Object[Simulation, Hybridization]
A simulation to predict the secondary structure of a given nucleic acid oligomer by considering the formation of potential intermolecular Watson-Crick pairing between nucleotides.
Organizational Information
Name
Name of this Object.
Format: Single
Class: String
Programmatic Pattern: _String
Pattern Description: A string.
ID
ID of this Object.
Format: Single
Class: String
Programmatic Pattern: _String
Pattern Description: The ID of this object.
Object
Object of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Simulation, Hybridization, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Simulation, Hybridization]
Pattern Description: Object[Simulation, Hybridization]
Notebook
Notebook this object belongs to.
Format: Single
Class: Link
Programmatic Pattern: _Link
Pattern Description: An object of that matches ObjectP[Object[LaboratoryNotebook]].
Relation: Object[LaboratoryNotebook][Objects]
Status
The current status of the simulation.
Format: Single
Class: Expression
Programmatic Pattern: ProtocolStatusP
Author
The person who requested this simulation.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[User][SimulationsAuthored]
DateConfirmed
The date on which the simulation first entered processing or a backlog.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateEnqueued
The date on which the simulation first entered processing or a backlog.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateStarted
Date when this simulation was started.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateCompleted
Date when this simulation was completed.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateCanceled
Date when this simulation was canceled.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
TimeElapsed
The time that was required to complete the simulation.
Format: Computable
Programmatic Pattern: GreaterEqualP[0 Day]
Expression: SafeEvaluate[{Field[DateCompleted], Field[DateStarted]}, Computables`Private`timeElapsed[Field[DateCompleted], Field[DateStarted]]]
Option Handling
UnresolvedOptions
The unresolved options entered into the simulation function that generated this object.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
ResolvedOptions
The options resolved automatically by this simulation or entered by the requestor.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
General
StartingMaterials
The objects containing the source structure used in this simulation.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
InitialStructures
The starting structures of the nucleic acid oligomers which will be used to initialize hybridization.
Format: Multiple
Class: Expression
Programmatic Pattern: StructureP
HybridizationDomain
The domain of positions within the strands for which hybridization calculations are restricted to.
Format: Multiple
[[1]] Strand Index
Header: Strand Index
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
[[2]] Starting Base Number
Header: Starting Base Number
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterP[0 Nucleotide, 1 Nucleotide]
[[3]] Ending Base Number
Header: Ending Base Number
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterP[0 Nucleotide, 1 Nucleotide]
Temperature
Temperature at which Gibbs free energy of hybridized structure will be calculated.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterP[0 Kelvin]
Method
Determine whether the returned hybridized structures are sorted by ascending energy or descending number of bonds.
Format: Single
Class: Expression
Programmatic Pattern: HybridizationMethodP
Depth
Number of times to recursively hybridize the structures when simulating.
Format: Single
Class: Expression
Programmatic Pattern: GreaterEqualP[1, 1] | {GreaterEqualP[1, 1]} | Infinity
Consolidate
Determine if all hybridizations are extended to their maximum length so that the neighbouring bases of each bond cannot be further paired.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
MaxMismatch
Maximum number of mismatches allowed in any given duplex.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
MinPieceSize
Minimum number of consecutive paired bases required in a duplex containing mismatches.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
MinLevel
Minimum number of bases required in each duplex.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
Simulation Results
MostStableStructure
The returned structure which has the minimum Gibbs free energy or maximum number of bonds depending on Method option.
Format: Single
Class: Expression
Programmatic Pattern: StructureP
HybridizedStructures
The final hybridized structures resulting from the simulation starting from the initial structures.
Format: Multiple
Class: Expression
Programmatic Pattern: StructureP
HybridizedEnergies
For each member of HybridizedStructures, the free energy of hybridization starting from the initial structure to the hybridized structure.
Format: Multiple
Class: Real
Unit: 1 thermochemical kilocalorie per mole
Programmatic Pattern: EnergyP
HybridizedNumberOfBonds
For each member of HybridizedStructures, the number of bonds in the hybridized structure.
Format: Multiple
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
HybridizedPercentage
For each member of HybridizedStructures, the percent composition of the hybridized structure at equilibrium.
Format: Multiple
Class: Real
Unit: 1 percent
Programmatic Pattern: GreaterEqualP[0 Percent]
HybridizationMechanism
The ReactionMechanism summarizing the series of reactions in the hybridization process.
Format: Single
Class: Expression
Programmatic Pattern: ReactionMechanismP
Last modified on Mon 26 Sep 2022 15:43:53