nuget
Main class for predicting Gibbs free energies of biochemical reactions. Implements the Component Contribution method for thermodynamic calculations.
ComponentContribution
01 Syntax
Emily.eQuilibrator.Core.ComponentContribution
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| .ctor | 2 | Creates a new ComponentContribution instance |
| GetCompound | 1 | Gets a compound by its identifier |
| SearchCompounds | 1 | Searches for compounds by name or identifier |
| ParseFormula | 1 | Parses a reaction formula string |
| Reaction | 1 | Creates a PhasedReaction from a formula string |
| StandardDgPrime | 2 | 组件贡献法：计算反应在指定条件下的标准变换 Gibbs 自由能 ΔrG'°。 每个化合物优先采用其微物种 Legendre 分区函数（组件贡献），无微物种时回退到基团向量（组贡献）。 质子/水作为参考物种取 ΔfG'° = 0。 |
| StandardDgPrimeGroupContribution | 2 | 组贡献法：计算反应在指定条件下的标准变换 Gibbs 自由能 ΔrG'°。 每个化合物优先采用基团向量估算（组贡献），无基团向量时回退到组件贡献。 |
| StandardDgPrimeCore | 1 | 核心计算：对反应中的每个化合物求和 ΔfG'° × 化学计量系数。 |
| GetReactionDirection | 1 | Calculates the direction of a reaction at given conditions |
| CalculatePValue | 1 | Calculates the p-value for a Gibbs energy estimate |
| NormalCdf | 1 | Standard normal cumulative distribution function |
| CreateStoichiometricMatrix | 2 | Creates a stoichiometric matrix from parsed reactions |
| GetCompoundIds | 1 | Gets the compound IDs used in the stoichiometric matrix |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| Cache | 1 | The compound cache for looking up compound properties |
| PH | 1 | The pH value for calculations |
| PMg | 1 | The pMg value for calculations |
| IonicStrength | 1 | The ionic strength in molar |
| Temperature | 1 | The temperature in Kelvin |
04 Fields
| Name | Overloads | Summary |
|---|---|---|
| _parser | 1 | The reaction parser |
05 Members
#ctor
Creates a new ComponentContribution instance
#ctor(CompoundCache)
Creates a new ComponentContribution instance with a custom cache
Parameters
| Name | Type | Description |
|---|---|---|
cache | CompoundCache | The compound cache to use |
GetCompound(
String)Gets a compound by its identifier
Parameters
| Name | Type | Description |
|---|---|---|
compoundId | String | The compound identifier |
Returns
The compound, or null if not found
SearchCompounds(
String)Searches for compounds by name or identifier
Parameters
| Name | Type | Description |
|---|---|---|
query | String | The search query |
Returns
A list of matching compounds
ParseFormula(
String)Parses a reaction formula string
Parameters
| Name | Type | Description |
|---|---|---|
formula | String | The reaction formula |
Returns
A ParsedReaction object
Reaction(
String)Creates a PhasedReaction from a formula string
Parameters
| Name | Type | Description |
|---|---|---|
formula | String | The reaction formula |
Returns
A PhasedReaction object
StandardDgPrime(PhasedReaction)
组件贡献法：计算反应在指定条件下的标准变换 Gibbs 自由能 ΔrG'°。 每个化合物优先采用其微物种 Legendre 分区函数（组件贡献），无微物种时回退到基团向量（组贡献）。 质子/水作为参考物种取 ΔfG'° = 0。
StandardDgPrime(
String)计算反应公式（字符串）对应的标准变换 Gibbs 自由能（组件贡献法）。
StandardDgPrimeGroupContribution(PhasedReaction)
组贡献法：计算反应在指定条件下的标准变换 Gibbs 自由能 ΔrG'°。 每个化合物优先采用基团向量估算（组贡献），无基团向量时回退到组件贡献。
StandardDgPrimeGroupContribution(
String)计算反应公式（字符串）对应的标准变换 Gibbs 自由能（组贡献法）。
StandardDgPrimeCore(PhasedReaction,
Boolean)核心计算：对反应中的每个化合物求和 ΔfG'° × 化学计量系数。
GetReactionDirection(PhasedReaction)
Calculates the direction of a reaction at given conditions
Parameters
| Name | Type | Description |
|---|---|---|
reaction | PhasedReaction | The reaction |
Returns
The reaction direction (forward, reverse, or equilibrium)
CalculatePValue(
Double, Double)Calculates the p-value for a Gibbs energy estimate
NormalCdf(
Double)Standard normal cumulative distribution function
CreateStoichiometricMatrix(
IEnumerable(Of String))Creates a stoichiometric matrix from reaction formulas
Parameters
| Name | Type | Description |
|---|---|---|
formulas | IEnumerable(Of String) | The reaction formulas |
Returns
A stoichiometric matrix as a 2D array
CreateStoichiometricMatrix(
IEnumerable(Of ParsedReaction))Creates a stoichiometric matrix from parsed reactions
Parameters
| Name | Type | Description |
|---|---|---|
reactions | IEnumerable(Of ParsedReaction) | The parsed reactions |
Returns
A stoichiometric matrix as a 2D array
GetCompoundIds(
IEnumerable(Of String))Gets the compound IDs used in the stoichiometric matrix
Parameters
| Name | Type | Description |
|---|---|---|
formulas | IEnumerable(Of String) | The reaction formulas |
Returns
List of compound IDs in order
Cache
The compound cache for looking up compound properties
PH
The pH value for calculations
PMg
The pMg value for calculations
IonicStrength
The ionic strength in molar
Temperature
The temperature in Kelvin
_parser
The reaction parser