding to MolResidue  
descriptor Line 1..1 ChemComp descriptor - part of ChemCompVar key. Describes topological variant (e,g, protonation state) of ChemCompVar. For Polymer-type ChemComps (those that have 'next' or 'prev' LinkEnds) also describes non-polymer part of substitution pattern.  
linking ccp.api.molecule.ChemComp.ChemCompLinking 1..1 Residue linking code. For polymers distinguishes between terminal (start), terminal (end) and internal residues. For nonpolymers defines substitution pattern. Part of key for ChemCompVar. May be modified after sequence definition.  
molType ccp.api.molecule.ChemComp.MolType 1..1 Derived. molType of ChemComp corresponding to MolResidue  
seqCode Int 1..1 The seqCode is the residue number given by the user. For linear polymers normally used to give the position of the residue in the molecule sequence.  
seqInsertCode Line 1..1 Sequence insert code - entered by user. Serves to distinguish residues that the user prefers to give the same seqCode. Defaults to a single space.  
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
chemComp ccp.api.molecule.ChemComp.ChemComp 1..1 ChemComp that describes the type of the MolResidue  
chemCompVar ccp.api.molecule.ChemComp.ChemCompVar 1..1 Derived. ChemCompVar corresponding to MolResidue  
isotopeLabels ccp.api.lims.RefSampleComponent.IsotopeLabel 0..* Isotope label objects relevant to MolResidue  
molFeatures ccp.api.general.Annotation.MolFeature 0..* The MolFeature associated to a MolResidue.  
molResLinkEnds MolResLinkEnd 0..* (Child link). child link to class MolResLinkEnd  
molSeqFragment MolSeqFragment 0..1 MolSeqFragment delimited by MolResidue  
molecule Molecule 1..1 (Parent link). parent link  
parent Molecule 1..1 link to parent object - synonym for molecule  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
ccpCode
getCcpCode LongWord - non-std.
descriptor
getDescriptor Line -
setDescriptor - Line
linking
getLinking ccp.api.molecule.ChemComp.ChemCompLinking -
setLinking - ccp.api.molecule.ChemComp.ChemCompLinking
molType
getMolType ccp.api.molecule.ChemComp.MolType - non-std.
seqCode
getSeqCode Int -
setSeqCode - Int
seqInsertCode
getSeqInsertCode Line -
setSeqInsertCode - Line
serial
getSerial Int -
setSerial - Int

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
chemComp
getChemComp ccp.api.molecule.ChemComp.ChemComp -
setChemComp - ccp.api.molecule.ChemComp.ChemComp
chemCompVar
getChemCompVar ccp.api.molecule.ChemComp.ChemCompVar - non-std.
setChemCompVar - ccp.api.molecule.ChemComp.ChemCompVar non-std.
isotopeLabels
getIsotopeLabels ccp.api.lims.RefSampleComponent.IsotopeLabel Set -
setIsotopeLabels - ccp.api.lims.RefSampleComponent.IsotopeLabel Set
sortedIsotopeLabels ccp.api.lims.RefSampleComponent.IsotopeLabel List -
addIsotopeLabel - ccp.api.lims.RefSampleComponent.IsotopeLabel
removeIsotopeLabel - ccp.api.lims.RefSampleComponent.IsotopeLabel
findFirstIsotopeLabel ccp.api.lims.RefSampleComponent.IsotopeLabel keyword=value pairs
findAllIsotopeLabels ccp.api.lims.RefSampleComponent.IsotopeLabel Set keyword=value pairs
molFeatures
getMolFeatures ccp.api.general.Annotation.MolFeature Set -
setMolFeatures - ccp.api.general.Annotation.MolFeature Set
sortedMolFeatures ccp.api.general.Annotation.MolFeature List -
findFirstMolFeature ccp.api.general.Annotation.MolFeature keyword=value pairs
findAllMolFeatures ccp.api.general.Annotation.MolFeature Set keyword=value pairs
molResLinkEnds
getMolResLinkEnds MolResLinkEnd Set -
sortedMolResLinkEnds MolResLinkEnd List -
findFirstMolResLinkEnd MolResLinkEnd keyword=value pairs
findAllMolResLinkEnds MolResLinkEnd Set keyword=value pairs
molSeqFragment
getMolSeqFragment MolSeqFragment -
setMolSeqFragment - MolSeqFragment
molecule
getMolecule Molecule -
parent
getParent Molecule -

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey MolResidue 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
newMolResLinkEnd MolResLinkEnd linkCode, ...

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:54_00044

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

if self.molecule.isFinalised:
  raise ApiError("MolResidues may not be added once Molecule has been finalised")

for ca in self.chemCompVar.chemAtoms:
  if isinstance(ca,ccp.api.molecule.ChemComp.LinkAtom):
    linkEnd = ca.boundLinkEnd
    if linkEnd is not None:
      MolResLinkEnd(self, linkCode=linkEnd.linkCode)

Special destructor code:

# The following code interacts directly with the deletion implementation (use of 'objsToBeDeleted').
# This is bad, but the only way to accomplish the desired result.
if self.molecule not in objsToBeDeleted and not self.root.override:
  raise ApiError("MolResidue %s: MolResidues can only be deleted when the Molecule is deleted." % self)

Special postDestructor code:

None

Constraints:

None
Known inward one-way links: ccp.api.molecule.LabeledMolecule.ResLabel.molResidueccp.api.molecule.MolSystem.Residue.molResidue
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Fri Mar 28 11:18:11 2014    from data model package  ccp.api.molecule.Molecule.MolResidue   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk