Repository navigation
Drop each complex without an ortholog under the drop policy - #25
Merged
Merged
Conversation
The policy drop removes each complex that has a subunit without an ortholog and removes the reaction when no complex remains. It removed the reaction as soon as one subunit had no ortholog.
This was referenced Nov 5, 2026
Contributor
Function test results539 tests 532 ✅ 2m 43s ⏱️ Results for commit a037baa. ♻️ This comment has been updated with latest results. |
edkerk
added a commit
to CompMetEng/raven-docs
that referenced
this pull request
Nov 8, 2026
The guide to reconstruction from homology states that the policy `drop` removes each complex with a missing subunit and removes the reaction when no complex remains. The text follows [RAVEN#25](CompMetEng/RAVEN#25) and the matching change in raven-toolbox, and it merges after both. The page [Update the binary bundles](https://github.com/CompMetEng/raven-docs/blob/docs/homology-drop/docs/installation/updating-binaries.md) names the bundled executables, the platforms that `build_binary_bundles.py` builds, the file that records the provenance, the entry of HMMER 3.3.2 for Windows, and the edits that a new version or a new tool needs. The page [Update the KEGG assets](https://github.com/CompMetEng/raven-docs/blob/docs/homology-drop/docs/installation/updating-kegg-assets.md) gives the arguments of the check functions and says that RAVEN reads the manifest once per session. The paragraphs on the ecModel YAML name the readers of the empty `enzymes` forms and of double-quoted values, and state that the upgrade of a GECKO 3 model is in memory.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
getModelFromHomologywithcomplexPolicydropremoves each complex that has a subunit without an ortholog, and removes the reaction only when no complex remains. For the rule(A and B) or (C and D)without an ortholog ofB, the draft has the orthologs ofCandD. Before, the reaction was removed as soon as one subunit had no ortholog.The step that removes the placeholder genes of isozymes reads the rule as a tree, in which
andbinds tighter thanor. For the rule(A or B and C) and Dwithout an ortholog ofB, the draft rule is(nA or (OLD_T_B and nC)) and nDunderflag,(nA or nC) and nDunderkeepandnA and nDunderdrop. The result differs from before only for rules with unbracketedandandoror with nestedorgroups.The same policy is implemented in raven-toolbox#199.