diversity_selection
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diversity_selection [2012/07/02 20:42] – [Advanced options] rkiss | diversity_selection [2012/07/02 20:50] – [Algorithm] rkiss | ||
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We plan to introduce more descriptors and more similarity measure types in the future. | We plan to introduce more descriptors and more similarity measure types in the future. | ||
- | * **Molecular descriptor**: | + | * **Molecular descriptor**: |
==== Default options ==== | ==== Default options ==== | ||
- | The default descriptor used is the linear fingerprint implemented in Open Babel ((Open Babel v2.3.90 http:// | + | The default descriptor used is the linear fingerprint implemented in OpenBabel |
- | + | ||
- | If you have no suggestions to use another setup, you can rely on our choices. After implementation and evaluation of new fingerprints and metrics, the default setup can be changed. This can be tracked at the end of this document, in the Changelog section. | + | |
==== Algorithm ==== | ==== Algorithm ==== | ||
- | We use an optimized implementation of the stepwise elimination algorithm((R. J. Taylor, J. Chem. Inf. Comput. Sci., 1995, 35, 59 67.)), which can be described as follows: | + | We use an optimized implementation of the stepwise elimination algorithm((R. J. Taylor, J. Chem. Inf. Comput. Sci., 1995, 35, 59-67.)), which can be described as follows: |
- | - calculate | + | - Calculate |
- | - process | + | - Process |
- | - select | + | - Select |
- | - eliminate | + | - Eliminate |
- | - go to step I. if off-diagonal elements remained | + | - Go to step I. if off-diagonal elements remained |
- | - sort the list of eliminated molecules by similarity values associated to the elimination steps in increasing order | + | - Sort the list of eliminated molecules by similarity values associated to the elimination steps in increasing order |
During this process, the size of the collection is reduced and diversity increases. Each elimination step throws out a compound that has close analogues in the remaining set. In result, we get a single compound, and a list of compounds with decreasing similarity values, which can be interpreted as the increasing diversity of the remaining set. | During this process, the size of the collection is reduced and diversity increases. Each elimination step throws out a compound that has close analogues in the remaining set. In result, we get a single compound, and a list of compounds with decreasing similarity values, which can be interpreted as the increasing diversity of the remaining set. |