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Improvements in Superimposition Quality
Mateusz Bieniek edited this page Nov 30, 2020
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SupTop - Superimposed Topology
Slight refinement to the search/overlap algorithm
- Assume that a component X in the molecules, in terms of the general atom types, is symmetric and present in both molecules. When this happens, they would be classified as mirrors, but it is not always easy to know which is which. Here, use the charges and other information to see if they are a better match. For example, since we are working on a general atom type, check if the specific atom types are different and allow you to discredit one of the solutions, or if you have 2 hydrogen-pairs, see if two of them match better in terms of charges.
Multiple solutions:
- Assume that you have a chain-like molecule with 3 overlaid Strongly Connected Components A-B-C matched to A-B'-C, such that A might have multiple solutions. Their matching will be arbitrary but some solutions will be preferable.
Scoring SupTops should take into account:
- Overlap size
- New inserted areas, (or cavities created?)
- FF terms can be used to compare the atoms as well (see Parmed)
Test Cases
- Scan for Unit Tests in other packages out there (FESetup, others?)