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Class: MolSeqFragment


    Block of molResidues with consecutive serials in a molecule . For linear polymers this is guaranteed to be a connected fragment of the molecule. For other molecules the set of Molresidues selected may or may not be connected, depending on how the molecule was created. MolSeqFragments are disjoint and no residue can be a member of more than one.
Attributes
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Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link molecule to class Molecule
Main key: limitResidues
Mandatory Attributes: limitResidues
Known Subclasses: None
Children: None
Constructor: newObj = MolSeqFragment( molecule,limitResidues=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
organismName Line 0..1 Derived. Common name of source organism (e.g. 'mouse', 'human',...).  
organismSciName Line 0..1 Derived. Scientific name of source organism (e.g. 'mus musculus', 'homo sapiens',...).  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
alignments Alignment 0..* Alignments relevant to MolSeqFragment  
limitResidues MolResidue 2..2 MolResidues belonging to Polymer Sequence Block.  
molecule Molecule 1..1 (Parent link). parent link  
naturalSource ccp.api.general.Taxonomy.NaturalSource 0..1 Natural Source that MolSeqFragment refers to.  
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
organismName
getOrganismName Line - non-std.
organismSciName
getOrganismSciName Line - non-std.

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
alignments
getAlignments Alignment Set -
setAlignments - Alignment Set
sortedAlignments Alignment List -
addAlignment - Alignment
removeAlignment - Alignment
findFirstAlignment Alignment keyword=value pairs
findAllAlignments Alignment Set keyword=value pairs
limitResidues
getLimitResidues MolResidue Set -
setLimitResidues - MolResidue Set
sortedLimitResidues MolResidue List -
findFirstLimitResidue MolResidue keyword=value pairs
findAllLimitResidues MolResidue Set keyword=value pairs
molecule
getMolecule Molecule -
naturalSource
getNaturalSource ccp.api.general.Taxonomy.NaturalSource -
setNaturalSource - ccp.api.general.Taxonomy.NaturalSource
parent
getParent Molecule -

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey MolSeqFragment 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
None

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_00045

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraint name:

MolSeqFragments_are_disjoint
Constraint code: ll = [x.serial for x in self.limitResidues]
min0 = min(ll)
max0 = max(ll)
for seqBlock in self.molecule.molSeqFragments:
  if seqBlock is not self:
    (i1, i2) = [x.serial for x in seqBlock.limitResidues]
    if not ((i1 > max0 and i2 > max0) or (i1 < min0 and i2 < min0)):
      isValid = False
      break
else:
  isValid = True
Known inward one-way links: None
  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.MolSeqFragment   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk