nuget
Represents a chemical reaction with phase information for thermodynamic calculations. Contains stoichiometry, reaction direction, and methods for Gibbs energy calculations.
PhasedReaction
01 Syntax
Emily.eQuilibrator.Core.Models.PhasedReaction
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| IsReversible | 1 | Indicates whether the reaction is reversible |
| .ctor | 1 | Creates a new PhasedReaction |
| FromSparse | 1 | Creates a PhasedReaction from a stoichiometry dictionary with compound IDs |
| Parse | 1 | Parses a reaction formula string and creates a PhasedReaction |
| GetCoefficient | 1 | Gets the coefficient for a specific compound |
| ContainsCompound | 1 | Checks if the reaction contains a specific compound |
| GetAtomBalance | 1 | Gets the net atom balance for this reaction |
| IsBalanced | 1 | Checks if the reaction is atom-balanced |
| GetNetCharge | 1 | Gets the net charge of this reaction |
| GetNetProtons | 1 | Gets the net proton count for this reaction |
| CalculateConcentrationCorrection | 1 | Calculates the concentration correction for Gibbs energy |
| CalculatePhysiologicalCorrection | 1 | Calculates the physiological concentration correction |
| SetCompoundConcentration | 1 | Sets the concentration for a compound in this reaction |
| SetConcentrations | 1 | Sets concentrations for multiple compounds |
| Reverse | 1 | Creates a reversed version of this reaction |
| Scale | 1 | Scales the reaction by a factor |
| Combine | 1 | Combines this reaction with another reaction |
| Serialize | 1 | Serializes this reaction to a list of dictionaries |
| ToString | 1 | Formats this reaction as a formula string |
| Equals | 1 | |
| GetHashCode | 1 |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| Sparse | 1 | The stoichiometry of the reaction as a sparse vector. |
| Arrow | 1 | The arrow type used in the reaction formula |
| ReactionId | 1 | The reaction identifier |
| Name | 1 | The reaction name |
| Compounds | 1 | Gets all compounds in this reaction |
| Reactants | 1 | Gets the reactants (compounds with negative coefficients) |
| Products | 1 | Gets the products (compounds with positive coefficients) |
04 Members
IsReversible
Indicates whether the reaction is reversible
#ctor(
Dictionary(Of PhasedCompound, Double), String, String)Creates a new PhasedReaction
Parameters
| Name | Type | Description |
|---|---|---|
sparse | Dictionary(Of PhasedCompound, Double) | The stoichiometry dictionary |
arrow | String | The arrow type |
rid | String | Optional reaction identifier |
FromSparse(
Dictionary(Of String, Double), Func(Of String, PhasedCompound), String, String)Creates a PhasedReaction from a stoichiometry dictionary with compound IDs
Parameters
| Name | Type | Description |
|---|---|---|
sparse | Dictionary(Of String, Double) | Dictionary mapping compound IDs to coefficients |
compoundLookup | Func(Of String, PhasedCompound) | Function to lookup compounds by ID |
arrow | String | The arrow type |
rid | String | Optional reaction identifier |
Parse(
String, Func(Of String, PhasedCompound))Parses a reaction formula string and creates a PhasedReaction
Parameters
| Name | Type | Description |
|---|---|---|
formula | String | The reaction formula |
compoundLookup | Func(Of String, PhasedCompound) | Function to lookup compounds by ID |
Returns
A new PhasedReaction
GetCoefficient(PhasedCompound)
Gets the coefficient for a specific compound
Parameters
| Name | Type | Description |
|---|---|---|
compound | PhasedCompound | The compound to look up |
Returns
The stoichiometric coefficient
ContainsCompound(PhasedCompound)
Checks if the reaction contains a specific compound
Parameters
| Name | Type | Description |
|---|---|---|
compound | PhasedCompound | The compound to check |
Returns
True if the compound is in the reaction
GetAtomBalance
Gets the net atom balance for this reaction
Returns
Dictionary mapping element symbols to net counts
IsBalanced(
Double)Checks if the reaction is atom-balanced
Parameters
| Name | Type | Description |
|---|---|---|
tolerance | Double | Tolerance for floating point comparison |
Returns
True if the reaction is balanced
GetNetCharge
Gets the net charge of this reaction
Returns
The net charge
GetNetProtons
Gets the net proton count for this reaction
Returns
The net proton count
CalculateConcentrationCorrection
Calculates the concentration correction for Gibbs energy
Returns
The correction in RT units
CalculatePhysiologicalCorrection
Calculates the physiological concentration correction
Returns
The correction in RT units
SetCompoundConcentration(PhasedCompound,
Double)Sets the concentration for a compound in this reaction
Parameters
| Name | Type | Description |
|---|---|---|
compound | PhasedCompound | The compound |
concentration | Double | The concentration in molar |
SetConcentrations(
Dictionary(Of PhasedCompound, Double))Sets concentrations for multiple compounds
Parameters
| Name | Type | Description |
|---|---|---|
concentrations | Dictionary(Of PhasedCompound, Double) | Dictionary mapping compounds to concentrations |
Reverse
Creates a reversed version of this reaction
Returns
A new PhasedReaction with reversed stoichiometry
Scale(
Double)Scales the reaction by a factor
Parameters
| Name | Type | Description |
|---|---|---|
factor | Double | The scaling factor |
Returns
A new scaled PhasedReaction
Combine(PhasedReaction)
Combines this reaction with another reaction
Parameters
| Name | Type | Description |
|---|---|---|
other | PhasedReaction | The other reaction |
Returns
A new combined PhasedReaction
Serialize
Serializes this reaction to a list of dictionaries
Returns
A list of compound dictionaries with coefficients
ToString
Formats this reaction as a formula string
Returns
The reaction formula string
Sparse
The stoichiometry of the reaction as a sparse vector. Negative values indicate reactants, positive values indicate products.
Arrow
The arrow type used in the reaction formula
ReactionId
The reaction identifier
Name
The reaction name
Compounds
Gets all compounds in this reaction
Reactants
Gets the reactants (compounds with negative coefficients)
Products
Gets the products (compounds with positive coefficients)
Equals(
Object)GetHashCode()