Class
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Description
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AbstractComponent
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The abstract component is used to define the details which characterise all components, these are name, any synonyms and a CAS number. There are 4 subclasses of abstract component: Molecular component (MolComponent), Cell, Substance and Composite.
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Cell
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Cell is a subclass of AbstractComponent. The information on the cell component.
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ComponentDbRef
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The link between a database reference (DbRef) and a component.
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Composite
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Composite is a subclass of AbstractComponent. It is a non-covalent complex of any kind. E.g. A DNA duplex, a micelle, possibly containing other molecules. A protein with an inhibitor bound. A cell containing plasmids.
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CompositeElement
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One element of the composite.
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CompositeInteraction
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The interaction between two composite elements.
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Construct
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This is a subtype of MolComponent. It is used to summarise information about a construct such as an expression vector plasmid.
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IsotopeLabel
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Isotope label or labeling pattern. Refers to elements of a type given by elementSymbol. If self.molResidues is set the substitution is limited to these residues. If self.atomNames is set the substitution is limited to atoms with these names.
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Label
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Label (isotopic, fluorophore, X-ray anomalous scatterer, or other) attached to AbstractComponent. Isotope labeling given in SpecificLabelGroup and IsotopeLabel must be consistent with labeling given in the Label class, as both are valid together.
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MolCompFeature
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The MolCompFeature is used to assign information to each part of the MolComponent sequence, as defined by a series of MolResidues with consecutive serials.
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MolComponent
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One type of component. A Molecular component (MolComponent) represents a pure component of known melecular structure. This includes most chemicals, proteins, DNA, RNA, DNA/RNA and also enzymes, constructs and primers. Restriction enzymes, primers and constructs are subtypes of MolCOmponent with additional features recorded. NaCl is a MolComponent, so is lysozyme.
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Primer
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This is a subtype of MolComponent. A specific oligonucleotide or primer such as a PCR-primer used to amplify nucleic acid fragments.
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RefSampleComponentStore
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TopObject for RefSampleComponent package
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RestrictionEnzyme
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This is a subtype of MolComponent. Restriction enzymes are known to cleave nucleic acide sequences at certain positions.
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SpecificLabelGroup
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Group of specific isotope labels that apply together to an individual molecule. Molecules that are mixtures of isotopomers may have several SpecificLabelGroups. Isotope labeling given in SpecificLabelGroup and IsotopeLabel must be consistent with labeling given in the Label class, as both are valid together.
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Substance
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A Substance should be limited to cases that cannot be put under any of the others. Typically: bovine calf serum, light petroleum, wheat germ extract, algal hydrolysate.
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