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Stoichiometry #683

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qai222 opened this issue Jun 6, 2023 · 1 comment
Closed

Stoichiometry #683

qai222 opened this issue Jun 6, 2023 · 1 comment
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enhancement New feature or request

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@qai222
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qai222 commented Jun 6, 2023

Is your feature request related to a problem? Please describe.
Record the stoichiometric coefficients of the main chemical equation (assumed following #682) to have a balanced equation.

Describe the solution you'd like
A field at the Compound level. The coefficient should be additive for the same Compound.

  1. (without modifying the current schema) convention: for the main chemical equation, the stoichiometric coefficient of a Compound is recorded as a custom CompoundIdentifier whose value is the stringified stoichiometric coefficient.
  2. extend Amount.kind to include stoichiometric coefficients.

Describe alternatives you've considered
Something at the Reaction level, ex. a balanced reaction SMILES as a ReactionIdentifier. The problem here is although I can have a balanced equation,

  1. I have to have all Compounds identified by SMILES.
  2. If the same Compound appears in multiple ReactionInputs, I have no way to know the exact coefficient of one Compound in a specific ReactionInput.
@qai222 qai222 added the enhancement New feature or request label Jun 6, 2023
@qai222
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qai222 commented Jun 7, 2023

Convention for compound stoichiometry:

  • The preferred field for compound stoichiometry is the map Compound.features.
  • The key should be "stoichiometric_coefficient" or "stoichiometric_ratio".
  • The value should be a Data mesaage with its float_value representing the compound's stoichiometric coefficient or ratio.

(from discussion during OH)

@qai222 qai222 closed this as completed Jun 7, 2023
@qai222 qai222 mentioned this issue Jun 22, 2023
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