Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

All reactions (not just reversible ones) have now forward_variable and r... #27

Merged
merged 3 commits into from
Apr 10, 2015

Conversation

phantomas1234
Copy link
Collaborator

...everse_variable.

Also the following major changes have been introduced:

  • reversible_encoding has been eliminated. Everything needs to use v_fwd - v_rev now to model the flux of a reaction.
  • reaction.variable is deprecated. Start using reactions.forward_variable

All test miraculously pass ... which is weird. I anticipated flux_variability_analysis would fail because it is not using v_fwd - v_rev explicitily. It doesn't fail though because the objective is set with reactions and SolverBasedModel.objective = reaction will use v_fwd - v_rev

…d reverse_variable.

Also the following major changes have been introduced:

- reversible_encoding has been eliminated. Everything needs to use v_fwd - v_rev now to model the flux of a reaction.
- reaction.variable is deprecated. Start using reactions.forward_variable

All test miraculously pass ... which is weird. I anticipated flux_variability_analysis would fail because it is not using v_fwd - v_rev explicitily. It doesn't fail though because the objective is set with reactions and SolverBasedModel.objective = reaction will use  v_fwd - v_rev
phantomas1234 added a commit that referenced this pull request Apr 10, 2015
All reactions (not just reversible ones) have now forward_variable and r...
@phantomas1234 phantomas1234 merged commit d1d64c6 into devel Apr 10, 2015
@phantomas1234 phantomas1234 deleted the reverse_variables_for_everyone branch July 28, 2015 11:03
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

1 participant