Comments (2)
I know we probably want to be clever here, and I think that Daniel is working on a strategy for catching duplicate paths from kMC that would work, but after spending some time digging through paths the past couple of days, there is something pretty obvious that should work - just prune paths with identical costs. For example:
0 3.4620678646635246894
1 3.4620678646635246894
2 3.4736261363211290221
3 3.75510952395117456
4 3.7861278042505688611
5 3.7861278042505688611
6 4.2238517847547954525
7 4.3857509970409720313
8 4.3857509970409720313
9 4.477374250818638558
10 4.477374250818638558
paths 0 and 1 are duplicates, paths 4 and 5 are duplicates, paths 7 and 8 are duplicates, paths 9 and 10 are duplicates.
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Here is how i solve this: I have a integer index for each reaction. A pathway is then a list of indices which you can convert into a frozen set. frozen sets are hashable, so you can easily detect duplicates and count how many times each pathway happens
I think i like Sam's solution better for path finding though
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Related Issues (20)
- Remove deprecated function calls HOT 3
- Add OpenBabel to tests HOT 1
- Improved cost functions
- Sweeeeeeeet Logo
- Better core interfaces
- Checkpointing for PR solving
- Functions to change temperature and electron free energy for a reaction network
- Computable properties of huge reaction networks
- Accelerate PR solving for exponential cost functions
- Add tool to visualize reaction networks
- Catching BP/PR cancelation beyond just the shortest path HOT 1
- Split reaction nodes could be re-unified to nearly halve the number of nodes/edges HOT 2
- Make concerted reactions only allowed for a consistent reaction center
- Considering ion charge when deducing reactions
- Considering conformers, cis/trans isomers, and stereoisomers when deducing reactions
- Hetal isn't getting credit for her contributions
- Concerted reaction tests should also test against reaction free energy
- N shortest paths should implicitly remove duplicates
- Replace pickles with msgpak
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