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User defined degradation/creation leads to wrong stoichiometry #192

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formersbach opened this issue Sep 13, 2022 · 0 comments · Fixed by #193
Closed

User defined degradation/creation leads to wrong stoichiometry #192

formersbach opened this issue Sep 13, 2022 · 0 comments · Fixed by #193
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bug Something isn't working text2model Text-to-model conversion

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@formersbach
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Description:

When using '0' or '∅' in a user defined reaction, 0/∅ is added to the list of species and to the stoichiometric matrix.

Reproduce:

Text file containing:

@rxn 0 --> A: p[kf]

Convert to model:

from biomass import Text2Model, create_model
model = Text2Model("test.txt")
model.convert(overwrite=True)
print(model.stoichiometry_matrix.toarray(), model.species)

Expected:

model.stoichiometry : [1]
model.species: A

Observed:

model.stoichiometry : [-1, 1]
model.species: 0, A
@formersbach formersbach added bug Something isn't working text2model Text-to-model conversion labels Sep 13, 2022
@formersbach formersbach linked a pull request Sep 13, 2022 that will close this issue
Fixes #192 #193
Merged
himoto pushed a commit that referenced this issue Sep 14, 2022
@formersbach @pre-commit-ci
Fixes #192 (#193)
389d20b 
* 0 and ∅ not added as species for user defined function

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Change explicit list to self.nothing

* Fix merge conflict of last commit

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Fixes #192 biomass-dev/biomass
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@formersbach