Data Model version 2.1.2
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Class: Molecule


    Abstract molecule, with defined topology but no location, coordinates, etc.
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link memopsRoot to class memops.api.Implementation.MemopsRoot
Main key: name
Mandatory Attributes: name
Partitions Children: True
Known Subclasses: None
Children:
link alignments to class Alignment
link molResLinks to class MolResLink
link molResidues to class MolResidue
link molSeqFragments to class MolSeqFragment
link moleculeSysNames to class MoleculeSysName
Constructor: newObj = Molecule( memopsRoot,name=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
calcIsoelectricPoint Float 0..1 Calculated isoelectric point of molecule. The pI indicates the value of pH at which the net charge of the molecule would be neutralized, if the molecule would have a conformation with each amino acid fully exposed to the solvent. NB This is derived information, this should be moved when this gets developed.  
commonNames Line 0..* List of molecule common names.  
details String 0..1 Free text, for notes, explanatory comments, etc.  
empiricalFormula Line 0..1 Derived. Empirical formula for molecule.  
formalCharge Int 1..1 Derived. Formal charge of molecule.  
fragmentDetails Text 0..1 Details on what (if anything) this Molecule is a fragment of).  
functions Line 0..* Keywords describing functions for molecule. e.g. 'enzyme', 'structure', ...  
hasNonStdChemComp Boolean 1..1 Derived. Does molecule contain non-standard ChemComp? Note that this will be true whenever the molecule does not consist entirely of StdChemComps. Since only molTypes protein, DNA, and RNA have any StdChemComps at all, this attribute will be True but meaningless for any Molecule that contains ChemComps of other types.  
hasNonStdChirality Boolean 0..1 Derived. Does molecule contain ChemComp of non-standard chirality? Note that this will be true also when the Molecule contains a ChemComp where no StdChirality is defined.  
isAromatic Boolean 1..1 Derived. Does molecule contain aromatic groups?  
isFinalised Boolean 1..1 Non-finalised molecules may not have links to Samples etc. Finalised molecules can no longer have residues added or removed. Note that you can add MolResidues to non-finalised molecules even if they already have chains, but that you must make sure of adding new MolSystem.Residues as necessary.  
isParamagnetic Boolean 1..1 Derived. Does Molecule contain paramagnetic groups?  
isStdCyclic Boolean 0..1 Derived. Is Molecule a Std Cyclic polymer, i.e. a Std Linear polymer with a polymer-type link between the last and the first residue?  
isStdLinear Boolean 1..1 Derived. Is the molecule a standard linear polymer? A linear polymer must contain a linear sequence where MolResidues with successive serials are linked by linear polymer type links (linkCodes 'next' and 'prev'). Linear polymers may be heavily crosslinked but all the sequential links must be present and of the correct type. The component MolResidues may be of any type or a mixture of types (peptide, nucleotide, styrene monomers, ...) provided the 'next' and/or 'prev' links are present. The following are not linear polymers: - A strand of DNA with a break in the middle of the sequence numbering, even if the strand is circular. - A protein with one peptide bond replaced by a bond going through an Aspartate side chain COOH. - A glycoprotein. - A linear polysaccharide.  
keywords Line 0..* Keywords for searching molecule. e.g. 'DNA binding', 'receptor', 'Zinc finger'...  
longName Text 0..1 Long form of molecule name.  
molType MolType 0..1 Derived. molType of ChemComps making up Molecule. Possible values: 'protein', 'DNA', 'RNA', 'DNA/RNA', 'other'. The values are returned if *all* ChemComps are of the correct molType(s). 'other' is returned if the Molecule contains neither protein, not DNA, nor RNA ChemComps. If the Molecule contains a mixture of molTypes (except for DNA/RNA) the value is None (not set). Note that the molType says nothing about how the ChemComps are linked, and that e.g. a Molecule of molType 'protein' need not contain a single peptide bond. If e.g. molType is 'protein' and isStdLinear' is True, on the other hand, the Molecule is a single unbroken polypeptide (which may or may not contain crosslinks).  
molecularMass Float 1..1 Derived. Molecular mass, in atomic units. This is the sum of the atomic weights of the atoms that form this molecule.  
mutationDetails Text 0..1 Details on mutations in the sequence (e.g. this is A54K relative to the wildtype).  
name Line 1..1 Name of Molecule. Used as key. Should be correct and informative, but may be an abbreviation or an acronym if the alternative is too long. Recommended e.g. NaCl, Lysozyme, Lac headpiece, morphine.  
seqDetails Text 0..1 Details, notes, comments etc. about the sequence.  
seqLength Int 1..1 Derived. Number of MolResidues in Molecule. For linear polymers equal to sequence length.  
seqString String 0..1 Derived. String holding sequence one-letter-codes with '*' for non-standard residues. The attribute is always defined, but is equal to the empty string except for linear polymers of defined molType. Note that one-letter codes are only defined for std ChemComps, which are only found for peptides and nucleotides, so the value for linear polymers of type 'other' is likely to be meaningless.  
smiles String 0..1 SMILES (Simplified Molecular Input Line Entry Specification) string describing molecule.  
smilesType SmilesType 0..1 Type of Smiles string in smiles attribute  
stdSeqString String 0..1 Derived. String holding sequence one-letter-codes with non-standard ChemComps replaced by one-letter-code of corresponding standard derivative, or by '*' if there is no standard derivative. The attribute is always defined, but is equal to the empty string except for linear polymers of defined molType. Note that one-letter codes are only defined for std ChemComps, which are only found for peptides and nucleotides, so the value for linear polymers of type 'other' is likely to be meaningless.  

Inherited Attributes (not in package): applicationDataclassNamecreatedByfieldNamesguidinConstructorisDeletedisLoadedisModifiableisModifiedisReadinglastUnlockedBymetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
alignments Alignment 0..* (Child link). child link to class Alignment  
chains ccp.api.molecule.MolSystem.Chain 0..* MolSystem Chains corresponding to Molecule  
citations ccp.api.general.Citation.Citation 0..* Citations describing molecule.  
entryMolecules ccp.api.nmr.NmrEntry.EntryMolecule 0..* Connection to NmrEntries that reference this Molecule  
memopsRoot memops.api.Implementation.MemopsRoot 1..1 (Parent link). parent link  
molComponents ccp.api.lims.RefSampleComponent.MolComponent 0..* The list of MolComponent associated to a particular Molecule.  
molResLinks MolResLink 0..* (Child link). child link to class MolResLink  
molResidues MolResidue 0..* (Child link). child link to class MolResidue  
molSeqFragments MolSeqFragment 0..* (Child link). child link to class MolSeqFragment  
moleculeSysNames MoleculeSysName 0..* (Child link). child link to class MoleculeSysName  
naturalSource ccp.api.general.Taxonomy.NaturalSource 0..1 Natural source for molecule  
parent memops.api.Implementation.MemopsRoot 1..1 link to parent object - synonym for memopsRoot  

Inherited Attributes (not in package): accessactiveAccessactiveRepositoriespackageLocatorroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
calcIsoelectricPoint
getCalcIsoelectricPoint Float -
setCalcIsoelectricPoint - Float
commonNames
getCommonNames Line Tuple -
setCommonNames - Line List
addCommonName - Line
removeCommonName - Line
details
getDetails String -
setDetails - String
empiricalFormula
getEmpiricalFormula Line - non-std.
formalCharge
getFormalCharge Int - non-std.
fragmentDetails
getFragmentDetails Text -
setFragmentDetails - Text
functions
getFunctions Line Tuple -
setFunctions - Line List
addFunction - Line
removeFunction - Line
hasNonStdChemComp
getHasNonStdChemComp Boolean - non-std.
hasNonStdChirality
getHasNonStdChirality Boolean - non-std.
isAromatic
getIsAromatic Boolean - non-std.
isFinalised
getIsFinalised Boolean -
setIsFinalised - Boolean
isParamagnetic
getIsParamagnetic Boolean - non-std.
isStdCyclic
getIsStdCyclic Boolean - non-std.
isStdLinear
getIsStdLinear Boolean - non-std.
keywords
getKeywords Line Tuple -
setKeywords - Line List
addKeyword - Line
removeKeyword - Line
longName
getLongName Text -
setLongName - Text
molType
getMolType MolType - non-std.
molecularMass
getMolecularMass Float - non-std.
mutationDetails
getMutationDetails Text -
setMutationDetails - Text
name
getName Line -
setName - Line
seqDetails
getSeqDetails Text -
setSeqDetails - Text
seqLength
getSeqLength Int - non-std.
seqString
getSeqString String - non-std.
smiles
getSmiles String -
setSmiles - String
smilesType
getSmilesType SmilesType -
setSmilesType - SmilesType
stdSeqString
getStdSeqString String - non-std.

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
alignments
getAlignments Alignment Set -
sortedAlignments Alignment List -
findFirstAlignment Alignment keyword=value pairs
findAllAlignments Alignment Set keyword=value pairs
chains
getChains ccp.api.molecule.MolSystem.Chain Set -
setChains - ccp.api.molecule.MolSystem.Chain Set
sortedChains ccp.api.molecule.MolSystem.Chain List -
findFirstChain ccp.api.molecule.MolSystem.Chain keyword=value pairs
findAllChains ccp.api.molecule.MolSystem.Chain Set keyword=value pairs
citations
getCitations ccp.api.general.Citation.Citation Set -
setCitations - ccp.api.general.Citation.Citation Set
sortedCitations ccp.api.general.Citation.Citation List -
findFirstCitation ccp.api.general.Citation.Citation keyword=value pairs
findAllCitations ccp.api.general.Citation.Citation Set keyword=value pairs
entryMolecules
getEntryMolecules ccp.api.nmr.NmrEntry.EntryMolecule Set -
setEntryMolecules - ccp.api.nmr.NmrEntry.EntryMolecule Set
sortedEntryMolecules ccp.api.nmr.NmrEntry.EntryMolecule List -
findFirstEntryMolecule ccp.api.nmr.NmrEntry.EntryMolecule keyword=value pairs
findAllEntryMolecules ccp.api.nmr.NmrEntry.EntryMolecule Set keyword=value pairs
memopsRoot
getMemopsRoot memops.api.Implementation.MemopsRoot -
molComponents
getMolComponents ccp.api.lims.RefSampleComponent.MolComponent Set -
setMolComponents - ccp.api.lims.RefSampleComponent.MolComponent Set
sortedMolComponents ccp.api.lims.RefSampleComponent.MolComponent List -
addMolComponent - ccp.api.lims.RefSampleComponent.MolComponent
removeMolComponent - ccp.api.lims.RefSampleComponent.MolComponent
findFirstMolComponent ccp.api.lims.RefSampleComponent.MolComponent keyword=value pairs
findAllMolComponents ccp.api.lims.RefSampleComponent.MolComponent Set keyword=value pairs
molResLinks
getMolResLinks MolResLink Set -
sortedMolResLinks MolResLink List -
findFirstMolResLink MolResLink keyword=value pairs
findAllMolResLinks MolResLink Set keyword=value pairs
molResidues
getMolResidues MolResidue Set -
sortedMolResidues MolResidue List -
findFirstMolResidue MolResidue keyword=value pairs
findAllMolResidues MolResidue Set keyword=value pairs
molSeqFragments
getMolSeqFragments MolSeqFragment Set -
sortedMolSeqFragments MolSeqFragment List -
findFirstMolSeqFragment MolSeqFragment keyword=value pairs
findAllMolSeqFragments MolSeqFragment Set keyword=value pairs
moleculeSysNames
getMoleculeSysNames MoleculeSysName Set -
sortedMoleculeSysNames MoleculeSysName List -
findFirstMoleculeSysName MoleculeSysName keyword=value pairs
findAllMoleculeSysNames MoleculeSysName Set keyword=value pairs
naturalSource
getNaturalSource ccp.api.general.Taxonomy.NaturalSource -
setNaturalSource - ccp.api.general.Taxonomy.NaturalSource
parent
getParent memops.api.Implementation.MemopsRoot -

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey Molecule memops.api.Implementation.MemopsRoot, 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
newAlignment Alignment dbRef, ...
newMolResLink MolResLink molResLinkEnds, ...
newMolResidue MolResidue descriptor, linking, seqCode, chemComp, ...
newMolSeqFragment MolSeqFragment limitResidues, ...
newMoleculeSysName MoleculeSysName namingSystem, ...

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_00039

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraint name:

molResidue_serials_must_be_consecutive
Constraint code: ll = self.sortedMolResidues()
if ll:
  isValid = (len(ll) == (ll[-1].serial - ll[0].serial + 1))
else:
  isValid = True

Constraint name:

seqCode_and_seqInsertCode_form_secondary_key_for_molResidues
Constraint code: ll = self.molResidues
aset = frozenset((x.seqCode, x.seqInsertCode) for x in ll)
isValid = (len(aset) == len(ll))

Constraint name:

smiles_goes_with_smilesType
Constraint code: (self.smiles is None) == (self.smilesType is None)
Known inward one-way links: ccp.api.molecule.LabeledMolecule.LabeledMolecule.moleculememops.api.Implementation.MemopsRoot.currentMolecule
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Thu Oct 2 16:09:21 2014    from data model package  ccp.api.molecule.Molecule.Molecule   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk