Fix bug RMG-database #81 #517
Merged
Conversation
This file contains 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
also change variables names to reflect that the variables are the Family/Library objects rather than the corresponding strings.
the "library" variable from the reaction dict is a string. it needs to be converted to the corresponding object before we can check whether it is a Family or Library.
idem dito for reactants0/products0
The test generates radical addition reactions between the 3 reactants. One of the radical addition reactions is also present in the seed mech The test checks whether the reaction will only appear once in the final model.
prevents attempting to load the (singleton) database more than once.
nickvandewiele
force-pushed
the
fixbug_RMG-database_81
branch
from
2f6592e to
97f0dd8
Compare
nickvandewiele
added a commit
that referenced
this pull request
Jan 8, 2016
…tabase_81 Fix bug RMG-database #81
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Outdated suggestions cannot be applied.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.
This PR fixes the duplicated reactions that were erroneously not discovered as already existing reactions in the reaction database.
This issue was mentioned here and in #513.
An attempt at creating a unit test that reproduces this is found in the testGenerateReactions module for lack of a better place.
The added unit test generates reactions for 3 input reactants (
HCJ=O, CH2O, and [CH2]OC=O) through a single reaction family (radical addition to double bond). The one reactionHCJ=O + CH2O <=> [CH2]OC=Othat results from applying this reaction family, is also present in the seed mechanism (
methylformate) that is imported. It is checked whether the total number of reactions in the final model is equal to the expected number.Importing the library as a reaction library rather than a seed mechanism and only generating 1 reaction is currently not working due to #515.